Flawfinder version 2.0.10, (C) 2001-2019 David A. Wheeler.
Number of rules (primarily dangerous function names) in C/C++ ruleset: 223
Examining data/vg-1.27.1+ds/test/build_graph.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/utility.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/test/unit/MWTExploreTestsMultiAction.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/test/unit/MWTExploreTests.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/utility.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/library/ezexample_predict.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/library/test_search.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/library/ezexample_predict_threaded.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/library/test.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/library/search_generate.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/library/library_example.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/library/recommend.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/library/ezexample_train.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/library/gd_mf_weights.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/library/libsearch.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/spanning_tree.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lrq.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/multilabel.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/multilabel.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parser_helper.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/action_score.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/print.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/error_reporting.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/sender.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/active.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/spanning_tree.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/beam.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cbify.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/baseline.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_graph.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb_explore.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/reductions.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/svrg.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/active.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/allreduce_threads.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/floatbits.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/allreduce_sockets.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/best_constant.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/audit_regressor.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/interact.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_primitives.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_example_json.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/boosting.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/noop.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/vw_validate.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/print.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/vw_versions.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_meta.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/correctedMath.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/oaa.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/accumulate.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_example_json.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/unique_sort.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/mf.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/feature_group.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/global_data.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/explore_eval.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/mwt.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/array_parameters.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd_predict.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/scorer.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cs_active.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/interactions.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/example_predict.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/comp_io.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/interact.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb_adf.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cache.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_meta.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb_adf.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb_algs.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/topk.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/audit_regressor.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/scorer.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/rand48.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cache.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cost_sensitive.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/oaa.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/vw.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/binary.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd_mf.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/main.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/ect.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parser.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_dep_parser.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_primitives.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/loss_functions.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_sequencetask.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_graph.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/io_buf.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb_explore_adf.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/memory.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/noop.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/autolink.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/csoaa.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_hooktask.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/nn.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/simple_label.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/vw_allreduce.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_entityrelationtask.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/label_dictionary.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lrqfa.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/interactions.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/loss_functions.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/primitives.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/svrg.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/autolink.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_hooktask.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lrqfa.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/OjaNewton.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_example.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/accumulate.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parser_helper.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lrq.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/comp_io.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_multiclasstask.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/learner.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/label_dictionary.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/ect.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/OjaNewton.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb_explore_adf.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bs.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/unique_sort.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/ftrl.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/stagewise_poly.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/mf.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_dispatch_loop.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/example.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/main_predict.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/multiclass.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_entityrelationtask.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/baseline.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/topk.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/confidence.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/v_hashmap.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/nn.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_dep_parser.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/hash.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gen_cs_example.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/example.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/vw_exception.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/crossplat_compat.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/multilabel_oaa.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/network.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb_algs.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/recall_tree.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/vwdll.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb_explore.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/classweight.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/explore_eval.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/constant.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/active_interactor.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/vw_exception.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/vw_validate.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/ftrl.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parser.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/primitives.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/best_constant.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_sequencetask.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_example.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/vwdll.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/label_parser.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/rand48.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/interactions_predict.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/v_array.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gen_cs_example.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/active_cover.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/io_buf.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/recall_tree.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bs.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/multiclass.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/multilabel_oaa.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/csoaa.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/action_score.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_multiclasstask.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/expreplay.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/example_predict.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/network.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/allreduce.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/classweight.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/array_parameters_dense.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/simple_label.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cs_active.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd_mf.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/ezexample.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/boosting.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/active_cover.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/learner.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/sender.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/mwt.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/stagewise_poly.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cbify.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/confidence.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/hash.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/binary.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/global_data.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cost_sensitive.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cluster/spanning_tree_main.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractfeatures.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractpixels.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/c_test/sample.c
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_exception.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vowpalwabbit.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/clr_io.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_builder.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_base.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_cbutil.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_builder.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_label.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vld_clr.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_arguments.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/clr_io_memory.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vld_clr.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/spanning_tree_clr.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_clr.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/spanning_tree_clr.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_settings.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vowpalwabbit.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_model.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_interface.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_example.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_prediction.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/resource.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_example.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_base.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_model.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_prediction.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_cbutil.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/vw_labelcomparator.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/clr_io_memory.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/AssemblyInfo.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/cs/cli/clr_io.cpp
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/python/pylibvw.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWScalarsLearner.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/jni_base_learner.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWActionProbsLearner.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWActionScoresLearner.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/jni_base_learner.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWMulticlassLearner.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWMulticlassLearner.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWMultilabelsLearner.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWProbLearner.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWScalarsLearner.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWProbLearner.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWMultilabelsLearner.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWActionScoresLearner.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_VW.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWLearners.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWActionProbsLearner.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_VW.h
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWLearners.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWScalarLearner.cc
Examining data/vg-1.27.1+ds/deps/vowpal_wabbit/java/src/main/c++/vowpalWabbit_learner_VWScalarLearner.h
Examining data/vg-1.27.1+ds/deps/mmmultimap/src/mmmultiset.hpp
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Examining data/vg-1.27.1+ds/deps/mmmultimap/src/main.cpp
Examining data/vg-1.27.1+ds/deps/xg/src/main.cpp
Examining data/vg-1.27.1+ds/deps/xg/src/xg.hpp
Examining data/vg-1.27.1+ds/deps/xg/src/xg.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfakluge.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/pliib.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/examples/getseq.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/examples/index.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfa_builder.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/main.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfak_test.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/gfakluge/gtest.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/handle.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/util.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/types.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/BBHash/example_custom_hash.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h
Examining data/vg-1.27.1+ds/deps/xg/deps/BBHash/example.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/BBHash/bootest.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/cst-bfs-iterator.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/k2_treap_in_mem.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/sa-int-construct-from-file.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/write_structure.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/intersect.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/louds-tree.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/node_iterator.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/construct-in-memory.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/int-vector-buffer.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/isa_access.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/bit-vector.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/wt_ap.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/hugepages.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/csa-alphabet-strategy.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/fm-index.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/sd_vector_benchmark.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/int-vector-buffer-iterator.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/int-vector-mapper.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/store_to_file.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/c++11-initializer-list.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/fm-rmq-index.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/memory-visualization.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/sa-construct-space-efficient.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/text-statistics.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/standalone_lcp.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/int-vector-entry.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/uint64-array2int_vector.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/storage-visualization.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/print_wt.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/range-minimum-queries.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/cst-node-child-iterator.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/memory_management.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/wm_int.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/wt_helper.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/structure_tree.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/suffix_arrays.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/ram_fs.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/k2_tree.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/vlc_vector.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/rrr_vector.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/rrr_vector_15.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/lcp.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/coder.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/inv_perm_support.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/rmq_support.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/csa_wt.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/csa_sada.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/cst_iterators.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/hyb_vector.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/wt_hutu.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/construct_isa.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/construct_lcp.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/rank_support_scan.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/lcp_wt.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/select_support.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/wavelet_trees.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/lcp_support_tree.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/bp_support_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/coder_elias_gamma.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/csa_sampling_strategy.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/k2_treap_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/rrr_helper.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/k2_treap_helper.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/bp_support.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/config.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/wt_rlmn.hpp
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Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/wt_int.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/rmq_succinct_sada.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/sorted_stack_support.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/lcp_vlc.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/coder_elias_delta.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/suffix_trees.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/sorted_int_stack.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/bp_support_sada.hpp
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Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/bit_vector_il.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/lcp_bitcompressed.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/fast_cache.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/uint256_t.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/construct_bwt.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/bit_vectors.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/construct_config.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/suffix_tree_helper.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/cst_fully.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/sorted_multi_stack_support.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/io.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/util.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/nearest_neighbour_dictionary.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/qsufsort.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/sfstream.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/construct_sa_se.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/rmq_support_sparse_table.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/raster_img.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/rank_support_v5.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/wt_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/construct.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/wt_blcd.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/louds_tree.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/construct_lcp_helper.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/k2_tree_helper.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/iterators.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/sdsl_concepts.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/wt_gmr.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/nn_dict_dynamic.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/cst_sct3.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/wt_pc.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/coder_comma.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/cst_sada.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/suffix_tree_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/sd_vector.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/ram_filebuf.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/select_support_mcl.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/bits.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/uint128_t.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/lcp_support_tree2.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/dac_vector.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/rank_support_v.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/lcp_byte.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/vectors.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/uintx_t.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/bp_support_g.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/csa_alphabet_strategy.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/bp_support_gg.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/construct_sa.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/rmq_succinct_sct.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/lcp_dac.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/csa_bitcompressed.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/enc_vector.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-09.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-07.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/rmq-example.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-23.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-24.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-11.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/int-vector-buffer.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-16.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-18.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/document_listing/doc_list_index.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/use-a-wavelet-tree.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-01.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-06.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-08.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/cst-search.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-19.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-17.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-10.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-25.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-22.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-13.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-14.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-21.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-26.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-05.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-02.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/csx-printf.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-20.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-15.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-12.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-03.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/expl-04.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/cst-traversal.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/src/gmock-cardinalities.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/src/gmock-all.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/src/gmock_main.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/src/gmock-spec-builders.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/src/gmock.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/src/gmock-internal-utils.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/src/gmock-matchers.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock_link2_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-internal-utils_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-nice-strict_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock_stress_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-generated-internal-utils_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock_output_test_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-generated-actions_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-generated-matchers_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock_link_test.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock_link_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-more-actions_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-cardinalities_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock_all_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-actions_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock_ex_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock_leak_test_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-spec-builders_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-matchers_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-generated-function-mockers_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-port_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/gmock-cardinalities.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/gmock-actions.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/gmock-generated-matchers.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/gmock-more-matchers.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/gmock-generated-function-mockers.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/gmock-generated-nice-strict.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/gmock-generated-actions.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/gmock-more-actions.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/gmock-matchers.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/internal/custom/gmock-port.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/internal/custom/gmock-matchers.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/internal/custom/gmock-generated-actions.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/internal/gmock-port.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/gmock-spec-builders.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/include/gmock/gmock.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/codegear/gtest_all.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/codegear/gtest_link.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-test-part.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest_main.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-all.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-typed-test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample4.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample4.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample4_unittest.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample3-inl.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample6_unittest.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample9_unittest.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample2.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample2_unittest.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample1.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample2.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample1_unittest.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample10_unittest.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample3_unittest.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample5_unittest.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/prime_tables.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample1.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample8_unittest.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample7_unittest.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-typed-test_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/production.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-listener_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_break_on_failure_unittest_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_environment_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_no_test_unittest.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_shuffle_test_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-param-test_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_ex_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_throw_on_failure_test_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-port_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-test-part_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_xml_output_unittest_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_env_var_test_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_premature_exit_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_filter_unittest_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-message_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_sole_header_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_output_test_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_catch_exceptions_test_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_uninitialized_test_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_list_tests_unittest_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-typed-test2_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_xml_outfile2_test_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_xml_outfile1_test_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/production.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_color_test_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_stress_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_repeat_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-unittest-api_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-tuple_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-typed-test_test.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_all_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_prod_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_help_test_.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-options_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_pred_impl_unittest.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_main_unittest.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_throw_on_failure_ex_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-param-test_test.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-param-test2_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-linked_ptr_test.cc
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-printers.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest_pred_impl.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-typed-test.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port-arch.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/custom/gtest-printers.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/custom/gtest-port.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/custom/gtest.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-param-util-generated.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-death-test-internal.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-internal.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-tuple.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-filepath.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-string.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-param-util.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-type-util.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-spi.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-test-part.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest_prod.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-param-test.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-message.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-death-test.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget_test.cc
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Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/libdivsufsort/include/divsufsort_private.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/libdivsufsort/lib/utils.c
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/libdivsufsort/lib/sssort.c
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/libdivsufsort/lib/divsufsort.c
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/libdivsufsort/lib/trsort.c
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/libdivsufsort/examples/bwt.c
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/libdivsufsort/examples/sasearch.c
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/libdivsufsort/examples/unbwt.c
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/libdivsufsort/examples/suftest.c
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/libdivsufsort/examples/mksary.c
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/CMakeModules/check_mode_ti.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/lcp/src/create_lcp.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/lcp/src/create_sa_bwt.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/rrr_vector/src/rrr_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_extract/src/info.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_extract/src/interface.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_extract/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/suffix_trees/src/build_cst.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/suffix_trees/src/time_and_space_cst.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/suffix_trees/src/depth_stats.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/document_retrieval/src/size_of_idx.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/document_retrieval/src/gen_pattern.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/document_retrieval/src/word_pat2char_pat.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_sort.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_greedy.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_sada.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/document_retrieval/src/query_idx.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_qprobing.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/document_retrieval/src/build_idx.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/self_delimiting_codes/src/sdc_benchmark.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/k2_trees/src/k2_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/k2_trees/src/gen_k2t.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_locate/src/interface.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_locate/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_locate/src/pattern_random.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_locate/src/info.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_count/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_count/src/info.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_count/src/interface.h
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/wavelet_trees/src/wt_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/wavelet_trees/src/gen_bwt.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/uint256_t.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/nn_dict_dynamic.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/ram_fs.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/bp_support_algorithm.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/louds_tree.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/uint128_t.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/construct_sa_se.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/config.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sd_vector.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/io.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/ram_filebuf.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/construct_config.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/lcp_support_tree.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/construct_sa.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/bits.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/wt_helper.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/rrr_vector_15.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/construct_lcp_helper.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/construct_isa.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/construct_lcp.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/memory_management.cpp
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Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/util.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/wt_byte_test.cpp
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Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/lcp_construct_test.cpp
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Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/sorted_int_stack_test.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/rank_support_test.cpp
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Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/sa_construct_test.cpp
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Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/coder_test.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_buffer_test.cpp
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Examining data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/rmq_test.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmmultimap.hpp
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Examining data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/main.cpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/base_case.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/thread_pool.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/sequential.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/local_classification.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/bucket_pointers.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/cleanup_margins.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/utils.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/config.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/empty_block_movement.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/sampling.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/parallel.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/synchronization.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/buffers.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/ips4o_fwd.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/partitioning.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/classifier.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/memory.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/ips4o.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/block_permutation.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/args/examples/completion.cxx
Examining data/vg-1.27.1+ds/deps/xg/deps/args/examples/gitlike.cxx
Examining data/vg-1.27.1+ds/deps/xg/deps/args/test.cxx
Examining data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp
Examining data/vg-1.27.1+ds/deps/xg/deps/args/test/multiple_inclusion_2.cxx
Examining data/vg-1.27.1+ds/deps/xg/deps/args/test/multiple_inclusion_1.cxx
Examining data/vg-1.27.1+ds/deps/xg/deps/args/test/windows_h.cxx
Examining data/vg-1.27.1+ds/deps/BBHash/example.cpp
Examining data/vg-1.27.1+ds/deps/BBHash/BooPHF.h
Examining data/vg-1.27.1+ds/deps/BBHash/bootest.cpp
Examining data/vg-1.27.1+ds/deps/BBHash/example_custom_hash.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/src/packed_graph.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/src/is_single_stranded.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/src/vectorizable_overlays.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/src/test_libbdsg.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/src/packed_path_position_overlay.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/src/packed_structs.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/src/strand_split_overlay.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/src/node.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/src/utility.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/src/path_position_overlays.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/src/eades_algorithm.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/src/packed_subgraph_overlay.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/iostream.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/options.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/eval.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/detail/descr.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/detail/typeid.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/detail/init.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/detail/internals.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/detail/common.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/detail/class.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/embed.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/functional.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/chrono.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/operators.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/cast.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/attr.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/complex.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/stl.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/pytypes.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/stl_bind.h
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/numpy.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/common.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/buffer_info.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/eigen.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_embed/test_interpreter.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_embed/external_module.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_embed/catch.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_stl_binders.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_async.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/constructor_stats.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_local_bindings.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/object.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_modules.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_cmake_build/embed.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_cmake_build/main.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_chrono.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/pybind11_cross_module_tests.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_buffers.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_sequences_and_iterators.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_multiple_inheritance.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_smart_ptr.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_methods_and_attributes.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/pybind11_tests.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/local_bindings.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_iostream.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_stl.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_call_policies.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_virtual_functions.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_constants_and_functions.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_union.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_exceptions.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_eval.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/cross_module_gil_utils.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_enum.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_gil_scoped.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_pytypes.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_eigen.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_numpy_array.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_builtin_casters.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_factory_constructors.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_callbacks.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_operator_overloading.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_copy_move.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_pickling.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_kwargs_and_defaults.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/pybind11_tests.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_docstring_options.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_class.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_numpy_vectorize.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_opaque_types.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_numpy_dtypes.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_tagbased_polymorphic.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/piecewise.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/serialize_file.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/serialize_large.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/serialize_stream.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/hash_std.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/movable.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/insert_rvalue.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/emplace.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_stdint.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_utils.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_timer.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_traits.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_smartptr.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_memory.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_config.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_dlalloc.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_bitset_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_alloc_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/perftest1.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_relative_include_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/hopscotch_growth_policy.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/hopscotch_map.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/hopscotch_set.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/hopscotch_hash.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/bhopscotch_map.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/bhopscotch_set.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/tests/main.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/tests/hopscotch_set_tests.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/tests/utils.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/tests/policy_tests.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/tests/hopscotch_map_tests.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/tests/custom_allocator_tests.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/rle_lz77_v1.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/benchmark.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/rle_bwt.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/debug.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/h0_lz77.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/cw-bwt.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/fm_index.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/wm_string.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/bwt.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/sparse_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/spsi.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/succinct_bitvector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/lciv.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/alphabet_encoder.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/packed_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/includes.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/rle_string.hpp
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/spsi_check.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/gap_bitvector.hpp
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/hacked_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/structures/ContextAutomata.h
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/structures/HuffmanTree.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/structures/PartialSums.h
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/structures/BackwardFileIterator.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/cw_bwt.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/rle_lz77_v1.hpp
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/h0_lz77.hpp
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/rle_lz77_v2.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/handle.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/util.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/types.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/bootest.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/example.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/example_custom_hash.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/document_retrieval/src/build_idx.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_sort.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/document_retrieval/src/size_of_idx.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/document_retrieval/src/query_idx.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_qprobing.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/document_retrieval/src/gen_pattern.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_greedy.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_sada.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/document_retrieval/src/word_pat2char_pat.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/k2_trees/src/gen_k2t.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/k2_trees/src/k2_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/self_delimiting_codes/src/sdc_benchmark.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_extract/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_extract/src/info.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_extract/src/interface.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/suffix_trees/src/depth_stats.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/suffix_trees/src/build_cst.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/suffix_trees/src/time_and_space_cst.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_count/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_count/src/interface.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_count/src/info.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_locate/src/info.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_locate/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_locate/src/interface.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_locate/src/pattern_random.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/wavelet_trees/src/wt_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/wavelet_trees/src/gen_bwt.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/rrr_vector/src/rrr_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/lcp/src/create_sa_bwt.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/lcp/src/create_lcp.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/document_listing/doc_list_index.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-03.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-04.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-15.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-12.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/cst-search.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/int-vector-buffer.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-20.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-05.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-02.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-21.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-26.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/cst-traversal.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-13.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-14.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-25.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/use-a-wavelet-tree.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-22.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-19.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-17.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-10.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-01.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-06.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-08.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/csx-printf.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-11.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-16.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-18.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/rmq-example.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-23.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-24.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-09.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/expl-07.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_uninitialized_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_ex_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-unittest-api_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_catch_exceptions_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-typed-test2_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-port_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_filter_unittest_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-typed-test_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_sole_header_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_all_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-param-test_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-typed-test_test.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_throw_on_failure_ex_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_repeat_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-param-test_test.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_color_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_stress_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_throw_on_failure_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_premature_exit_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_xml_outfile2_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_main_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-options_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_environment_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_no_test_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_xml_outfile1_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_xml_output_unittest_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_env_var_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-test-part_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/production.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-param-test2_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/production.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_prod_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_output_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-message_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_shuffle_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-listener_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_list_tests_unittest_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_help_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_pred_impl_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-linked_ptr_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_break_on_failure_unittest_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-tuple_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/codegear/gtest_all.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/codegear/gtest_link.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-param-test.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-death-test.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-test-part.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-message.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/custom/gtest.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/custom/gtest-port.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/custom/gtest-printers.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-param-util.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-death-test-internal.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-type-util.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-filepath.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-string.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-internal.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-tuple.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-param-util-generated.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port-arch.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-spi.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-printers.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest_pred_impl.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-typed-test.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest_prod.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-test-part.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-typed-test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest_main.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-all.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/libdivsufsort/examples/suftest.c
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/libdivsufsort/include/divsufsort_private.h
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/libdivsufsort/lib/sssort.c
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/libdivsufsort/lib/divsufsort.c
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/standalone_lcp.cpp
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/storage-visualization.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/construct-in-memory.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/fm-index.cpp
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/k2_treap_in_mem.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/write_structure.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/node_iterator.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/sa-int-construct-from-file.cpp
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/hugepages.cpp
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/louds-tree.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/isa_access.cpp
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/config.cpp
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/construct_isa.cpp
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/construct_sa.cpp
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/CMakeModules/check_mode_ti.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/memory_management.hpp
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Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/rank_support_v.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/wm_int.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/vectors.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/coder_elias_gamma.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/uintx_t.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/lcp.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/bit_vectors.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/csa_wt.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/rmq_succinct_sct.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/k2_tree_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/rmq_succinct_sada.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/construct_bwt.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/suffix_tree_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/construct_sa_se.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/wt_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/wt_blcd.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/coder_elias_delta.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/sorted_stack_support.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/wt_gmr.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/qsufsort.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/wavelet_trees.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/rrr_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/sd_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/sfstream.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/util.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/bp_support.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/suffix_tree_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/csa_alphabet_strategy.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/uint128_t.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/construct_isa.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/lcp_bitcompressed.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/construct_lcp.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/k2_treap.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/bp_support_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/k2_treap_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/suffix_trees.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/nearest_neighbour_dictionary.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/construct.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/structure_tree.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/iterators.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/io.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/k2_treap_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/wt_ap.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/inv_perm_support.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/k2_tree.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/lcp_byte.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/uint256_t.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/suffix_arrays.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/wt_pc.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/wt_rlmn.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/suffix_array_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/rrr_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/lcp_support_tree.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/cst_fully.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/bits.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/cst_sct3.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/cst_sada.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/construct_sa.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/lcp_vlc.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/bp_support_g.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/hyb_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/wt_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/wt_hutu.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/select_support.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/cst_iterators.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/lcp_support_tree2.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/sorted_multi_stack_support.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/rmq_support_sparse_table.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/vlc_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/rmq_support.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/rrr_vector_15.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/csa_bitcompressed.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/cst_int_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/coder_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/cst_byte_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/search_bidirectional_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/wt_byte_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/select_support_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/sorted_stack_support_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/cst_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/lcp_construct_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/csa_byte_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/rank_support_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/bit_vector_generator.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/sa_construct_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/k2_treap_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/wt_int_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/bits_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/k2_tree_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/bit_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_generator.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/rmq_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/replace_int_vector_value.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/inv_perm_support_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_buffer_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/csa_int_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/sorted_int_stack_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/dac_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/sd_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/nn_dict_dynamic_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/std/bdsg/internal/binder_hook_bind.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/bdsg.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/handlegraph/path_handle_graph.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/handlegraph/path_position_handle_graph.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/handlegraph/handle_graph.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/handlegraph/serializable_handle_graph.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/handlegraph/types.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/handlegraph/mutable_path_mutable_handle_graph.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/bdsg/odgi.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/bdsg/internal/packed_structs.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/bdsg/internal/is_single_stranded.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/bdsg/internal/utility.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/bdsg/internal/wang_hash.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/bdsg/overlays/path_position_overlays.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/bdsg/overlays/packed_path_position_overlay.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/bdsg/overlays/vectorizable_overlays_1.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/bdsg/overlays/vectorizable_overlays.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/cmake_bindings/bdsg/overlays/packed_subgraph_overlay.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/tests/policy_tests.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/tests/utils.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/tests/hopscotch_map_tests.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/tests/custom_allocator_tests.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/tests/hopscotch_set_tests.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/tests/main.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/hopscotch_hash.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/hopscotch_map.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/hopscotch_set.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/hopscotch_growth_policy.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/bhopscotch_set.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/bhopscotch_map.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/perftest1.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_bitset_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_relative_include_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_alloc_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_smartptr.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_config.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_memory.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_dlalloc.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_timer.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_utils.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_traits.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_stdint.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/serialize_stream.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/emplace.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/insert_rvalue.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/hash_std.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/serialize_file.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/movable.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/serialize_large.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/piecewise.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_stl.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_numpy_dtypes.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_gil_scoped.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_callbacks.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_copy_move.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/pybind11_tests.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_opaque_types.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_exceptions.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_kwargs_and_defaults.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_call_policies.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_pickling.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_local_bindings.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_pytypes.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_factory_constructors.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_chrono.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_stl_binders.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_operator_overloading.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_iostream.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_tagbased_polymorphic.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_constants_and_functions.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_async.cpp
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Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-param-test.h
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Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_list_tests_unittest_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_env_var_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_xml_outfile2_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_catch_exceptions_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_all_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-listener_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_environment_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_no_test_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_shuffle_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-port_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_xml_output_unittest_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-typed-test2_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_help_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-linked_ptr_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_throw_on_failure_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-test-part_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_sole_header_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-message_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_output_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-tuple_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_ex_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_filter_unittest_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_color_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_stress_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_throw_on_failure_ex_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_uninitialized_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-options_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_repeat_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-param-test_test.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-param-test_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_pred_impl_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-typed-test_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_prod_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/production.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-param-test2_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_break_on_failure_unittest_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_main_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_xml_outfile1_test_.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-typed-test_test.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-unittest-api_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_premature_exit_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample9_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample6_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample1.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample4_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample10_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample1.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample3-inl.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample2.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample2_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample2.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample4.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample3_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/prime_tables.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample1_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample7_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample8_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample4.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample5_unittest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget_test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-all.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest_main.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-test-part.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-typed-test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/codegear/gtest_link.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/codegear/gtest_all.cc
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/libdivsufsort/include/divsufsort_private.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/libdivsufsort/examples/mksary.c
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/libdivsufsort/examples/unbwt.c
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/libdivsufsort/examples/suftest.c
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/libdivsufsort/examples/sasearch.c
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/libdivsufsort/examples/bwt.c
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/libdivsufsort/lib/utils.c
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/libdivsufsort/lib/sssort.c
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/libdivsufsort/lib/divsufsort.c
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/libdivsufsort/lib/trsort.c
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/CMakeModules/check_mode_ti.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/rrr_vector_15.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/coder_elias_gamma.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/sorted_multi_stack_support.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/k2_tree.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/suffix_trees.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/k2_treap_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/rrr_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/cst_iterators.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/k2_treap_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/rank_support_scan.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/hyb_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/ram_filebuf.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/coder_comma.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/select_support_scan.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/rmq_succinct_sada.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/vlc_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/rmq_succinct_sct.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/suffix_arrays.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/rrr_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/bp_support.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/wt_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/wt_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/rank_support_v.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/coder.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/sorted_int_stack.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/wt_hutu.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/wt_gmr.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/memory_management.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/lcp_support_sada.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/construct_lcp_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/construct_lcp.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/csa_sada.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/bit_vectors.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/suffix_array_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/construct_config.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/construct_isa.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/k2_tree_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/lcp_vlc.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/suffix_tree_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/csa_alphabet_strategy.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/bp_support_g.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/wavelet_trees.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/construct_sa.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/wt_rlmn.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/select_support_mcl.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/iterators.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/wt_pc.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/wt_huff.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/wm_int.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/fast_cache.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/rmq_support_sparse_table.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/construct_bwt.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/lcp_support_tree.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/lcp.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/construct.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/nn_dict_dynamic.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/ram_fs.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/csa_bitcompressed.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/uint128_t.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/lcp_support_tree2.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/lcp_byte.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/structure_tree.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/rank_support_v5.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/bit_vector_il.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/nearest_neighbour_dictionary.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/cst_sct3.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/sd_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/util.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/csa_wt.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/cst_sada.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/suffix_tree_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/wt_blcd.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/construct_sa_se.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/lcp_bitcompressed.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/lcp_wt.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/k2_treap.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/bp_support_gg.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/enc_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/csa_sampling_strategy.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/dac_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/bp_support_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/coder_elias_delta.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/config.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/sfstream.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/vectors.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/wt_int.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/uintx_t.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/bits.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/raster_img.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/io.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/rank_support.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/lcp_dac.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/qsufsort.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/inv_perm_support.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/uint256_t.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/sdsl_concepts.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/bp_support_sada.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/select_support.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/cst_fully.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/louds_tree.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/sorted_stack_support.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/wt_ap.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/rmq_support.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/uint64-array2int_vector.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/standalone_lcp.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/text-statistics.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/csa-alphabet-strategy.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/int-vector-buffer.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/print_wt.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/construct-in-memory.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/memory-visualization.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/cst-node-child-iterator.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/node_iterator.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/sa-int-construct-from-file.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/cst-bfs-iterator.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/louds-tree.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/sa-construct-space-efficient.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/sd_vector_benchmark.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/k2_treap_in_mem.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/intersect.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/range-minimum-queries.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/isa_access.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/storage-visualization.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/fm-index.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/int-vector-mapper.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/write_structure.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/store_to_file.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/int-vector-entry.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/fm-rmq-index.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/int-vector-buffer-iterator.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/c++11-initializer-list.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/bit-vector.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/hugepages.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/wt_ap.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_extract/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_extract/src/info.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_extract/src/interface.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/k2_trees/src/k2_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/k2_trees/src/gen_k2t.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/rrr_vector/src/rrr_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/wavelet_trees/src/wt_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/wavelet_trees/src/gen_bwt.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_count/src/interface.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_count/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_count/src/info.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/lcp/src/create_sa_bwt.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/lcp/src/create_lcp.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/document_retrieval/src/query_idx.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/document_retrieval/src/word_pat2char_pat.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/document_retrieval/src/build_idx.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/document_retrieval/src/size_of_idx.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_sada.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_qprobing.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/document_retrieval/src/gen_pattern.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_greedy.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_sort.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_locate/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_locate/src/pattern_random.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_locate/src/interface.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_locate/src/info.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/suffix_trees/src/time_and_space_cst.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/suffix_trees/src/depth_stats.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/suffix_trees/src/build_cst.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/self_delimiting_codes/src/sdc_benchmark.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/bits_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/sorted_stack_support_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/k2_tree_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/dac_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/search_bidirectional_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/cst_byte_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/csa_int_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/bit_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/lcp_construct_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/cst_int_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/bit_vector_generator.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/replace_int_vector_value.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/coder_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_generator.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/wt_byte_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/inv_perm_support_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/sd_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/k2_treap_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/sa_construct_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/rmq_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_buffer_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/wt_int_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/cst_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/rank_support_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/sorted_int_stack_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/csa_byte_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/select_support_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/nn_dict_dynamic_test.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/construct_isa.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/memory_management.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/construct_lcp.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/nn_dict_dynamic.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/util.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/lcp_support_tree.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sd_vector.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/uint128_t.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/bits.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/ram_filebuf.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/construct_sa_se.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/uint256_t.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/rrr_vector_15.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/construct_lcp_helper.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/io.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/louds_tree.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/config.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/ram_fs.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/wt_helper.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/construct_config.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_fibonacci.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/construct_sa.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/bp_support_algorithm.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/rle_lz77_v1.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/fm_index.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/ContextAutomata.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/BackwardIterator.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/BackwardStringIterator.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/HuffmanTree.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/PartialSums.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/BackwardFileIterator.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/DynamicString.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/wt_string.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/gap_bitvector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/spsi.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/packed_array.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/hacked_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/lciv.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/includes.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/wm_string.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/succinct_bitvector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/sparse_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/alphabet_encoder.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/packed_vector.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/spsi_check.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/bwt.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/rle_string.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/dynamic.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/algorithms/rle_lz77_v2.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/algorithms/h0_lz77.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/algorithms/cw_bwt.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/algorithms/rle_lz77_v1.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/h0_lz77.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/wm_string.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/rle_bwt.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/debug.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/cw-bwt.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/benchmark.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/rle_lz77_v2.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/handle.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/types.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/util.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/bootest.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/example_custom_hash.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/example.cpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/packed_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/overlays/packed_subgraph_overlay.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/overlays/path_position_overlays.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/overlays/strand_split_overlay.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/overlays/overlay_helper.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/overlays/vectorizable_overlays.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/overlays/packed_path_position_overlay.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/hash_graph.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/internal/endianness.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/internal/binder_hook_bind.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/internal/eades_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/internal/varint.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/internal/utility.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/internal/dynamic_types.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/internal/packed_structs.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/internal/wang_hash.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/internal/binder_hook_compile.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/internal/hash_map.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/internal/node.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/internal/is_single_stranded.hpp
Examining data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/odgi.hpp
Examining data/vg-1.27.1+ds/deps/lru_cache/main.cc
Examining data/vg-1.27.1+ds/deps/lru_cache/lru_cache.h
Examining data/vg-1.27.1+ds/deps/gcsa2/files.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/support.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/try_extend.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/algorithms.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/build_gcsa.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/dbg.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/utils.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/internal.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/dbg.h
Examining data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/files.h
Examining data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/gcsa.h
Examining data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/lcp.h
Examining data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/algorithms.h
Examining data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/path_graph.h
Examining data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/support.h
Examining data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/utils.h
Examining data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/internal.h
Examining data/vg-1.27.1+ds/deps/gcsa2/gcsa.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/lcp.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/benchmark/csa_query.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/benchmark/csa_builder.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/benchmark/count_kmers.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/benchmark/query_gcsa.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/gcsa_format.cpp
Examining data/vg-1.27.1+ds/deps/gcsa2/convert_graph.cpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/vpkg.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/loader.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/hfile_cppstream.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/alignment_io.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/protobuf_iterator.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/stream_multiplexer.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/gafkluge.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/stream.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/blocked_gzip_input_stream.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/fdstream.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/blocked_gzip_output_stream.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/basic_stream.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/edit.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/message_iterator.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/hfile_internal.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/registry.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/alignment_emitter.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/json2pb.h
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/protobuf_emitter.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/include/vg/io/message_emitter.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/util.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/types.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/handle.cpp
Examining data/vg-1.27.1+ds/deps/libvgio/src/hfile_cppstream.cpp
Examining data/vg-1.27.1+ds/deps/libvgio/src/registry.cpp
Examining data/vg-1.27.1+ds/deps/libvgio/src/basic_stream.cpp
Examining data/vg-1.27.1+ds/deps/libvgio/src/blocked_gzip_output_stream.cpp
Examining data/vg-1.27.1+ds/deps/libvgio/src/message_iterator.cpp
Examining data/vg-1.27.1+ds/deps/libvgio/src/vpkg.cpp
Examining data/vg-1.27.1+ds/deps/libvgio/src/bin2ascii.h
Examining data/vg-1.27.1+ds/deps/libvgio/src/json2pb.cpp
Examining data/vg-1.27.1+ds/deps/libvgio/src/stream.cpp
Examining data/vg-1.27.1+ds/deps/libvgio/src/alignment_io.cpp
Examining data/vg-1.27.1+ds/deps/libvgio/src/edit.cpp
Examining data/vg-1.27.1+ds/deps/libvgio/src/message_emitter.cpp
Examining data/vg-1.27.1+ds/deps/libvgio/src/blocked_gzip_input_stream.cpp
Examining data/vg-1.27.1+ds/deps/libvgio/src/alignment_emitter.cpp
Examining data/vg-1.27.1+ds/deps/libvgio/src/stream_multiplexer.cpp
Examining data/vg-1.27.1+ds/deps/gssw/src/gssw.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/check.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/simde-constify.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/hedley.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/simde-diagnostic.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/debug-trap.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/simde-detect-clang.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/simde-math.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/simde-arch.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/mvn.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/and.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/tst.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/sub.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/trn1.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/zip1.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/addl.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/mlal.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/shr_n.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/cgtz.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/shl.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/types.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/qmovn.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/mull.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/bsl.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/get_low.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/mla.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/rsra_n.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/max.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/trn2.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/zip2.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/uzp.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/ld1.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/mul.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/ceq.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/zip.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/pmax.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/combine.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/cge.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/cgez.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/shl_n.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/orr.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/uzp2.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/cltz.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/reinterpret.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/paddl.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/cgt.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/mlal_high.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/eor.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/st1_lane.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/cle.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/rshr_n.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/clez.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/get_lane.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/uzp1.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/sra_n.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/add.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/trn.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/get_high.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/pmin.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/neg.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/addw.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/dup_n.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/movl.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/st1.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/ceqz.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/padal.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/movl_high.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/min.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/abs.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/padd.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon/cagt.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/arm/neon.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/simde-features.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/sse4.2.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/avx512f.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/avx512bw.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/sse4.1.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/avx2.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/sse2.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/mmx.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/svml.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/gfni.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/ssse3.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/avx512cd.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/sse3.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/avx.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/fma.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/sse.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/avx512dq.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/x86/avx512vl.h
Examining data/vg-1.27.1+ds/deps/gssw/src/simde/simde-common.h
Examining data/vg-1.27.1+ds/deps/gssw/src/ssw_cpp.h
Examining data/vg-1.27.1+ds/deps/gssw/src/ssw_cpp.cpp
Examining data/vg-1.27.1+ds/deps/gssw/src/example.c
Examining data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c
Examining data/vg-1.27.1+ds/deps/gssw/src/example_adj.c
Examining data/vg-1.27.1+ds/deps/gssw/src/example.cpp
Examining data/vg-1.27.1+ds/deps/gssw/src/gssw.c
Examining data/vg-1.27.1+ds/deps/gssw/src/kseq.h
Examining data/vg-1.27.1+ds/deps/gssw/src/main.c
Examining data/vg-1.27.1+ds/deps/structures/src/stable_double.cpp
Examining data/vg-1.27.1+ds/deps/structures/src/union_find.cpp
Examining data/vg-1.27.1+ds/deps/structures/src/tests.cpp
Examining data/vg-1.27.1+ds/deps/structures/src/suffix_tree.cpp
Examining data/vg-1.27.1+ds/deps/structures/src/include/structures/rank_pairing_heap.hpp
Examining data/vg-1.27.1+ds/deps/structures/src/include/structures/suffix_tree.hpp
Examining data/vg-1.27.1+ds/deps/structures/src/include/structures/min_max_heap.hpp
Examining data/vg-1.27.1+ds/deps/structures/src/include/structures/stable_double.hpp
Examining data/vg-1.27.1+ds/deps/structures/src/include/structures/immutable_list.hpp
Examining data/vg-1.27.1+ds/deps/structures/src/include/structures/updateable_priority_queue.hpp
Examining data/vg-1.27.1+ds/deps/structures/src/include/structures/union_find.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/rle_bwt.cpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/rle_lz77_v1.cpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/benchmark.cpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/debug.cpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/rle_lz77_v2.cpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/cw-bwt.cpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/h0_lz77.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/rle_lz77_v1.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/rle_lz77_v2.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/cw_bwt.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/HuffmanTree.h
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/PartialSums.h
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/ContextAutomata.h
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/BackwardIterator.h
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/BackwardFileIterator.h
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/DynamicString.h
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/BackwardStringIterator.h
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/dynamic.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/packed_vector.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/includes.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/sparse_vector.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/lciv.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/bwt.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/wm_string.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/succinct_bitvector.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/spsi.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/hacked_vector.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/packed_array.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/fm_index.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/rle_string.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/alphabet_encoder.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/spsi_check.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/wt_string.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/gap_bitvector.hpp
Examining data/vg-1.27.1+ds/deps/DYNAMIC/h0_lz77.cpp
Examining data/vg-1.27.1+ds/deps/gfakluge/gtest.cpp
Examining data/vg-1.27.1+ds/deps/gfakluge/src/gfak_test.cpp
Examining data/vg-1.27.1+ds/deps/gfakluge/src/gfa_builder.hpp
Examining data/vg-1.27.1+ds/deps/gfakluge/src/gfakluge.hpp
Examining data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/examples/getseq.cpp
Examining data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/examples/index.cpp
Examining data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/pliib.hpp
Examining data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp
Examining data/vg-1.27.1+ds/deps/gfakluge/src/main.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/variants.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/gbwt.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/remove_seq.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/build_ri.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/cached_gbwt.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/metadata.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_huff.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/enc_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_byte.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/rank_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/ram_filebuf.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/construct_config.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/config.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/bp_support_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_comma.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/dac_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/memory_management.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_int.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/cst_sct3.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_tree_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/io.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/cst_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/select_support_scan.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_arrays.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/rrr_vector_15.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/sorted_int_stack.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/select_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_tree_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/louds_tree.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_wt.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/sorted_stack_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_support_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/cst_iterators.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/csa_alphabet_strategy.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/raster_img.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/bit_vectors.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/rank_support_scan.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/construct_lcp.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/qsufsort.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_treap_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/construct_isa.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/sfstream.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_blcd.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/csa_wt.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/select_support_mcl.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_elias_gamma.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/rmq_succinct_sct.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/wavelet_trees.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/fast_cache.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/wm_int.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_treap.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_dac.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/rmq_support_sparse_table.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/vectors.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/uintx_t.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/structure_tree.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/ram_fs.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/coder.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/rmq_succinct_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/cst_fully.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/inv_perm_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/construct_lcp_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/uint256_t.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_elias_delta.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_tree.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_bitcompressed.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/construct_sa.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/rank_support_v.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/bp_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/bit_vector_il.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/rrr_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/util.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/csa_sampling_strategy.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/construct_sa_se.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/bp_support_g.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/bp_support_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/construct_bwt.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_tree_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_pc.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/nearest_neighbour_dictionary.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_gmr.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/hyb_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/nn_dict_dynamic.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/bits.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/sd_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/csa_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_ap.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/sorted_multi_stack_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/sdsl_concepts.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_hutu.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/rrr_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_treap_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/rmq_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/uint128_t.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/construct.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/vlc_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_vlc.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_trees.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/rank_support_v5.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/bp_support_gg.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/csa_bitcompressed.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_rlmn.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/iterators.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_support_tree2.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_support_tree.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/bp_support_algorithm.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/memory_management.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/louds_tree.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/construct_sa_se.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/lcp_support_tree.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/construct_sa.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/ram_filebuf.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/io.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/nn_dict_dynamic.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/wt_helper.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/construct_lcp_helper.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sd_vector.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/uint128_t.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/util.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/ram_fs.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/construct_lcp.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/construct_isa.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/uint256_t.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/bits.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/rrr_vector_15.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/config.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/construct_config.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/info.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/interface.h
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/k2_trees/src/k2_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/k2_trees/src/gen_k2t.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/suffix_trees/src/build_cst.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/suffix_trees/src/depth_stats.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/suffix_trees/src/time_and_space_cst.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/interface.h
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/pattern_random.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/info.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/wavelet_trees/src/gen_bwt.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/wavelet_trees/src/wt_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/self_delimiting_codes/src/sdc_benchmark.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/lcp/src/create_sa_bwt.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/lcp/src/create_lcp.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/rrr_vector/src/rrr_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/interface.h
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/info.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/gen_pattern.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/word_pat2char_pat.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_sort.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/size_of_idx.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_qprobing.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_greedy.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/build_idx.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/query_idx.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index.hpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/CMakeModules/check_mode_ti.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/cst-node-child-iterator.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/sa-int-construct-from-file.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/node_iterator.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/memory-visualization.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/louds-tree.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/fm-index.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/csa-alphabet-strategy.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/isa_access.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/uint64-array2int_vector.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/sd_vector_benchmark.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/bit-vector.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/int-vector-mapper.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/cst-bfs-iterator.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/text-statistics.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/wt_ap.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/range-minimum-queries.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/int-vector-buffer-iterator.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/fm-rmq-index.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/store_to_file.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/intersect.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/c++11-initializer-list.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/int-vector-entry.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/print_wt.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/storage-visualization.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/standalone_lcp.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/sa-construct-space-efficient.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/int-vector-buffer.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/write_structure.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/construct-in-memory.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/hugepages.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/k2_treap_in_mem.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/int-vector-buffer.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-07.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-09.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-24.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-23.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-18.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/rmq-example.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-16.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-11.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/cst-search.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-08.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-06.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-01.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-10.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-17.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-19.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-22.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-25.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/document_listing/doc_list_index.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-14.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-13.cpp
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Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-21.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/use-a-wavelet-tree.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-02.cpp
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Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/cst-traversal.cpp
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Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-12.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/csx-printf.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-15.cpp
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/expl-04.cpp
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Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/include/divsufsort_private.h
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/lib/utils.c
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/lib/divsufsort.c
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/lib/trsort.c
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Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/unbwt.c
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Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/mksary.c
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Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/sasearch.c
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/src/gmock-cardinalities.cc
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/src/gmock_main.cc
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/src/gmock-spec-builders.cc
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/src/gmock.cc
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/src/gmock-internal-utils.cc
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Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/test/gmock-nice-strict_test.cc
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/test/gmock-generated-internal-utils_test.cc
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/test/gmock-cardinalities_test.cc
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/test/gmock-more-actions_test.cc
Examining data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/test/gmock_ex_test.cc
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Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-01.cpp
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Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-08.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-25.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-22.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-19.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-17.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-10.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/csx-printf.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-09.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-07.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-11.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-16.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-18.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-23.cpp
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Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-15.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-12.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-20.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/use-a-wavelet-tree.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/document_listing/doc_list_index.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/int-vector-buffer.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-03.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-04.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-21.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/cst-traversal.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-26.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/cst-search.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-13.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/expl-14.cpp
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Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/rmq-example.cpp
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Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/samples/sample5_unittest.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-spi.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-death-test.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-param-test.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest_prod.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-test-part.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-message.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest_pred_impl.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-tuple.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-param-util-generated.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-death-test-internal.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-filepath.h
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Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-string.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-param-util.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-internal.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/custom/gtest.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/custom/gtest-printers.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/custom/gtest-port.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port-arch.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-printers.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest-typed-test.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-all.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest_main.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-typed-test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-test-part.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/lib/sssort.c
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/lib/divsufsort.c
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/lib/trsort.c
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/lib/utils.c
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/include/divsufsort_private.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/unbwt.c
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/mksary.c
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/bwt.c
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/suftest.c
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/sasearch.c
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/c++11-initializer-list.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/bit-vector.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/construct-in-memory.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/memory-visualization.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/sa-int-construct-from-file.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/range-minimum-queries.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/sa-construct-space-efficient.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/uint64-array2int_vector.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/int-vector-mapper.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/node_iterator.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/write_structure.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/k2_treap_in_mem.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/int-vector-entry.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/louds-tree.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/isa_access.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/fm-index.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/wt_ap.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/cst-node-child-iterator.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/storage-visualization.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/sd_vector_benchmark.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/intersect.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/cst-bfs-iterator.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/int-vector-buffer-iterator.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/int-vector-buffer.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/store_to_file.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/text-statistics.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/standalone_lcp.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/fm-rmq-index.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/hugepages.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/print_wt.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/csa-alphabet-strategy.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_hutu.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/construct_config.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/construct_isa.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/rmq_support_sparse_table.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_treap_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/construct_lcp.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_pc.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/wavelet_trees.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/fast_cache.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/construct_sa.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/sorted_int_stack.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/memory_management.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/bp_support_g.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_rlmn.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_support_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/bit_vectors.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/csa_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_vlc.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_tree_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/bp_support_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/sorted_multi_stack_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/enc_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/csa_alphabet_strategy.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/dac_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/rmq_succinct_sct.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_arrays.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_trees.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_tree.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_treap_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_tree_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/rmq_succinct_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_gmr.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/sorted_stack_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/rank_support_scan.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/rank_support_v.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/louds_tree.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/io.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_ap.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/rrr_vector_15.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_elias_gamma.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/ram_filebuf.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/raster_img.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_comma.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/cst_iterators.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/cst_fully.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/structure_tree.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/nn_dict_dynamic.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/hyb_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/select_support_scan.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/util.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/inv_perm_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/csa_wt.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/uint256_t.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_blcd.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_treap.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_tree_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/nearest_neighbour_dictionary.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/sdsl_concepts.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/rrr_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/vlc_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/rank_support_v5.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_elias_delta.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/ram_fs.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/rmq_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/vectors.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/qsufsort.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/uintx_t.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/rank_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_bitcompressed.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/sfstream.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/bp_support_gg.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/wm_int.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_dac.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/sd_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/construct_lcp_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/bp_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_int.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/rrr_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/csa_bitcompressed.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/select_support_mcl.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/config.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_support_tree2.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/bit_vector_il.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_huff.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/select_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/construct_sa_se.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/bits.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/uint128_t.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/coder.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/construct.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/construct_bwt.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/cst_sct3.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/cst_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/csa_sampling_strategy.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/bp_support_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_wt.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_byte.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/iterators.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_support_tree.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/coder_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/search_bidirectional_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/sorted_stack_support_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/sorted_int_stack_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/cst_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/k2_tree_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/sd_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/k2_treap_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/csa_int_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/inv_perm_support_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/bits_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/csa_byte_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/cst_int_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_buffer_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/nn_dict_dynamic_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/rmq_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/lcp_construct_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_generator.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/wt_byte_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/replace_int_vector_value.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/select_support_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/dac_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/rank_support_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/cst_byte_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/bit_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/sa_construct_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/wt_int_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/bit_vector_generator.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/config.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/ram_filebuf.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/construct_sa.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/rrr_vector_15.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/louds_tree.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/construct_isa.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/construct_lcp.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/lcp_support_tree.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/wt_helper.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/ram_fs.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/bp_support_algorithm.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/util.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sd_vector.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/construct_config.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/uint128_t.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/memory_management.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/nn_dict_dynamic.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/io.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/uint256_t.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/bits.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/construct_sa_se.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/construct_lcp_helper.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/CMakeModules/check_mode_ti.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/size_of_idx.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_sort.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/gen_pattern.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/query_idx.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_greedy.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/word_pat2char_pat.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/build_idx.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_qprobing.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/self_delimiting_codes/src/sdc_benchmark.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/lcp/src/create_sa_bwt.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/lcp/src/create_lcp.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/pattern_random.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/info.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/interface.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/info.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/interface.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/rrr_vector/src/rrr_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/interface.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/info.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/wavelet_trees/src/gen_bwt.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/wavelet_trees/src/wt_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/suffix_trees/src/depth_stats.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/suffix_trees/src/time_and_space_cst.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/suffix_trees/src/build_cst.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/k2_trees/src/gen_k2t.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/k2_trees/src/k2_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/gbwt.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/tests/test_metadata.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/tests/test_queries.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/tests/test_bwtmerge.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/tests/test_variants.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/tests/test_support.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/utils.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/internal.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/gbwt.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/cached_gbwt.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/variants.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/metadata.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/support.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/files.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/algorithms.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/bwtmerge.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/dynamic_gbwt.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/bwtmerge.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/metadata.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/metadata_tool.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/suffix_trees/src/time_and_space_cst.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/suffix_trees/src/build_cst.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/suffix_trees/src/depth_stats.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_count/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_count/src/interface.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_count/src/info.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_locate/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_locate/src/info.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_locate/src/interface.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_locate/src/pattern_random.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/wavelet_trees/src/gen_bwt.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/wavelet_trees/src/wt_time_and_space.cpp
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Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/tutorial/expl-01.cpp
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Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/samples/sample4.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/samples/sample1_unittest.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/samples/prime_tables.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/samples/sample2_unittest.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/samples/sample3-inl.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/samples/sample10_unittest.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/samples/sample1.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/samples/sample6_unittest.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/samples/sample9_unittest.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/samples/sample2.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/samples/sample4_unittest.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_xml_outfile1_test_.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-listener_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_shuffle_test_.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-linked_ptr_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_output_test_.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_all_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-message_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_env_var_test_.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_prod_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_pred_impl_unittest.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-tuple_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/production.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_help_test_.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-param-test2_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-test-part_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_no_test_unittest.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_environment_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_ex_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_premature_exit_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/production.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-param-test_test.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_list_tests_unittest_.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_throw_on_failure_ex_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_throw_on_failure_test_.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-unittest-api_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_sole_header_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-typed-test_test.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_main_unittest.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-port_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-options_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_filter_unittest_.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_break_on_failure_unittest_.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-typed-test_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_color_test_.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_stress_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-typed-test2_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-param-test_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_xml_outfile2_test_.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_uninitialized_test_.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_catch_exceptions_test_.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_xml_output_unittest_.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_repeat_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget_test.cc
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget.h
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/vectors.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/louds_tree.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/suffix_array_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/lcp_byte.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/uintx_t.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/lcp_support_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/lcp_dac.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/raster_img.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/cst_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/bp_support_g.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/cst_sct3.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/k2_treap_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/uint256_t.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/sorted_int_stack.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/config.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/construct_sa.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/cst_fully.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/wt_int.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/sdsl_concepts.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/wt_blcd.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/dac_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/lcp.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/memory_management.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/wt_ap.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/wt_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/enc_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/bp_support_gg.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/nearest_neighbour_dictionary.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/construct_config.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/lcp_wt.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/rank_support_v.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/k2_treap_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/uint128_t.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/qsufsort.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/csa_wt.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/sorted_stack_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/sfstream.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/sorted_multi_stack_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/wt_pc.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/rmq_succinct_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/rmq_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/sd_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/bit_vector_il.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/csa_alphabet_strategy.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/construct_bwt.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/iterators.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/k2_treap.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/ram_fs.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/k2_tree_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/rank_support_scan.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/wt_huff.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/suffix_trees.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/rmq_succinct_sct.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/bp_support_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/wm_int.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/fast_cache.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/coder_elias_gamma.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/construct.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/suffix_tree_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/construct_isa.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/coder_comma.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/util.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/rank_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/ram_filebuf.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/construct_lcp.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/suffix_tree_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/lcp_vlc.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/wavelet_trees.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/select_support_scan.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/coder.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/nn_dict_dynamic.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/wt_rlmn.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/wt_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/coder_elias_delta.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/structure_tree.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/rmq_support_sparse_table.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/wt_gmr.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/wt_hutu.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/rank_support_v5.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/rrr_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/inv_perm_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/lcp_bitcompressed.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/bp_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/construct_sa_se.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/lcp_support_tree.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/csa_sampling_strategy.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/vlc_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/bit_vectors.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/select_support_mcl.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/csa_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/lcp_support_tree2.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/suffix_arrays.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/csa_bitcompressed.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/io.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/bits.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/k2_tree.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/construct_lcp_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/rrr_vector_15.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/hyb_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/bp_support_sada.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/rrr_vector.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/cst_iterators.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/select_support.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/wt_ap.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/csa-alphabet-strategy.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/node_iterator.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/uint64-array2int_vector.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/int-vector-mapper.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/cst-node-child-iterator.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/int-vector-buffer-iterator.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/standalone_lcp.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/k2_treap_in_mem.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/construct-in-memory.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/int-vector-entry.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/fm-rmq-index.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/print_wt.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/c++11-initializer-list.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/write_structure.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/storage-visualization.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/bit-vector.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/intersect.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/cst-bfs-iterator.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/store_to_file.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/range-minimum-queries.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/sa-int-construct-from-file.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/int-vector-buffer.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/fm-index.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/sa-construct-space-efficient.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/memory-visualization.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/sd_vector_benchmark.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/hugepages.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/isa_access.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/text-statistics.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/louds-tree.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/CMakeModules/check_mode_ti.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/cst_byte_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/search_bidirectional_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/replace_int_vector_value.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/inv_perm_support_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/k2_tree_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/sorted_int_stack_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/csa_int_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/rmq_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/sd_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/bit_vector_generator.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_buffer_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/nn_dict_dynamic_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/sorted_stack_support_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_generator.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/k2_treap_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/lcp_construct_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/wt_int_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/wt_byte_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/cst_helper.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/csa_byte_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/select_support_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/bits_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/rank_support_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/dac_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/cst_int_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/sa_construct_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/bit_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/coder_test.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/util.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/ram_fs.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/construct_sa.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_fibonacci.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/config.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/construct_lcp_helper.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/construct_config.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/louds_tree.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/wt_helper.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/bits.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/ram_filebuf.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sd_vector.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/lcp_support_tree.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/uint128_t.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/io.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/rrr_vector_15.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/nn_dict_dynamic.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/uint256_t.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/construct_lcp.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/construct_isa.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/memory_management.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/bp_support_algorithm.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/construct_sa_se.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/handle.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/types.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/util.hpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/gfa2gbwt.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/gfa.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/minimizer.cpp
Examining data/vg-1.27.1+ds/deps/gbwtgraph/utils.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/CMakeModules/check_mode_ti.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/rmq-example.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-05.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-02.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-21.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/cst-search.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-26.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-13.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-14.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-03.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-04.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-15.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-12.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/cst-traversal.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-20.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/document_listing/doc_list_index.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-18.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-11.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-16.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/int-vector-buffer.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-23.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-24.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-07.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/csx-printf.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-09.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-25.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-22.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-17.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-10.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-19.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-08.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-01.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/expl-06.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/use-a-wavelet-tree.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/construct-in-memory.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/csa-alphabet-strategy.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/print_wt.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/c++11-initializer-list.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/int-vector-buffer.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/memory-visualization.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/write_structure.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/int-vector-entry.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/store_to_file.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/k2_treap_in_mem.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/int-vector-buffer-iterator.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/range-minimum-queries.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/isa_access.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/cst-bfs-iterator.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/storage-visualization.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/sd_vector_benchmark.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/fm-index.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/fm-rmq-index.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/hugepages.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/louds-tree.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/cst-node-child-iterator.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/intersect.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/sa-construct-space-efficient.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/standalone_lcp.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/text-statistics.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/bit-vector.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/int-vector-mapper.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/node_iterator.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/wt_ap.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/sa-int-construct-from-file.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/examples/uint64-array2int_vector.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/util.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/construct.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/sorted_multi_stack_support.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/lcp_wt.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/rrr_vector_15.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/suffix_trees.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/lcp_support_tree.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/cst_iterators.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/iterators.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/wt_blcd.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/memory_management.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/sd_vector.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/wt_int.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/select_support_mcl.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/config.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/lcp_dac.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/k2_treap_helper.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/suffix_arrays.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/rrr_helper.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/bit_vectors.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/uintx_t.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/bp_support.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/uint128_t.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/vectors.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/select_support_scan.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/coder_elias_gamma.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/wm_int.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/coder.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/wt_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/vlc_vector.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/k2_tree_helper.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/ram_fs.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/rank_support_scan.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/wt_huff.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/bits.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/suffix_array_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/construct_isa.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/construct_lcp_helper.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/cst_fully.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/suffix_tree_helper.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/rank_support_v.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/uint256_t.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/construct_lcp.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/rmq_succinct_sada.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/inv_perm_support.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/suffix_tree_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/hyb_vector.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/csa_alphabet_strategy.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/wavelet_trees.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/csa_wt.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/coder_comma.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/rrr_vector.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/bp_support_g.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/construct_sa.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/csa_sada.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/ram_filebuf.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/lcp_bitcompressed.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/louds_tree.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/construct_bwt.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/rmq_support_sparse_table.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/wt_pc.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/nearest_neighbour_dictionary.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/structure_tree.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/wt_hutu.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/raster_img.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/io.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/rank_support_v5.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/wt_gmr.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/coder_elias_delta.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/lcp.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/cst_sct3.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/wt_rlmn.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/dac_vector.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/rmq_support.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/cst_sada.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/k2_treap_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/enc_vector.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/lcp_byte.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/lcp_vlc.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/rmq_succinct_sct.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/nn_dict_dynamic.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/bit_vector_il.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/sorted_stack_support.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/sorted_int_stack.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/k2_treap.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/bp_support_sada.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/select_support.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/k2_tree.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/csa_sampling_strategy.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/bp_support_gg.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/lcp_support_sada.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/wt_helper.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/csa_bitcompressed.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/construct_sa_se.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/bp_support_algorithm.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/construct_config.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/rank_support.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/lcp_support_tree2.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/wt_ap.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/fast_cache.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/qsufsort.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/sfstream.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/sdsl_concepts.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/self_delimiting_codes/src/sdc_benchmark.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/suffix_trees/src/time_and_space_cst.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/suffix_trees/src/build_cst.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/suffix_trees/src/depth_stats.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_count/src/interface.h
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_count/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_count/src/info.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/rrr_vector/src/rrr_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_locate/src/pattern_random.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_locate/src/interface.h
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_locate/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_locate/src/info.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/lcp/src/create_lcp.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/lcp/src/create_sa_bwt.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/wavelet_trees/src/wt_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/wavelet_trees/src/gen_bwt.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_extract/src/interface.h
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_extract/src/info.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_extract/src/build_index_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/document_retrieval/src/size_of_idx.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_sort.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/document_retrieval/src/gen_pattern.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_greedy.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_qprobing.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/document_retrieval/src/word_pat2char_pat.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/document_retrieval/src/doc_list_index_sada.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/document_retrieval/src/build_idx.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/document_retrieval/src/query_idx.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/k2_trees/src/k2_time_and_space.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/k2_trees/src/gen_k2t.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/wt_int_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/wt_byte_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/sorted_int_stack_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/nn_dict_dynamic_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/dac_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/inv_perm_support_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/bit_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/sorted_stack_support_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_generator.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/cst_helper.hpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/search_bidirectional_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/cst_int_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/csa_byte_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/rmq_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/bit_vector_generator.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/coder_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/replace_int_vector_value.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/select_support_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/k2_treap_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/k2_tree_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/csa_int_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/rank_support_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/bits_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_buffer_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/lcp_construct_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/sa_construct_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/cst_byte_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/test/sd_vector_test.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/bits.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/nn_dict_dynamic.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/sd_vector.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/uint128_t.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/lcp_support_tree.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/uint256_t.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_sa_se.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/util.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/io.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/config.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/rrr_vector_15.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_sa.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/bp_support_algorithm.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_lcp.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_config.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/memory_management.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_isa.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/csa_alphabet_strategy.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/ram_filebuf.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/louds_tree.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/ram_fs.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/wt_helper.cpp
Examining data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp
Examining data/vg-1.27.1+ds/deps/sha1/sha1.cpp
Examining data/vg-1.27.1+ds/deps/sha1/sha1.hpp
Examining data/vg-1.27.1+ds/deps/sha1/test_sha1.cpp
Examining data/vg-1.27.1+ds/deps/sha1/demo_sha1.cpp
Examining data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_mutable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_deletable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/path_position_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/deletable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/iteratee.hpp
Examining data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/expanding_overlay_graph.hpp
Examining data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/util.hpp
Examining data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/types.hpp
Examining data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/mutable_path_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/mutable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp
Examining data/vg-1.27.1+ds/deps/libhandlegraph/src/handle.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/allele.hpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/row_set.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/probability.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/math.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/math.hpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/probability.hpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/allele.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/row_set.hpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/interface.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/DP_map.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/DP_map.hpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/haplotype_state_node.hpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/delay_multiplier.hpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/serialize_index.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/input_haplotype.hpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/interface.h
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/reference.hpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/input_haplotype.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/haplotype_manager.hpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/haplotype_state_tree.hpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/reference.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/reference_sequence.hpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/penalty_set.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/profiler.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/test.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/tree_tests.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/speed_tree.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/reference_sequence.cpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/linhapexample.c
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/set_of_extensions.hpp
Examining data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/penalty_set.hpp
Examining data/vg-1.27.1+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected/inc/3_Absorb3edge2x.h
Examining data/vg-1.27.1+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected/impl/3_Absorb3edge2x.c
Examining data/vg-1.27.1+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected/tests/allTests.c
Examining data/vg-1.27.1+ds/deps/pinchesAndCacti/externalTools/threeEdgeConnected/tests/3_Absorb3edge2xTest.c
Examining data/vg-1.27.1+ds/deps/pinchesAndCacti/tests/allTests.c
Examining data/vg-1.27.1+ds/deps/pinchesAndCacti/tests/stPinchGraphsTest.c
Examining data/vg-1.27.1+ds/deps/pinchesAndCacti/tests/stCactusGraphsTest.c
Examining data/vg-1.27.1+ds/deps/pinchesAndCacti/inc/stPinchGraphs.h
Examining data/vg-1.27.1+ds/deps/pinchesAndCacti/inc/stCactusGraphs.h
Examining data/vg-1.27.1+ds/deps/pinchesAndCacti/impl/stPinchGraphs.c
Examining data/vg-1.27.1+ds/deps/pinchesAndCacti/impl/stCactusGraphs.c
Examining data/vg-1.27.1+ds/deps/dozeu/log.h
Examining data/vg-1.27.1+ds/deps/dozeu/unittest.h
Examining data/vg-1.27.1+ds/deps/dozeu/example.protein.c
Examining data/vg-1.27.1+ds/deps/dozeu/simde/simde-arch.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/simde-diagnostic.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/hedley.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/check.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/simde-common.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/simde-features.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/debug-trap.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/simde-math.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/ssse3.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/sse4.2.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/avx512f.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/avx512bw.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/gfni.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/sse4.1.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/svml.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/sse2.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/sse3.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/mmx.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/avx512cd.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/sse.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/avx2.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/fma.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/avx.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/avx512vl.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/x86/avx512dq.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/paddl.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/add.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/combine.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/mlal_high.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/trn.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/uzp2.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/get_high.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/neg.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/get_lane.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/cltz.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/shl_n.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/get_low.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/min.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/abs.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/reinterpret.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/st1.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/rshr_n.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/clez.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/uzp1.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/cgt.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/sra_n.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/movl_high.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/pmin.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/orr.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/movl.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/addw.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/cle.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/padal.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/st1_lane.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/ceqz.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/dup_n.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/eor.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/cagt.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/padd.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/uzp.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/ld1.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/mul.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/trn1.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/bsl.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/mlal.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/addl.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/mla.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/max.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/zip1.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/types.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/cge.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/qmovn.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/cgtz.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/ceq.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/zip.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/rsra_n.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/shr_n.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/mull.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/sub.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/trn2.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/and.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/mvn.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/tst.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/zip2.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/pmax.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/shl.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon/cgez.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/arm/neon.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/simde-detect-clang.h
Examining data/vg-1.27.1+ds/deps/dozeu/simde/simde-constify.h
Examining data/vg-1.27.1+ds/deps/dozeu/dozeu.h
Examining data/vg-1.27.1+ds/deps/dozeu/example.c
Examining data/vg-1.27.1+ds/deps/dozeu/example.2bit.c
Examining data/vg-1.27.1+ds/deps/sparsepp/examples/serialize_file.cc
Examining data/vg-1.27.1+ds/deps/sparsepp/examples/serialize_stream.cc
Examining data/vg-1.27.1+ds/deps/sparsepp/examples/serialize_large.cc
Examining data/vg-1.27.1+ds/deps/sparsepp/examples/hash_std.cc
Examining data/vg-1.27.1+ds/deps/sparsepp/examples/emplace.cc
Examining data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_timer.h
Examining data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_utils.h
Examining data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_memory.h
Examining data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_dlalloc.h
Examining data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_config.h
Examining data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp.h
Examining data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_stdint.h
Examining data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_smartptr.h
Examining data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_traits.h
Examining data/vg-1.27.1+ds/deps/sparsepp/tests/spp_alloc_test.cc
Examining data/vg-1.27.1+ds/deps/sparsepp/tests/perftest1.cc
Examining data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc
Examining data/vg-1.27.1+ds/deps/sparsepp/tests/spp_bitset_test.cc
Examining data/vg-1.27.1+ds/deps/sparsepp/tests/spp_relative_include_test.cc
Examining data/vg-1.27.1+ds/deps/progress_bar/progress_bar.cpp
Examining data/vg-1.27.1+ds/deps/progress_bar/progress_bar.hpp
Examining data/vg-1.27.1+ds/deps/progress_bar/main.cpp
Examining data/vg-1.27.1+ds/src/banded_global_aligner.cpp
Examining data/vg-1.27.1+ds/src/funnel.hpp
Examining data/vg-1.27.1+ds/src/deconstructor.cpp
Examining data/vg-1.27.1+ds/src/mem.cpp
Examining data/vg-1.27.1+ds/src/index_manager.hpp
Examining data/vg-1.27.1+ds/src/nodetraversal.hpp
Examining data/vg-1.27.1+ds/src/kmer.hpp
Examining data/vg-1.27.1+ds/src/sampler.hpp
Examining data/vg-1.27.1+ds/src/phase_unfolder.hpp
Examining data/vg-1.27.1+ds/src/minimizer_mapper.hpp
Examining data/vg-1.27.1+ds/src/phased_genome.cpp
Examining data/vg-1.27.1+ds/src/packer.cpp
Examining data/vg-1.27.1+ds/src/stream_sorter.hpp
Examining data/vg-1.27.1+ds/src/constructor.cpp
Examining data/vg-1.27.1+ds/src/augment.hpp
Examining data/vg-1.27.1+ds/src/wang_hash.hpp
Examining data/vg-1.27.1+ds/src/annotation.hpp
Examining data/vg-1.27.1+ds/src/dagified_graph.hpp
Examining data/vg-1.27.1+ds/src/traversal_support.cpp
Examining data/vg-1.27.1+ds/src/variant_adder.cpp
Examining data/vg-1.27.1+ds/src/source_sink_overlay.hpp
Examining data/vg-1.27.1+ds/src/subcommand/surject_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/annotate_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/help_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/index_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/subcommand.hpp
Examining data/vg-1.27.1+ds/src/subcommand/trace_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/test_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/benchmark_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/pack_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/gampcompare_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/sift_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/gbwt_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/prune_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/explode_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/locify_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/subcommand.cpp
Examining data/vg-1.27.1+ds/src/subcommand/ids_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/concat_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/deconstruct_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/sort_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/view_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/viz_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/sim_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/augment_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/giraffe_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/mpmap_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/find_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/call_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/rna_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/map_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/kmers_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/gamcompare_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/compare_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/convert_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/gamsort_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/mod_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/translate_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/vectorize_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/minimizer_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/align_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/snarls_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/depth_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/circularize_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/combine_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/stats_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/bugs_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/version_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/crash_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/filter_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/recalibrate_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/simplify_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/validate_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/dotplot_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/paths_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/msga_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/mcmc_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/chunk_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/cluster_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/genotype_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/construct_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/join_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/inject_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/add_main.cpp
Examining data/vg-1.27.1+ds/src/subcommand/srpe_main.cpp
Examining data/vg-1.27.1+ds/src/alignment.cpp
Examining data/vg-1.27.1+ds/src/entropy.hpp
Examining data/vg-1.27.1+ds/src/haplotype_extracter.hpp
Examining data/vg-1.27.1+ds/src/progressive.hpp
Examining data/vg-1.27.1+ds/src/convert.hpp
Examining data/vg-1.27.1+ds/src/prune.cpp
Examining data/vg-1.27.1+ds/src/vectorizer.cpp
Examining data/vg-1.27.1+ds/src/minimizer_mapper.cpp
Examining data/vg-1.27.1+ds/src/phase_unfolder.cpp
Examining data/vg-1.27.1+ds/src/kmer.cpp
Examining data/vg-1.27.1+ds/src/sampler.cpp
Examining data/vg-1.27.1+ds/src/stream_sorter.cpp
Examining data/vg-1.27.1+ds/src/constructor.hpp
Examining data/vg-1.27.1+ds/src/packer.hpp
Examining data/vg-1.27.1+ds/src/phased_genome.hpp
Examining data/vg-1.27.1+ds/src/mem.hpp
Examining data/vg-1.27.1+ds/src/deconstructor.hpp
Examining data/vg-1.27.1+ds/src/banded_global_aligner.hpp
Examining data/vg-1.27.1+ds/src/funnel.cpp
Examining data/vg-1.27.1+ds/src/index_manager.cpp
Examining data/vg-1.27.1+ds/src/small_bitset.hpp
Examining data/vg-1.27.1+ds/src/alignment.hpp
Examining data/vg-1.27.1+ds/src/vectorizer.hpp
Examining data/vg-1.27.1+ds/src/prune.hpp
Examining data/vg-1.27.1+ds/src/progressive.cpp
Examining data/vg-1.27.1+ds/src/haplotype_extracter.cpp
Examining data/vg-1.27.1+ds/src/entropy.cpp
Examining data/vg-1.27.1+ds/src/augment.cpp
Examining data/vg-1.27.1+ds/src/variant_adder.hpp
Examining data/vg-1.27.1+ds/src/source_sink_overlay.cpp
Examining data/vg-1.27.1+ds/src/traversal_support.hpp
Examining data/vg-1.27.1+ds/src/dagified_graph.cpp
Examining data/vg-1.27.1+ds/src/variant_recall.hpp
Examining data/vg-1.27.1+ds/src/rare_variant_simplifier.hpp
Examining data/vg-1.27.1+ds/src/indexed_vg.cpp
Examining data/vg-1.27.1+ds/src/swap_remove.hpp
Examining data/vg-1.27.1+ds/src/unittest/incremental_subgraph.cpp
Examining data/vg-1.27.1+ds/src/unittest/packed_graph.cpp
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Examining data/vg-1.27.1+ds/src/unittest/hfile_cppstream.cpp
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Examining data/vg-1.27.1+ds/src/unittest/dagified_graph.cpp
Examining data/vg-1.27.1+ds/src/unittest/phase_unfolder.cpp
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Examining data/vg-1.27.1+ds/src/unittest/blocked_gzip_input_stream.cpp
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Examining data/vg-1.27.1+ds/src/unittest/three_edge_connected_components.cpp
Examining data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp
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Examining data/vg-1.27.1+ds/src/unittest/path_index.cpp
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Examining data/vg-1.27.1+ds/src/unittest/blocked_gzip_output_stream.cpp
Examining data/vg-1.27.1+ds/src/unittest/driver.hpp
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Examining data/vg-1.27.1+ds/src/unittest/flow_sort_test.cpp
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Examining data/vg-1.27.1+ds/src/unittest/minimizer_mapper.cpp
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Examining data/vg-1.27.1+ds/src/unittest/driver.cpp
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Examining data/vg-1.27.1+ds/src/unittest/packed_structs.cpp
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Examining data/vg-1.27.1+ds/src/unittest/tree_subgraph.cpp
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Examining data/vg-1.27.1+ds/src/unittest/mapper.cpp
Examining data/vg-1.27.1+ds/src/unittest/cluster.cpp
Examining data/vg-1.27.1+ds/src/unittest/annotation.cpp
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Examining data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp
Examining data/vg-1.27.1+ds/src/unittest/splicing.cpp
Examining data/vg-1.27.1+ds/src/unittest/k_widest_paths.cpp
Examining data/vg-1.27.1+ds/src/unittest/msa_converter.cpp
Examining data/vg-1.27.1+ds/src/unittest/random_graph.cpp
Examining data/vg-1.27.1+ds/src/unittest/path_component_index.cpp
Examining data/vg-1.27.1+ds/src/unittest/mcmc_genotyper.cpp
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Examining data/vg-1.27.1+ds/src/unittest/copy_graph.cpp
Examining data/vg-1.27.1+ds/src/unittest/gfa.cpp
Examining data/vg-1.27.1+ds/src/unittest/genotyper.cpp
Examining data/vg-1.27.1+ds/src/unittest/position.cpp
Examining data/vg-1.27.1+ds/src/unittest/dagify.cpp
Examining data/vg-1.27.1+ds/src/unittest/constructor.cpp
Examining data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp
Examining data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp
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Examining data/vg-1.27.1+ds/src/unittest/multipath_alignment.cpp
Examining data/vg-1.27.1+ds/src/unittest/genome_state.cpp
Examining data/vg-1.27.1+ds/src/unittest/vcf_buffer.cpp
Examining data/vg-1.27.1+ds/src/unittest/vpkg.cpp
Examining data/vg-1.27.1+ds/src/unittest/dozeu_pinning_overlay.cpp
Examining data/vg-1.27.1+ds/src/unittest/multipath_alignment_graph.cpp
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Examining data/vg-1.27.1+ds/src/unittest/test_aligner.hpp
Examining data/vg-1.27.1+ds/src/gbwt_helper.cpp
Examining data/vg-1.27.1+ds/src/vg_set.cpp
Examining data/vg-1.27.1+ds/src/genome_state.hpp
Examining data/vg-1.27.1+ds/src/snarl_caller.cpp
Examining data/vg-1.27.1+ds/src/multipath_alignment_graph.cpp
Examining data/vg-1.27.1+ds/src/incremental_subgraph.hpp
Examining data/vg-1.27.1+ds/src/multipath_alignment.cpp
Examining data/vg-1.27.1+ds/src/small_snarl_simplifier.cpp
Examining data/vg-1.27.1+ds/src/index.hpp
Examining data/vg-1.27.1+ds/src/memusage.cpp
Examining data/vg-1.27.1+ds/src/colors.hpp
Examining data/vg-1.27.1+ds/src/region.cpp
Examining data/vg-1.27.1+ds/src/watchdog.hpp
Examining data/vg-1.27.1+ds/src/name_mapper.cpp
Examining data/vg-1.27.1+ds/src/cactus.cpp
Examining data/vg-1.27.1+ds/src/aligner.cpp
Examining data/vg-1.27.1+ds/src/chunker.hpp
Examining data/vg-1.27.1+ds/src/graph_caller.hpp
Examining data/vg-1.27.1+ds/src/graph_synchronizer.hpp
Examining data/vg-1.27.1+ds/src/haplotype_indexer.hpp
Examining data/vg-1.27.1+ds/src/multipath_mapper.cpp
Examining data/vg-1.27.1+ds/src/flow_sort.cpp
Examining data/vg-1.27.1+ds/src/subgraph.cpp
Examining data/vg-1.27.1+ds/src/snarls.cpp
Examining data/vg-1.27.1+ds/src/vcf_buffer.cpp
Examining data/vg-1.27.1+ds/src/multipath_alignment_graph.hpp
Examining data/vg-1.27.1+ds/src/incremental_subgraph.cpp
Examining data/vg-1.27.1+ds/src/snarl_caller.hpp
Examining data/vg-1.27.1+ds/src/main.cpp
Examining data/vg-1.27.1+ds/src/genome_state.cpp
Examining data/vg-1.27.1+ds/src/crash.hpp
Examining data/vg-1.27.1+ds/src/vg_set.hpp
Examining data/vg-1.27.1+ds/src/multipath_alignment.hpp
Examining data/vg-1.27.1+ds/src/rare_variant_simplifier.cpp
Examining data/vg-1.27.1+ds/src/variant_recall.cpp
Examining data/vg-1.27.1+ds/src/gbwt_helper.hpp
Examining data/vg-1.27.1+ds/src/indexed_vg.hpp
Examining data/vg-1.27.1+ds/src/multipath_mapper.hpp
Examining data/vg-1.27.1+ds/src/graph_synchronizer.cpp
Examining data/vg-1.27.1+ds/src/haplotype_indexer.cpp
Examining data/vg-1.27.1+ds/src/vcf_buffer.hpp
Examining data/vg-1.27.1+ds/src/subgraph.hpp
Examining data/vg-1.27.1+ds/src/snarls.hpp
Examining data/vg-1.27.1+ds/src/flow_sort.hpp
Examining data/vg-1.27.1+ds/src/region.hpp
Examining data/vg-1.27.1+ds/src/memusage.hpp
Examining data/vg-1.27.1+ds/src/small_snarl_simplifier.hpp
Examining data/vg-1.27.1+ds/src/index.cpp
Examining data/vg-1.27.1+ds/src/chunker.cpp
Examining data/vg-1.27.1+ds/src/graph_caller.cpp
Examining data/vg-1.27.1+ds/src/name_mapper.hpp
Examining data/vg-1.27.1+ds/src/cactus.hpp
Examining data/vg-1.27.1+ds/src/aligner.hpp
Examining data/vg-1.27.1+ds/src/watchdog.cpp
Examining data/vg-1.27.1+ds/src/mcmc_caller.hpp
Examining data/vg-1.27.1+ds/src/types.hpp
Examining data/vg-1.27.1+ds/src/gff_reader.hpp
Examining data/vg-1.27.1+ds/src/homogenizer.hpp
Examining data/vg-1.27.1+ds/src/translator.hpp
Examining data/vg-1.27.1+ds/src/mcmc_genotyper.cpp
Examining data/vg-1.27.1+ds/src/multipath_alignment_emitter.cpp
Examining data/vg-1.27.1+ds/src/hts_alignment_emitter.cpp
Examining data/vg-1.27.1+ds/src/identity_overlay.cpp
Examining data/vg-1.27.1+ds/src/statistics.hpp
Examining data/vg-1.27.1+ds/src/ssw_aligner.hpp
Examining data/vg-1.27.1+ds/src/benchmark.cpp
Examining data/vg-1.27.1+ds/src/position.cpp
Examining data/vg-1.27.1+ds/src/extra_node_graph.cpp
Examining data/vg-1.27.1+ds/src/path.cpp
Examining data/vg-1.27.1+ds/src/haplotypes.hpp
Examining data/vg-1.27.1+ds/src/split_strand_graph.hpp
Examining data/vg-1.27.1+ds/src/path_index.cpp
Examining data/vg-1.27.1+ds/src/integrated_snarl_finder.cpp
Examining data/vg-1.27.1+ds/src/build_index.cpp
Examining data/vg-1.27.1+ds/src/seed_clusterer.cpp
Examining data/vg-1.27.1+ds/src/hash_map.hpp
Examining data/vg-1.27.1+ds/src/scanner.cpp
Examining data/vg-1.27.1+ds/src/feature_set.hpp
Examining data/vg-1.27.1+ds/src/utility.cpp
Examining data/vg-1.27.1+ds/src/dozeu_interface.hpp
Examining data/vg-1.27.1+ds/src/subgraph_overlay.hpp
Examining data/vg-1.27.1+ds/src/option.cpp
Examining data/vg-1.27.1+ds/src/position.hpp
Examining data/vg-1.27.1+ds/src/algorithms/normalize.hpp
Examining data/vg-1.27.1+ds/src/algorithms/find_tips.hpp
Examining data/vg-1.27.1+ds/src/algorithms/extract_connecting_graph.hpp
Examining data/vg-1.27.1+ds/src/algorithms/weakly_connected_components.hpp
Examining data/vg-1.27.1+ds/src/algorithms/distance_to_tail.hpp
Examining data/vg-1.27.1+ds/src/algorithms/to_gfa.hpp
Examining data/vg-1.27.1+ds/src/algorithms/dfs.cpp
Examining data/vg-1.27.1+ds/src/algorithms/coverage_depth.hpp
Examining data/vg-1.27.1+ds/src/algorithms/count_walks.hpp
Examining data/vg-1.27.1+ds/src/algorithms/subgraph.cpp
Examining data/vg-1.27.1+ds/src/algorithms/sorted_id_ranges.hpp
Examining data/vg-1.27.1+ds/src/algorithms/dijkstra.hpp
Examining data/vg-1.27.1+ds/src/algorithms/simplify_siblings.hpp
Examining data/vg-1.27.1+ds/src/algorithms/weakly_connected_components.cpp
Examining data/vg-1.27.1+ds/src/algorithms/distance_to_tail.cpp
Examining data/vg-1.27.1+ds/src/algorithms/normalize.cpp
Examining data/vg-1.27.1+ds/src/algorithms/extract_connecting_graph.cpp
Examining data/vg-1.27.1+ds/src/algorithms/find_tips.cpp
Examining data/vg-1.27.1+ds/src/algorithms/sorted_id_ranges.cpp
Examining data/vg-1.27.1+ds/src/algorithms/subgraph.hpp
Examining data/vg-1.27.1+ds/src/algorithms/count_walks.cpp
Examining data/vg-1.27.1+ds/src/algorithms/simplify_siblings.cpp
Examining data/vg-1.27.1+ds/src/algorithms/dijkstra.cpp
Examining data/vg-1.27.1+ds/src/algorithms/dfs.hpp
Examining data/vg-1.27.1+ds/src/algorithms/to_gfa.cpp
Examining data/vg-1.27.1+ds/src/algorithms/coverage_depth.cpp
Examining data/vg-1.27.1+ds/src/algorithms/remove_high_degree.hpp
Examining data/vg-1.27.1+ds/src/algorithms/eades_algorithm.hpp
Examining data/vg-1.27.1+ds/src/algorithms/unchop.hpp
Examining data/vg-1.27.1+ds/src/algorithms/gfa_to_handle.cpp
Examining data/vg-1.27.1+ds/src/algorithms/three_edge_connected_components.hpp
Examining data/vg-1.27.1+ds/src/algorithms/id_sort.hpp
Examining data/vg-1.27.1+ds/src/algorithms/are_equivalent.hpp
Examining data/vg-1.27.1+ds/src/algorithms/walk.cpp
Examining data/vg-1.27.1+ds/src/algorithms/strongly_connected_components.hpp
Examining data/vg-1.27.1+ds/src/algorithms/reverse_complement.cpp
Examining data/vg-1.27.1+ds/src/algorithms/alignment_path_offsets.hpp
Examining data/vg-1.27.1+ds/src/algorithms/walk.hpp
Examining data/vg-1.27.1+ds/src/algorithms/are_equivalent.cpp
Examining data/vg-1.27.1+ds/src/algorithms/id_sort.cpp
Examining data/vg-1.27.1+ds/src/algorithms/three_edge_connected_components.cpp
Examining data/vg-1.27.1+ds/src/algorithms/strongly_connected_components.cpp
Examining data/vg-1.27.1+ds/src/algorithms/reverse_complement.hpp
Examining data/vg-1.27.1+ds/src/algorithms/eades_algorithm.cpp
Examining data/vg-1.27.1+ds/src/algorithms/remove_high_degree.cpp
Examining data/vg-1.27.1+ds/src/algorithms/gfa_to_handle.hpp
Examining data/vg-1.27.1+ds/src/algorithms/unchop.cpp
Examining data/vg-1.27.1+ds/src/algorithms/alignment_path_offsets.cpp
Examining data/vg-1.27.1+ds/src/algorithms/apply_bulk_modifications.cpp
Examining data/vg-1.27.1+ds/src/algorithms/append_graph.hpp
Examining data/vg-1.27.1+ds/src/algorithms/approx_path_distance.hpp
Examining data/vg-1.27.1+ds/src/algorithms/distance_to_head.hpp
Examining data/vg-1.27.1+ds/src/algorithms/jump_along_path.cpp
Examining data/vg-1.27.1+ds/src/algorithms/next_pos_chars.hpp
Examining data/vg-1.27.1+ds/src/algorithms/path_string.cpp
Examining data/vg-1.27.1+ds/src/algorithms/k_widest_paths.cpp
Examining data/vg-1.27.1+ds/src/algorithms/split_strands.cpp
Examining data/vg-1.27.1+ds/src/algorithms/expand_context.cpp
Examining data/vg-1.27.1+ds/src/algorithms/extract_extending_graph.hpp
Examining data/vg-1.27.1+ds/src/algorithms/is_acyclic.cpp
Examining data/vg-1.27.1+ds/src/algorithms/find_shortest_paths.hpp
Examining data/vg-1.27.1+ds/src/algorithms/next_pos_chars.cpp
Examining data/vg-1.27.1+ds/src/algorithms/jump_along_path.hpp
Examining data/vg-1.27.1+ds/src/algorithms/k_widest_paths.hpp
Examining data/vg-1.27.1+ds/src/algorithms/path_string.hpp
Examining data/vg-1.27.1+ds/src/algorithms/append_graph.cpp
Examining data/vg-1.27.1+ds/src/algorithms/apply_bulk_modifications.hpp
Examining data/vg-1.27.1+ds/src/algorithms/distance_to_head.cpp
Examining data/vg-1.27.1+ds/src/algorithms/approx_path_distance.cpp
Examining data/vg-1.27.1+ds/src/algorithms/is_acyclic.hpp
Examining data/vg-1.27.1+ds/src/algorithms/extract_extending_graph.cpp
Examining data/vg-1.27.1+ds/src/algorithms/find_shortest_paths.cpp
Examining data/vg-1.27.1+ds/src/algorithms/split_strands.hpp
Examining data/vg-1.27.1+ds/src/algorithms/expand_context.hpp
Examining data/vg-1.27.1+ds/src/algorithms/dagify.hpp
Examining data/vg-1.27.1+ds/src/algorithms/topological_sort.cpp
Examining data/vg-1.27.1+ds/src/algorithms/a_star.hpp
Examining data/vg-1.27.1+ds/src/algorithms/extract_containing_graph.cpp
Examining data/vg-1.27.1+ds/src/algorithms/merge.cpp
Examining data/vg-1.27.1+ds/src/algorithms/nearest_offsets_in_paths.cpp
Examining data/vg-1.27.1+ds/src/algorithms/is_single_stranded.hpp
Examining data/vg-1.27.1+ds/src/algorithms/extend.hpp
Examining data/vg-1.27.1+ds/src/algorithms/copy_graph.hpp
Examining data/vg-1.27.1+ds/src/algorithms/kmer.cpp
Examining data/vg-1.27.1+ds/src/algorithms/shortest_cycle.cpp
Examining data/vg-1.27.1+ds/src/algorithms/is_single_stranded.cpp
Examining data/vg-1.27.1+ds/src/algorithms/extend.cpp
Examining data/vg-1.27.1+ds/src/algorithms/topological_sort.hpp
Examining data/vg-1.27.1+ds/src/algorithms/dagify.cpp
Examining data/vg-1.27.1+ds/src/algorithms/nearest_offsets_in_paths.hpp
Examining data/vg-1.27.1+ds/src/algorithms/merge.hpp
Examining data/vg-1.27.1+ds/src/algorithms/extract_containing_graph.hpp
Examining data/vg-1.27.1+ds/src/algorithms/shortest_cycle.hpp
Examining data/vg-1.27.1+ds/src/algorithms/copy_graph.cpp
Examining data/vg-1.27.1+ds/src/algorithms/kmer.hpp
Examining data/vg-1.27.1+ds/src/ssw_aligner.cpp
Examining data/vg-1.27.1+ds/src/benchmark.hpp
Examining data/vg-1.27.1+ds/src/statistics.cpp
Examining data/vg-1.27.1+ds/src/extra_node_graph.hpp
Examining data/vg-1.27.1+ds/src/endianness.hpp
Examining data/vg-1.27.1+ds/src/translator.cpp
Examining data/vg-1.27.1+ds/src/gff_reader.cpp
Examining data/vg-1.27.1+ds/src/homogenizer.cpp
Examining data/vg-1.27.1+ds/src/mcmc_caller.cpp
Examining data/vg-1.27.1+ds/src/identity_overlay.hpp
Examining data/vg-1.27.1+ds/src/hts_alignment_emitter.hpp
Examining data/vg-1.27.1+ds/src/multipath_alignment_emitter.hpp
Examining data/vg-1.27.1+ds/src/mcmc_genotyper.hpp
Examining data/vg-1.27.1+ds/src/seed_clusterer.hpp
Examining data/vg-1.27.1+ds/src/build_index.hpp
Examining data/vg-1.27.1+ds/src/integrated_snarl_finder.hpp
Examining data/vg-1.27.1+ds/src/path_index.hpp
Examining data/vg-1.27.1+ds/src/option.hpp
Examining data/vg-1.27.1+ds/src/subgraph_overlay.cpp
Examining data/vg-1.27.1+ds/src/utility.hpp
Examining data/vg-1.27.1+ds/src/dozeu_interface.cpp
Examining data/vg-1.27.1+ds/src/feature_set.cpp
Examining data/vg-1.27.1+ds/src/scanner.hpp
Examining data/vg-1.27.1+ds/src/haplotypes.cpp
Examining data/vg-1.27.1+ds/src/path.hpp
Examining data/vg-1.27.1+ds/src/split_strand_graph.cpp
Examining data/vg-1.27.1+ds/src/xdrop_aligner.cpp
Examining data/vg-1.27.1+ds/src/graph.hpp
Examining data/vg-1.27.1+ds/src/tree_subgraph.cpp
Examining data/vg-1.27.1+ds/src/dozeu_pinning_overlay.cpp
Examining data/vg-1.27.1+ds/src/msa_converter.hpp
Examining data/vg-1.27.1+ds/src/dinucleotide_machine.hpp
Examining data/vg-1.27.1+ds/src/stream_index.cpp
Examining data/vg-1.27.1+ds/src/viz.hpp
Examining data/vg-1.27.1+ds/src/surjector.hpp
Examining data/vg-1.27.1+ds/src/io/register_libvg_io.cpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_gbwtgraph.cpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_vg.hpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_r_index.hpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_gbwtgraph.hpp
Examining data/vg-1.27.1+ds/src/io/register_libvg_io.hpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_r_index.cpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_vg.cpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_hash_graph.hpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_hash_graph.cpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_odgi.hpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_minimizer.hpp
Examining data/vg-1.27.1+ds/src/io/save_handle_graph.hpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_distance_index.cpp
Examining data/vg-1.27.1+ds/src/io/load_proto_to_graph.cpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_odgi.cpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_minimizer.cpp
Examining data/vg-1.27.1+ds/src/io/load_proto_to_graph.hpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_distance_index.hpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_gcsa.cpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_xg.cpp
Examining data/vg-1.27.1+ds/src/io/json_stream_helper.hpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_gbwt.hpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_snarl_manager.hpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_lcp.hpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_packed_graph.cpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_xg.hpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_gbwt.cpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_gcsa.hpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_lcp.cpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_snarl_manager.cpp
Examining data/vg-1.27.1+ds/src/io/register_loader_saver_packed_graph.hpp
Examining data/vg-1.27.1+ds/src/transcriptome.hpp
Examining data/vg-1.27.1+ds/src/genotyper.hpp
Examining data/vg-1.27.1+ds/src/reverse_graph.hpp
Examining data/vg-1.27.1+ds/src/splicing.hpp
Examining data/vg-1.27.1+ds/src/nested_traversal_finder.cpp
Examining data/vg-1.27.1+ds/src/vg.hpp
Examining data/vg-1.27.1+ds/src/null_masking_graph.cpp
Examining data/vg-1.27.1+ds/src/gapless_extender.cpp
Examining data/vg-1.27.1+ds/src/region_expander.hpp
Examining data/vg-1.27.1+ds/src/readfilter.hpp
Examining data/vg-1.27.1+ds/src/cactus_snarl_finder.cpp
Examining data/vg-1.27.1+ds/src/version.cpp
Examining data/vg-1.27.1+ds/src/mapper.cpp
Examining data/vg-1.27.1+ds/src/nodeside.hpp
Examining data/vg-1.27.1+ds/src/path_component_index.cpp
Examining data/vg-1.27.1+ds/src/genotypekit.hpp
Examining data/vg-1.27.1+ds/src/qual_adj_xdrop_aligner.cpp
Examining data/vg-1.27.1+ds/src/min_distance.cpp
Examining data/vg-1.27.1+ds/src/gfa.cpp
Examining data/vg-1.27.1+ds/src/filter.hpp
Examining data/vg-1.27.1+ds/src/path_subgraph.hpp
Examining data/vg-1.27.1+ds/src/traversal_finder.cpp
Examining data/vg-1.27.1+ds/src/memoizing_graph.hpp
Examining data/vg-1.27.1+ds/src/handle.hpp
Examining data/vg-1.27.1+ds/src/pictographs.hpp
Examining data/vg-1.27.1+ds/src/cluster.hpp
Examining data/vg-1.27.1+ds/src/splicing.cpp
Examining data/vg-1.27.1+ds/src/genotyper.cpp
Examining data/vg-1.27.1+ds/src/reverse_graph.cpp
Examining data/vg-1.27.1+ds/src/transcriptome.cpp
Examining data/vg-1.27.1+ds/src/null_masking_graph.hpp
Examining data/vg-1.27.1+ds/src/vg.cpp
Examining data/vg-1.27.1+ds/src/nested_traversal_finder.hpp
Examining data/vg-1.27.1+ds/src/msa_converter.cpp
Examining data/vg-1.27.1+ds/src/dinucleotide_machine.cpp
Examining data/vg-1.27.1+ds/src/dozeu_pinning_overlay.hpp
Examining data/vg-1.27.1+ds/src/tree_subgraph.hpp
Examining data/vg-1.27.1+ds/src/graph.cpp
Examining data/vg-1.27.1+ds/src/surjector.cpp
Examining data/vg-1.27.1+ds/src/viz.cpp
Examining data/vg-1.27.1+ds/src/stream_index.hpp
Examining data/vg-1.27.1+ds/src/path_subgraph.cpp
Examining data/vg-1.27.1+ds/src/cluster.cpp
Examining data/vg-1.27.1+ds/src/memoizing_graph.cpp
Examining data/vg-1.27.1+ds/src/traversal_finder.hpp
Examining data/vg-1.27.1+ds/src/mapper.hpp
Examining data/vg-1.27.1+ds/src/version.hpp
Examining data/vg-1.27.1+ds/src/cactus_snarl_finder.hpp
Examining data/vg-1.27.1+ds/src/region_expander.cpp
Examining data/vg-1.27.1+ds/src/gapless_extender.hpp
Examining data/vg-1.27.1+ds/src/filter.cpp
Examining data/vg-1.27.1+ds/src/gfa.hpp
Examining data/vg-1.27.1+ds/src/min_distance.hpp
Examining data/vg-1.27.1+ds/src/path_component_index.hpp
Examining data/vg-1.27.1+ds/src/genotypekit.cpp
Examining data/vg-1.27.1+ds/src/srpe.cpp
Examining data/vg-1.27.1+ds/src/readfilter.cpp
Examining data/vg-1.27.1+ds/src/srpe.hpp
Examining data/vg-1.27.1+ds/src/preflight.cpp
Examining data/vg-1.27.1+ds/src/preflight.hpp
Examining data/vg-1.27.1+ds/src/crash.cpp
Examining data/vg-1.27.1+ds/include/vg_git_version.hpp

FINAL RESULTS:

data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/gap_bitvector.hpp:82:12:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
      bool access(uint64_t i) const {
data/vg-1.27.1+ds/deps/dozeu/log.h:63:2:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
	fprintf(stderr, fmt, __VA_ARGS__); \
data/vg-1.27.1+ds/deps/dozeu/log.h:99:8:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	_s += sprintf(_s, "\n`%s' len: %" PRId64 "\n", #ptr, (int64_t)len); \
data/vg-1.27.1+ds/deps/dozeu/simde/check.h:66:40:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#    define simde_errorf(format, ...) (fprintf(stderr, format, __VA_ARGS__), abort())
data/vg-1.27.1+ds/deps/dozeu/simde/hedley.h:1217:79:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#  define HEDLEY_PRINTF_FORMAT(string_idx,first_to_check) __declspec(vaformat(printf,string_idx,first_to_check))
data/vg-1.27.1+ds/deps/dozeu/unittest.h:327:2:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
	fprintf(gconf->fp,
data/vg-1.27.1+ds/deps/dozeu/unittest.h:336:3:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
		vfprintf(gconf->fp, fmt, l);
data/vg-1.27.1+ds/deps/dozeu/unittest.h:392:3:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
		vfprintf(gconf->fp, fmt, l);
data/vg-1.27.1+ds/deps/dozeu/unittest.h:538:8:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	_s += sprintf(_s, "\n`%s' len: %" PRIu64 "\n", #ptr, (uint64_t)len); \
data/vg-1.27.1+ds/deps/dozeu/unittest.h:621:2:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
	strcpy(cmd, cmd_base);
data/vg-1.27.1+ds/deps/dozeu/unittest.h:622:2:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
	strcat(cmd, filename);
data/vg-1.27.1+ds/deps/dozeu/unittest.h:658:11:  [4] (shell) popen:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
	if((fp = popen(cmd, "r")) == NULL) {
data/vg-1.27.1+ds/deps/dozeu/unittest.h:659:3:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
		fprintf(stderr, ut_color(UT_RED, "ERROR") ": failed to open pipe.\n");
data/vg-1.27.1+ds/deps/dozeu/unittest.h:665:3:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
		fprintf(stderr, ut_color(UT_RED, "ERROR") ": failed to read nm output.\n");
data/vg-1.27.1+ds/deps/dozeu/unittest.h:671:3:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
		fprintf(stderr, ut_color(UT_RED, "ERROR") ": failed to close pipe.\n");
data/vg-1.27.1+ds/deps/dozeu/unittest.h:1103:4:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
			fprintf(stderr,
data/vg-1.27.1+ds/deps/dozeu/unittest.h:1132:3:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
		fprintf(stderr,
data/vg-1.27.1+ds/deps/dozeu/unittest.h:1212:4:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
			fprintf(stderr, ut_color(UT_RED, "ERROR") ": detected circular dependency between groups.\n");
data/vg-1.27.1+ds/deps/dozeu/unittest.h:1244:3:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
		fprintf(stderr, ut_color(UT_RED, "ERROR") ": detected circular dependency between groups.\n");
data/vg-1.27.1+ds/deps/dozeu/unittest.h:1319:4:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
			fprintf(stderr, ut_color(UT_YELLOW, "Warning") ": group `%s' not found.\n", buf);
data/vg-1.27.1+ds/deps/dozeu/unittest.h:1455:4:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
			fprintf(stderr, ut_color(UT_RED, "ERROR") ": failed to order tests. check if the depends_on options are sane.\n");
data/vg-1.27.1+ds/deps/dozeu/unittest.h:1464:3:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
		fprintf(stderr, ut_color(UT_RED, "ERROR") ": failed to order tests. check if the depends_on options are sane.\n");
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp:225:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:221:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:251:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s\n", &num_pos, &numchars, orig_file);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:224:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:254:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s\n", &num_pos, &numchars, orig_file);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-death-test-internal.h:165:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(\
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2387:20:  [4] (buffer) StrNCpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
inline const char* StrNCpy(char* dest, const char* src, size_t n) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2458:26:  [4] (format) _snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define GTEST_SNPRINTF_ _snprintf
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2460:26:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define GTEST_SNPRINTF_ snprintf
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:146:10:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define vsnprintf _vsnprintf
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2969:5:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    vprintf(fmt, args);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2989:3:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vprintf(fmt, args);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2996:3:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vprintf(fmt, args);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc:1310:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, InDeathTestChild() ? "Inside" : "Outside");
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc:1320:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, InDeathTestChild() ? "Inside" : "Outside");
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:352:13:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
            sprintf(tmp_file_name, "%s/tmp_mapper_file_%lu_XXXXXX.sdsl",dir.c_str(),util::pid());
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:71:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:82:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:116:63:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_psi_trait<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:151:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:163:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:200:65:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_saisa_trait<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:328:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:341:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:378:63:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_wt_traits<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/bit_vector_test.cpp:52:29:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
TYPED_TEST(bit_vector_test, access)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp:225:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:221:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:251:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s\n", &num_pos, &numchars, orig_file);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:224:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:254:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s\n", &num_pos, &numchars, orig_file);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-death-test-internal.h:165:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(\
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2387:20:  [4] (buffer) StrNCpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
inline const char* StrNCpy(char* dest, const char* src, size_t n) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2458:26:  [4] (format) _snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define GTEST_SNPRINTF_ _snprintf
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2460:26:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define GTEST_SNPRINTF_ snprintf
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:146:10:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define vsnprintf _vsnprintf
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2969:5:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    vprintf(fmt, args);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2989:3:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vprintf(fmt, args);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2996:3:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vprintf(fmt, args);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc:1310:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, InDeathTestChild() ? "Inside" : "Outside");
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc:1320:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, InDeathTestChild() ? "Inside" : "Outside");
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:352:13:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
            sprintf(tmp_file_name, "%s/tmp_mapper_file_%lu_XXXXXX.sdsl",dir.c_str(),util::pid());
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:71:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:82:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:116:63:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_psi_trait<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:151:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:163:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:200:65:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_saisa_trait<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:328:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:341:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:378:63:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_wt_traits<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/bit_vector_test.cpp:52:29:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
TYPED_TEST(bit_vector_test, access)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp:225:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:221:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:251:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s\n", &num_pos, &numchars, orig_file);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:224:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:254:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s\n", &num_pos, &numchars, orig_file);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-death-test-internal.h:165:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(\
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2387:20:  [4] (buffer) StrNCpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
inline const char* StrNCpy(char* dest, const char* src, size_t n) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2458:26:  [4] (format) _snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define GTEST_SNPRINTF_ _snprintf
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2460:26:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define GTEST_SNPRINTF_ snprintf
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:146:10:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define vsnprintf _vsnprintf
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2969:5:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    vprintf(fmt, args);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2989:3:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vprintf(fmt, args);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2996:3:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vprintf(fmt, args);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc:1310:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, InDeathTestChild() ? "Inside" : "Outside");
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc:1320:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, InDeathTestChild() ? "Inside" : "Outside");
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:352:13:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
            sprintf(tmp_file_name, "%s/tmp_mapper_file_%lu_XXXXXX.sdsl",dir.c_str(),util::pid());
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:71:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:82:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:116:63:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_psi_trait<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:151:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:163:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:200:65:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_saisa_trait<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:328:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:341:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:378:63:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_wt_traits<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/bit_vector_test.cpp:52:29:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
TYPED_TEST(bit_vector_test, access)
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:181:22:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
                std::strcpy(name, line.c_str());
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:187:22:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
                std::strcpy(entry->name, name);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:240:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
    strcpy(ret, fastaName);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:241:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
    strcpy(ret + len, file_ext);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:54:2:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
	vprintf(fmt, argp);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:72:2:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
	vprintf(fmt, argp);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:89:5:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    vprintf(fmt, argp);
data/vg-1.27.1+ds/deps/gssw/src/main.c:288:14:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
			case 'a': strcpy(mat_name, optarg); break;
data/vg-1.27.1+ds/deps/gssw/src/simde/check.h:66:40:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#    define simde_errorf(format, ...) (fprintf(stderr, format, __VA_ARGS__), abort())
data/vg-1.27.1+ds/deps/gssw/src/simde/hedley.h:1217:79:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
#  define HEDLEY_PRINTF_FORMAT(string_idx,first_to_check) __declspec(vaformat(printf,string_idx,first_to_check))
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/gap_bitvector.hpp:81:12:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
      bool access(uint64_t i) const {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp:225:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:221:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:251:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s\n", &num_pos, &numchars, orig_file);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:224:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:254:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s\n", &num_pos, &numchars, orig_file);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-death-test-internal.h:165:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(\
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2387:20:  [4] (buffer) StrNCpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
inline const char* StrNCpy(char* dest, const char* src, size_t n) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2458:26:  [4] (format) _snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define GTEST_SNPRINTF_ _snprintf
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2460:26:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define GTEST_SNPRINTF_ snprintf
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:146:10:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define vsnprintf _vsnprintf
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2969:5:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    vprintf(fmt, args);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2989:3:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vprintf(fmt, args);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2996:3:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vprintf(fmt, args);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc:1310:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, InDeathTestChild() ? "Inside" : "Outside");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc:1320:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, InDeathTestChild() ? "Inside" : "Outside");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:352:13:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
            sprintf(tmp_file_name, "%s/tmp_mapper_file_%lu_XXXXXX.sdsl",dir.c_str(),util::pid());
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:71:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:82:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:116:63:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_psi_trait<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:151:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:163:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:200:65:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_saisa_trait<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:328:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:341:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:378:63:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_wt_traits<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/bit_vector_test.cpp:52:29:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
TYPED_TEST(bit_vector_test, access)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:83:13:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    #define snprintf sprintf_s 
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/gap_bitvector.hpp:82:12:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
      bool access(uint64_t i) const {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp:225:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:221:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:251:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s\n", &num_pos, &numchars, orig_file);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:224:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:254:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s\n", &num_pos, &numchars, orig_file);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-death-test-internal.h:165:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(\
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2387:20:  [4] (buffer) StrNCpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
inline const char* StrNCpy(char* dest, const char* src, size_t n) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2458:26:  [4] (format) _snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define GTEST_SNPRINTF_ _snprintf
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2460:26:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define GTEST_SNPRINTF_ snprintf
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:146:10:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define vsnprintf _vsnprintf
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2969:5:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    vprintf(fmt, args);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2989:3:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vprintf(fmt, args);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2996:3:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vprintf(fmt, args);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc:1310:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, InDeathTestChild() ? "Inside" : "Outside");
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc:1320:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, InDeathTestChild() ? "Inside" : "Outside");
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:352:13:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
            sprintf(tmp_file_name, "%s/tmp_mapper_file_%lu_XXXXXX.sdsl",dir.c_str(),util::pid());
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:71:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:82:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:116:63:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_psi_trait<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:151:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:163:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:200:65:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_saisa_trait<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:328:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:341:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:378:63:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_wt_traits<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/bit_vector_test.cpp:52:29:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
TYPED_TEST(bit_vector_test, access)
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:83:13:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    #define snprintf sprintf_s 
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp:225:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:221:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:251:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s\n", &num_pos, &numchars, orig_file);
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:224:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:254:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s\n", &num_pos, &numchars, orig_file);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:352:13:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
            sprintf(tmp_file_name, "%s/tmp_mapper_file_%lu_XXXXXX.sdsl",dir.c_str(),util::pid());
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:71:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:82:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:116:63:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_psi_trait<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:151:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:163:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:200:65:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_saisa_trait<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:328:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:341:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:378:63:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_wt_traits<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/sdsl-lite/test/bit_vector_test.cpp:52:29:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
TYPED_TEST(bit_vector_test, access)
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:29:17:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        int j = fscanf(file, INT_STRING, iA + i);
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:39:9:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        fprintf(file, INT_STRING "\n", iA[i]);
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:262:9:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
    i = sscanf(*string, INT_STRING, j);
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:304:9:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    i = sscanf(*string, "%s", cA);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:28:9:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        vfprintf(stderr, failureMessage, ap);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:805:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(cA, "%s/", tempFilePath);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:832:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(cA, "rm -rf %s", tempDir);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:833:9:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
    i = system(cA);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:915:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(cA, "%s/tempC", rootDir);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:917:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
    strcpy(tempFileTree->rootDir, cA);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:926:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(cA, "%s", tempFileTree->rootDir); //defensive
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:928:9:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
        sprintf(cA2, "%s/c0", cA);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:953:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(cA, "rm -rf %s", tempFileTree->rootDir);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:954:9:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
    i = system(cA);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:987:21:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
                    sprintf(cA, "%s", tempFileTree->rootDir);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:989:25:  [4] (format) sprintf:
  Potential format string problem (CWE-134). Make format string constant.
                        sprintf(cA2, "%s/c" INT_STRING, cA,
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:998:13:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
            sprintf(cA, "%s", tempFileTree->rootDir);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:1000:17:  [4] (format) sprintf:
  Potential format string problem (CWE-134). Make format string constant.
                sprintf(cA2, "%s/c" INT_STRING, cA,
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:1007:13:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
            strcpy(cA4, cA);
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:81:19:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
    pA->contig1 = strcpy((char *)st_malloc(sizeof(char)*(1+strlen(contig1))), contig1);
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:86:19:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
    pA->contig2 = strcpy((char *)st_malloc(sizeof(char)*(1+strlen(contig2))), contig2);
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:147:8:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    if(fscanf(fileHandle, "cigar: %s %" PRIi64 " %" PRIi64 " %c %s %" PRIi64 " %" PRIi64 " %c %f",\
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:153:23:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
        pA->contig2 = strcpy((char *)st_malloc(sizeof(char)*(1+strlen(cA2))), cA2);
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:154:23:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
        pA->contig1 = strcpy((char *)st_malloc(sizeof(char)*(1+strlen(cA3))), cA3);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCommon.c:88:9:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        vfprintf(stderr, string, ap);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCommon.c:97:9:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        vfprintf(stderr, string, ap);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCommon.c:106:9:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
        vfprintf(stderr, string, ap);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCommon.c:114:5:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    vfprintf(stderr, string, ap);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCommon.c:123:5:  [4] (format) vsprintf:
  Potential format string problem (CWE-134). Make format string constant.
    vsprintf(cA, string, ap);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCommon.c:127:9:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
    i = system(cA);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCommon.c:135:5:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    vfprintf(stderr, format, ap);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCommon.c:144:5:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    vfprintf(stderr, format, ap);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_BigRecordFile.c:56:2:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	sprintf(recordPath, "%s/%s.%s%lld", basePath, name, RECORD_FILE_TAG,
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_BigRecordFile.c:80:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
				sprintf(filePathBuffer, "%s/%s", basePath, ep->d_name);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_MySql.c:33:23:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 2, 3)))
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_MySql.c:39:23:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 2, 3)))
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:20:16:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
        return strcpy(st_malloc(sizeof(char)*(1+strlen(string))), string);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:30:17:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    int64_t i = vsnprintf(cA, arraySize, string, ap);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:40:13:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
        i = vsnprintf(cA, arraySize, string, ap);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:51:17:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    int64_t i = vsnprintf(NULL, 0, string, ap);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:58:9:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    i = vsnprintf(ret, arraySize, string, ap);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibTreap.c:43:3:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
		strcat(path, node->value);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibTreap.c:53:3:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
		strcat(path, node->value);
data/vg-1.27.1+ds/deps/sonLib/C/impl/stPhylogeny.c:89:15:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function. If the scanf format is influenceable by an
  attacker, it's exploitable.
        ret = sscanf(stTree_getLabel(tree), "%" PRIi64, &indexInfo->matrixIndex);
data/vg-1.27.1+ds/deps/sonLib/C/impl/stSafeC.c:24:5:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    vsnprintf(buf, sizeof(buf), msg, args);
data/vg-1.27.1+ds/deps/sonLib/C/impl/stSafeC.c:66:14:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    int sz = vsnprintf(buffer, bufSize, format, args);
data/vg-1.27.1+ds/deps/sonLib/C/impl/stSafeC.c:90:18:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
        int sz = vsnprintf(buf, bufSize, format, argscp);
data/vg-1.27.1+ds/deps/sonLib/C/inc/stSafeC.h:35:23:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 1, 2)))
data/vg-1.27.1+ds/deps/sonLib/C/inc/stSafeC.h:87:23:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 3, 4)))
data/vg-1.27.1+ds/deps/sonLib/C/inc/stSafeC.h:103:23:  [4] (format) printf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
__attribute__((format(printf, 1, 2)))
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:24:2:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
	strcpy(newStr, old);
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:75:2:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
	strcat(str->buffer, text);
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:91:2:  [4] (format) vsprintf:
  Potential format string problem (CWE-134). Make format string constant.
	vsprintf(buf, format, argp);
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:152:2:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	sprintf(buf, "%s:%d: ", file, line);
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/align.c:97:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
    strcpy(aln->seqs[aln->numseqs]->name, tempname);
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/align.c:266:7:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
      strcpy( aln->seqs[thisseq]->name, name_ptr );
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/distancemat.c:390:5:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    fscanf( handle, "%s", identifier );
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/distancemat.c:395:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
    strcpy( (*aln_loc)->seqs[i]->name, identifier );
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/distancemat_merops.c:400:5:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    fscanf( handle, "%s", identifier );
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/distancemat_merops.c:405:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
    strcpy( (*aln_loc)->seqs[i]->name, identifier );
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/sequence.c:31:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
    strcpy( dest->name, source->name );
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/util.c:124:3:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vfprintf( stderr, fmt, args);
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/util.c:147:3:  [4] (format) vfprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vfprintf( stderr, fmt, args );
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:84:13:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    #define snprintf sprintf_s 
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/utility.h:29:19:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
#define sprintf_s snprintf
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/utility.h:29:19:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
#define sprintf_s snprintf
data/vg-1.27.1+ds/deps/vowpal_wabbit/library/test_search.cc:92:13:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
  int ret = system("../vowpalwabbit/vw -k -c --holdout_off --passes 20 --search 4 --search_task sequence -d sequence.data -f sequence.model");
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc:1047:7:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
      fprintf(stderr, header_fmt,
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/crossplat_compat.h:12:19:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
#define sprintf_s snprintf
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/crossplat_compat.h:13:20:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
#define vsprintf_s vsnprintf
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/multiclass.cc:8:19:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
#define sprintf_s snprintf
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:267:3:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
  strcpy(info.name, s);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:275:3:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
  strcpy(cstr, str.c_str());
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:1380:3:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
  strcpy(c+2, s.c_str());
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:1390:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(argv[i],"%s",foo[i].begin);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:432:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, header_fmt, "average", "since", "instance", "current true",  "current predicted", "cur",  "cur", "predic", "cache", "examples", "");
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:434:7:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
      fprintf(stderr, header_fmt, "loss",    "last",  "counter",  "output prefix",  "output prefix",    "pass", "pol", "made",    "hits",  "gener", "#run");
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:436:7:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
      fprintf(stderr, header_fmt, "loss",    "last",  "counter",  "output prefix",  "output prefix",    "pass", "pol", "made",    "hits",  "gener", "beta");
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:1547:11:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
          strcpy(priv.learn_condition_on_names.begin(), condition_on_names);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:2432:3:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
  strcpy(cstr, nf_string.c_str());
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:181:22:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
                std::strcpy(name, line.c_str());
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:187:22:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
                std::strcpy(entry->name, name);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:240:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
    strcpy(ret, fastaName);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:241:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
    strcpy(ret + len, file_ext);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp:225:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:221:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:251:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s\n", &num_pos, &numchars, orig_file);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:224:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s forbidden=", numpatt,
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:254:13:  [4] (buffer) fscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
    error = fscanf(stdin, "# number=%lu length=%lu file=%s\n", &num_pos, &numchars, orig_file);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-death-test-internal.h:165:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(\
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2387:20:  [4] (buffer) StrNCpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
inline const char* StrNCpy(char* dest, const char* src, size_t n) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2458:26:  [4] (format) _snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define GTEST_SNPRINTF_ _snprintf
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2460:26:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define GTEST_SNPRINTF_ snprintf
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:146:10:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
# define vsnprintf _vsnprintf
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2969:5:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    vprintf(fmt, args);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2989:3:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vprintf(fmt, args);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2996:3:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
  vprintf(fmt, args);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc:1310:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, InDeathTestChild() ? "Inside" : "Outside");
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-death-test_test.cc:1320:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    fprintf(stderr, InDeathTestChild() ? "Inside" : "Outside");
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:352:13:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
            sprintf(tmp_file_name, "%s/tmp_mapper_file_%lu_XXXXXX.sdsl",dir.c_str(),util::pid());
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:71:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:82:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:116:63:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_psi_trait<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:151:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:163:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:200:65:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_saisa_trait<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:328:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:341:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    static value_type access(const t_csa& csa,size_type i)
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/suffix_array_helper.hpp:378:63:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            return traverse_csa_wt_traits<t_csa,t_direction>::access(m_csa,i);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/bit_vector_test.cpp:52:29:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
TYPED_TEST(bit_vector_test, access)
data/vg-1.27.1+ds/deps/xg/src/xg.cpp:2533:9:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
        strcpy(tmpdirname, tmpdirname_cpp.c_str());
data/vg-1.27.1+ds/src/crash.cpp:106:21:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
                    system(command.str().c_str());
data/vg-1.27.1+ds/src/hts_alignment_emitter.cpp:81:5:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
    strcat(out_mode, out_format.c_str());
data/vg-1.27.1+ds/src/hts_alignment_emitter.cpp:86:9:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
        strcat(out_mode, tmp);
data/vg-1.27.1+ds/src/subcommand/bugs_main.cpp:73:12:  [4] (shell) system:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
    return system((open_command + " " + url).c_str());
data/vg-1.27.1+ds/src/utility.cpp:154:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
    strcpy(cstr, s.c_str());
data/vg-1.27.1+ds/deps/BBHash/bootest.cpp:33:22:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
#define srandomdev() srand((unsigned) time(NULL))
data/vg-1.27.1+ds/deps/BBHash/bootest.cpp:45:8:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	low = random();
data/vg-1.27.1+ds/deps/BBHash/bootest.cpp:46:9:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	high = random();
data/vg-1.27.1+ds/deps/DYNAMIC/benchmark.cpp:46:2:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	srand(time(NULL));
data/vg-1.27.1+ds/deps/DYNAMIC/debug.cpp:17:4:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
   srand(time(NULL));
data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/ContextAutomata.h:135:3:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
		srand(time(NULL));
data/vg-1.27.1+ds/deps/dozeu/unittest.h:1396:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
	while((c = getopt_long(argc, argv, opts_short, opts_long, &idx)) != -1) {
data/vg-1.27.1+ds/deps/dozeu/unittest.h:1400:14:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
			case 's': srand((unsigned int)atol(optarg)); break;
data/vg-1.27.1+ds/deps/gbwt/benchmark.cpp:71:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  while((c = getopt(argc, argv, "c:f:p:le:rsS")) != -1)
data/vg-1.27.1+ds/deps/gbwt/build_gbwt.cpp:66:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  while((c = getopt(argc, argv, "b:cefF:i:lL:o:pP:rs:Sv")) != -1)
data/vg-1.27.1+ds/deps/gbwt/build_ri.cpp:58:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  while((c = getopt(argc, argv, "t:v")) != -1)
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp:39:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(17);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/test/gmock-matchers_test.cc:5203:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(static_cast<int>(seed));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest.h:925:39:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  void ShuffleTests(internal::Random* random);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2426:27:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  const char* const env = getenv(name);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2429:10:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  return getenv(name);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:312:37:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void ShuffleRange(internal::Random* random, int begin, int end,
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:333:39:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
inline void Shuffle(internal::Random* random, std::vector<E>* v) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:334:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random, 0, static_cast<int>(v->size()), v);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:792:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  internal::Random* random() { return &random_; }
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:243:5:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
  ::InitializeCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:261:5:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
  ::EnterCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:293:11:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
        ::InitializeCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:194:44:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  const char* const testbridge_test_only = getenv(GTEST_TEST_FILTER_ENV_VAR_);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2790:47:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void TestCase::ShuffleTests(internal::Random* random) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2791:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  Shuffle(random, &test_indices_);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4626:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random()->Reseed(random_seed_);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4940:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random(), 0, last_death_test_case_ + 1, &test_case_indices_);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4943:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random(), last_death_test_case_ + 1,
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4948:34:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    test_cases_[i]->ShuffleTests(random());
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:425:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv("TZ"))
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:426:26:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      saved_tz_ = strdup(getenv("TZ"));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:713:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(42);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:715:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random.Generate(0),
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:718:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random.Generate(testing::internal::Random::kMaxRange + 1),
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:725:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(12345);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:727:15:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    EXPECT_LT(random.Generate(kRange), kRange) << " for iteration " << i;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:742:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(kSeed);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:744:17:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    values[i] = random.Generate(kRange);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:747:3:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  random.Reseed(kSeed);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:749:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    EXPECT_EQ(values[i], random.Generate(kRange)) << " for iteration " << i;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:814:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(1);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:817:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, -1, 1, &a),
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:820:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 4, 4, &a),
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:823:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 3, 2, &a),
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:826:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 3, 4, &a),
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:347:24:  [3] (tmpfile) GetTempFileName:
  Temporary file race condition in certain cases (e.g., if run as SYSTEM in
  many versions of Windows) (CWE-377).
            auto ret = GetTempFileName(dir.c_str(),"tmp_mapper_file_", 0 ,tmp_file_name);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:38:15:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        this->setstate(std::ios_base::failbit);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:71:21:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    if (fail) this->setstate(std::ios::failbit);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:98:23:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                this->setstate(err);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:103:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:125:23:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                this->setstate(err);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:130:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:168:15:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        this->setstate(std::ios_base::failbit);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:201:21:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    if (fail) this->setstate(std::ios::failbit);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:223:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:249:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:274:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/bit_vector_generator.cpp:52:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(4711);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_generator.cpp:43:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(seed);
data/vg-1.27.1+ds/deps/gbwt/merge_gbwt.cpp:54:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  while((c = getopt(argc, argv, "b:C:fiJ:M:o:pP:s:S:t:T:")) != -1)
data/vg-1.27.1+ds/deps/gbwt/metadata_tool.cpp:47:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  while((c = getopt(argc, argv, "s:h:c:PSCr")) != -1)
data/vg-1.27.1+ds/deps/gbwt/remove_seq.cpp:50:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  while((c = getopt(argc, argv, "c:o:rSC")) != -1)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/benchmark.cpp:68:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  while((c = getopt(argc, argv, "c:f:p:le:sS")) != -1)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/build_gbwt.cpp:70:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  while((c = getopt(argc, argv, "b:cfF:i:lL:o:pP:rs:Sv")) != -1)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp:39:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(17);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/test/gmock-matchers_test.cc:5203:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(static_cast<int>(seed));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest.h:925:39:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  void ShuffleTests(internal::Random* random);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2426:27:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  const char* const env = getenv(name);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2429:10:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  return getenv(name);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:312:37:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void ShuffleRange(internal::Random* random, int begin, int end,
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:333:39:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
inline void Shuffle(internal::Random* random, std::vector<E>* v) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:334:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random, 0, static_cast<int>(v->size()), v);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:792:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  internal::Random* random() { return &random_; }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:243:5:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
  ::InitializeCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:261:5:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
  ::EnterCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:293:11:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
        ::InitializeCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:194:44:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  const char* const testbridge_test_only = getenv(GTEST_TEST_FILTER_ENV_VAR_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2790:47:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void TestCase::ShuffleTests(internal::Random* random) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2791:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  Shuffle(random, &test_indices_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4626:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random()->Reseed(random_seed_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4940:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random(), 0, last_death_test_case_ + 1, &test_case_indices_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4943:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random(), last_death_test_case_ + 1,
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4948:34:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    test_cases_[i]->ShuffleTests(random());
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:425:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv("TZ"))
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:426:26:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      saved_tz_ = strdup(getenv("TZ"));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:713:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(42);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:715:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random.Generate(0),
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:718:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random.Generate(testing::internal::Random::kMaxRange + 1),
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:725:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(12345);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:727:15:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    EXPECT_LT(random.Generate(kRange), kRange) << " for iteration " << i;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:742:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(kSeed);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:744:17:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    values[i] = random.Generate(kRange);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:747:3:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  random.Reseed(kSeed);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:749:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    EXPECT_EQ(values[i], random.Generate(kRange)) << " for iteration " << i;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:814:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(1);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:817:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, -1, 1, &a),
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:820:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 4, 4, &a),
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:823:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 3, 2, &a),
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:826:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 3, 4, &a),
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:347:24:  [3] (tmpfile) GetTempFileName:
  Temporary file race condition in certain cases (e.g., if run as SYSTEM in
  many versions of Windows) (CWE-377).
            auto ret = GetTempFileName(dir.c_str(),"tmp_mapper_file_", 0 ,tmp_file_name);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:38:15:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        this->setstate(std::ios_base::failbit);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:71:21:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    if (fail) this->setstate(std::ios::failbit);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:98:23:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                this->setstate(err);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:103:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:125:23:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                this->setstate(err);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:130:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:168:15:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        this->setstate(std::ios_base::failbit);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:201:21:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    if (fail) this->setstate(std::ios::failbit);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:223:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:249:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:274:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/bit_vector_generator.cpp:52:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(4711);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_generator.cpp:43:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(seed);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/merge_gbwt.cpp:54:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  while((c = getopt(argc, argv, "b:C:fiJ:M:o:pP:s:S:t:T:")) != -1)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/metadata_tool.cpp:47:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  while((c = getopt(argc, argv, "s:h:c:PSCr")) != -1)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/remove_seq.cpp:50:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  while((c = getopt(argc, argv, "c:o:rSC")) != -1)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp:39:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(17);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googlemock/test/gmock-matchers_test.cc:5203:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(static_cast<int>(seed));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest.h:925:39:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  void ShuffleTests(internal::Random* random);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2426:27:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  const char* const env = getenv(name);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2429:10:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  return getenv(name);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:312:37:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void ShuffleRange(internal::Random* random, int begin, int end,
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:333:39:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
inline void Shuffle(internal::Random* random, std::vector<E>* v) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:334:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random, 0, static_cast<int>(v->size()), v);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:792:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  internal::Random* random() { return &random_; }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:243:5:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
  ::InitializeCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:261:5:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
  ::EnterCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:293:11:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
        ::InitializeCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:194:44:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  const char* const testbridge_test_only = getenv(GTEST_TEST_FILTER_ENV_VAR_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2790:47:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void TestCase::ShuffleTests(internal::Random* random) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2791:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  Shuffle(random, &test_indices_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4626:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random()->Reseed(random_seed_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4940:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random(), 0, last_death_test_case_ + 1, &test_case_indices_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4943:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random(), last_death_test_case_ + 1,
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4948:34:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    test_cases_[i]->ShuffleTests(random());
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:425:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv("TZ"))
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:426:26:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      saved_tz_ = strdup(getenv("TZ"));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:713:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(42);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:715:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random.Generate(0),
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:718:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random.Generate(testing::internal::Random::kMaxRange + 1),
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:725:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(12345);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:727:15:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    EXPECT_LT(random.Generate(kRange), kRange) << " for iteration " << i;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:742:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(kSeed);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:744:17:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    values[i] = random.Generate(kRange);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:747:3:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  random.Reseed(kSeed);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:749:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    EXPECT_EQ(values[i], random.Generate(kRange)) << " for iteration " << i;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:814:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(1);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:817:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, -1, 1, &a),
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:820:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 4, 4, &a),
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:823:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 3, 2, &a),
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:826:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 3, 4, &a),
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:347:24:  [3] (tmpfile) GetTempFileName:
  Temporary file race condition in certain cases (e.g., if run as SYSTEM in
  many versions of Windows) (CWE-377).
            auto ret = GetTempFileName(dir.c_str(),"tmp_mapper_file_", 0 ,tmp_file_name);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:38:15:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        this->setstate(std::ios_base::failbit);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:71:21:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    if (fail) this->setstate(std::ios::failbit);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:98:23:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                this->setstate(err);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:103:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:125:23:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                this->setstate(err);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:130:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:168:15:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        this->setstate(std::ios_base::failbit);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:201:21:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    if (fail) this->setstate(std::ios::failbit);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:223:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:249:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:274:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/bit_vector_generator.cpp:52:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(4711);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_generator.cpp:43:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(seed);
data/vg-1.27.1+ds/deps/gbwtgraph/gfa2gbwt.cpp:26:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  while((c = getopt(argc, argv, "")) != -1)
data/vg-1.27.1+ds/deps/gcsa2/benchmark/count_kmers.cpp:63:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  while((c = getopt(argc, argv, "fk:No:s:")) != -1)
data/vg-1.27.1+ds/deps/gcsa2/build_gcsa.cpp:69:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  while((c = getopt(argc, argv, "bto:d:m:s:B:LvD:l:T:V:")) != -1)
data/vg-1.27.1+ds/deps/gcsa2/gcsa_format.cpp:54:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  while((c = getopt(argc, argv, "gl")) != -1)
data/vg-1.27.1+ds/deps/gfakluge/src/main.cpp:183:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hvnpl:", long_options, &option_index);
data/vg-1.27.1+ds/deps/gfakluge/src/main.cpp:250:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hpv", long_options, &option_index);
data/vg-1.27.1+ds/deps/gfakluge/src/main.cpp:331:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hm:i:f:S:v:", long_options, &option_index);
data/vg-1.27.1+ds/deps/gfakluge/src/main.cpp:396:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hbf:S:v", long_options, &option_index);
data/vg-1.27.1+ds/deps/gfakluge/src/main.cpp:490:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hv", long_options, &option_index);
data/vg-1.27.1+ds/deps/gfakluge/src/main.cpp:575:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hvfbpwS:", long_options, &option_index);
data/vg-1.27.1+ds/deps/gfakluge/src/main.cpp:675:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hvbS:s:", long_options, &option_index);
data/vg-1.27.1+ds/deps/gfakluge/src/main.cpp:762:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hvS:", long_options, &option_index);
data/vg-1.27.1+ds/deps/gfakluge/src/main.cpp:841:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hvS:", long_options, &option_index);
data/vg-1.27.1+ds/deps/gfakluge/src/main.cpp:924:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hpaAnel", long_options, &option_index);
data/vg-1.27.1+ds/deps/gfakluge/src/main.cpp:1069:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "vs:e:hS:b", long_options, &option_index);
data/vg-1.27.1+ds/deps/gssw/src/main.c:282:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
	while ((l = getopt(argc, argv, "m:x:o:e:a:f:pcrsh")) >= 0) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/bootest.cpp:33:22:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
#define srandomdev() srand((unsigned) time(NULL))
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/bootest.cpp:45:8:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	low = random();
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/bootest.cpp:46:9:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	high = random();
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/benchmark.cpp:44:2:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	srand(time(NULL));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/debug.cpp:17:4:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
   srand(time(NULL));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/ContextAutomata.h:135:3:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
		srand(time(NULL));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/detail/init.h:286:6:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void setstate(value_and_holder &v_h, T &&result, bool need_alias) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/detail/init.h:293:6:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void setstate(value_and_holder &v_h, std::pair<T, O> &&result, bool need_alias) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/detail/init.h:327:13:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            setstate<Class>(v_h, func(std::forward<ArgState>(state)),
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/pybind11.h:1591:35:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                detail::initimpl::setstate<Base>(v_h, static_cast<Type>(arg),
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp:39:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(17);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-matchers_test.cc:5203:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(static_cast<int>(seed));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest.h:925:39:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  void ShuffleTests(internal::Random* random);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2426:27:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  const char* const env = getenv(name);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2429:10:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  return getenv(name);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:312:37:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void ShuffleRange(internal::Random* random, int begin, int end,
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:333:39:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
inline void Shuffle(internal::Random* random, std::vector<E>* v) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:334:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random, 0, static_cast<int>(v->size()), v);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:792:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  internal::Random* random() { return &random_; }
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:243:5:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
  ::InitializeCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:261:5:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
  ::EnterCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:293:11:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
        ::InitializeCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:194:44:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  const char* const testbridge_test_only = getenv(GTEST_TEST_FILTER_ENV_VAR_);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2790:47:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void TestCase::ShuffleTests(internal::Random* random) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2791:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  Shuffle(random, &test_indices_);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4626:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random()->Reseed(random_seed_);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4940:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random(), 0, last_death_test_case_ + 1, &test_case_indices_);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4943:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random(), last_death_test_case_ + 1,
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4948:34:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    test_cases_[i]->ShuffleTests(random());
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:425:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv("TZ"))
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:426:26:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      saved_tz_ = strdup(getenv("TZ"));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:713:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(42);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:715:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random.Generate(0),
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:718:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random.Generate(testing::internal::Random::kMaxRange + 1),
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:725:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(12345);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:727:15:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    EXPECT_LT(random.Generate(kRange), kRange) << " for iteration " << i;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:742:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(kSeed);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:744:17:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    values[i] = random.Generate(kRange);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:747:3:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  random.Reseed(kSeed);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:749:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    EXPECT_EQ(values[i], random.Generate(kRange)) << " for iteration " << i;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:814:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(1);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:817:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, -1, 1, &a),
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:820:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 4, 4, &a),
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:823:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 3, 2, &a),
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:826:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 3, 4, &a),
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:347:24:  [3] (tmpfile) GetTempFileName:
  Temporary file race condition in certain cases (e.g., if run as SYSTEM in
  many versions of Windows) (CWE-377).
            auto ret = GetTempFileName(dir.c_str(),"tmp_mapper_file_", 0 ,tmp_file_name);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:38:15:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        this->setstate(std::ios_base::failbit);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:71:21:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    if (fail) this->setstate(std::ios::failbit);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:98:23:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                this->setstate(err);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:103:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:125:23:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                this->setstate(err);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:130:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:168:15:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        this->setstate(std::ios_base::failbit);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:201:21:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    if (fail) this->setstate(std::ios::failbit);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:223:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:249:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:274:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/bit_vector_generator.cpp:52:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(4711);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_generator.cpp:43:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(seed);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/perftest1.cc:37:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/perftest1.cc:44:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/perftest1.cc:51:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(1);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/perftest1.cc:58:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/perftest1.cc:64:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/perftest1.cc:71:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(1);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/perftest1.cc:81:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/perftest1.cc:88:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/perftest1.cc:95:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(1);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_alloc_test.cc:35:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(43); // always same sequence of random numbers
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_bitset_test.cc:154:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(1);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_bitset_test.cc:204:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(1);
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/bootest.cpp:33:22:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
#define srandomdev() srand((unsigned) time(NULL))
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/bootest.cpp:45:8:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	low = random();
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/bootest.cpp:46:9:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	high = random();
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/benchmark.cpp:46:2:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	srand(time(NULL));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/debug.cpp:17:4:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
   srand(time(NULL));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/structures/ContextAutomata.h:135:3:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
		srand(time(NULL));
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/detail/init.h:286:6:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void setstate(value_and_holder &v_h, T &&result, bool need_alias) {
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/detail/init.h:293:6:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void setstate(value_and_holder &v_h, std::pair<T, O> &&result, bool need_alias) {
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/detail/init.h:327:13:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            setstate<Class>(v_h, func(std::forward<ArgState>(state)),
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/pybind11.h:1591:35:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                detail::initimpl::setstate<Base>(v_h, static_cast<Type>(arg),
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp:39:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(17);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-matchers_test.cc:5203:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(static_cast<int>(seed));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest.h:925:39:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  void ShuffleTests(internal::Random* random);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2426:27:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  const char* const env = getenv(name);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2429:10:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  return getenv(name);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:312:37:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void ShuffleRange(internal::Random* random, int begin, int end,
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:333:39:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
inline void Shuffle(internal::Random* random, std::vector<E>* v) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:334:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random, 0, static_cast<int>(v->size()), v);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:792:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  internal::Random* random() { return &random_; }
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:243:5:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
  ::InitializeCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:261:5:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
  ::EnterCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:293:11:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
        ::InitializeCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:194:44:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  const char* const testbridge_test_only = getenv(GTEST_TEST_FILTER_ENV_VAR_);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2790:47:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void TestCase::ShuffleTests(internal::Random* random) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2791:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  Shuffle(random, &test_indices_);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4626:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random()->Reseed(random_seed_);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4940:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random(), 0, last_death_test_case_ + 1, &test_case_indices_);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4943:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random(), last_death_test_case_ + 1,
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4948:34:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    test_cases_[i]->ShuffleTests(random());
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:425:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv("TZ"))
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:426:26:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      saved_tz_ = strdup(getenv("TZ"));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:713:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(42);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:715:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random.Generate(0),
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:718:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random.Generate(testing::internal::Random::kMaxRange + 1),
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:725:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(12345);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:727:15:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    EXPECT_LT(random.Generate(kRange), kRange) << " for iteration " << i;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:742:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(kSeed);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:744:17:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    values[i] = random.Generate(kRange);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:747:3:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  random.Reseed(kSeed);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:749:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    EXPECT_EQ(values[i], random.Generate(kRange)) << " for iteration " << i;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:814:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(1);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:817:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, -1, 1, &a),
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:820:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 4, 4, &a),
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:823:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 3, 2, &a),
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:826:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 3, 4, &a),
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:347:24:  [3] (tmpfile) GetTempFileName:
  Temporary file race condition in certain cases (e.g., if run as SYSTEM in
  many versions of Windows) (CWE-377).
            auto ret = GetTempFileName(dir.c_str(),"tmp_mapper_file_", 0 ,tmp_file_name);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:38:15:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        this->setstate(std::ios_base::failbit);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:71:21:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    if (fail) this->setstate(std::ios::failbit);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:98:23:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                this->setstate(err);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:103:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:125:23:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                this->setstate(err);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:130:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:168:15:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        this->setstate(std::ios_base::failbit);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:201:21:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    if (fail) this->setstate(std::ios::failbit);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:223:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:249:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:274:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/bit_vector_generator.cpp:52:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(4711);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_generator.cpp:43:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(seed);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/perftest1.cc:37:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/perftest1.cc:44:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/perftest1.cc:51:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(1);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/perftest1.cc:58:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/perftest1.cc:64:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/perftest1.cc:71:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(1);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/perftest1.cc:81:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/perftest1.cc:88:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/perftest1.cc:95:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(1);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_alloc_test.cc:35:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(43); // always same sequence of random numbers
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_bitset_test.cc:154:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(1);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_bitset_test.cc:204:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(1);
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp:39:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(17);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:347:24:  [3] (tmpfile) GetTempFileName:
  Temporary file race condition in certain cases (e.g., if run as SYSTEM in
  many versions of Windows) (CWE-377).
            auto ret = GetTempFileName(dir.c_str(),"tmp_mapper_file_", 0 ,tmp_file_name);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:38:15:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        this->setstate(std::ios_base::failbit);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:71:21:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    if (fail) this->setstate(std::ios::failbit);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:98:23:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                this->setstate(err);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:103:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:125:23:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                this->setstate(err);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:130:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:168:15:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        this->setstate(std::ios_base::failbit);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:201:21:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    if (fail) this->setstate(std::ios::failbit);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:223:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:249:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:274:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/sdsl-lite/test/bit_vector_generator.cpp:52:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(4711);
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_generator.cpp:43:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(seed);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:859:25:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
        if (!((tmpdir = getenv("TMPDIR")))) {
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:860:22:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
            tmpdir = getenv("TMP");
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibExcept.c:85:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv("ST_ABORT_UNCAUGHT") != NULL) {
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibExcept.c:93:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv("ST_ABORT") != NULL) {
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibRandom.c:12:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(seed);
data/vg-1.27.1+ds/deps/sonLib/C/tests/kvDatabaseTestCommon.c:77:22:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
    while ((optKey = getopt_long(argc, argv, "t:d:H:P:i:r:b:u:p:h", longOptions, &optIndex)) >= 0) {
data/vg-1.27.1+ds/deps/sonLib/C/tests/sonLibConnectivityTests.c:214:2:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	srand(time(NULL));
data/vg-1.27.1+ds/deps/sparsepp/tests/perftest1.cc:37:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/sparsepp/tests/perftest1.cc:44:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/sparsepp/tests/perftest1.cc:51:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(1);
data/vg-1.27.1+ds/deps/sparsepp/tests/perftest1.cc:58:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/sparsepp/tests/perftest1.cc:64:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/sparsepp/tests/perftest1.cc:71:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(1);
data/vg-1.27.1+ds/deps/sparsepp/tests/perftest1.cc:81:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/sparsepp/tests/perftest1.cc:88:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(0);
data/vg-1.27.1+ds/deps/sparsepp/tests/perftest1.cc:95:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(1);
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_alloc_test.cc:35:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(43); // always same sequence of random numbers
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_bitset_test.cc:154:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(1);
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_bitset_test.cc:204:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(1);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:8620:18:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            std::srand( config.rngSeed() );
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h:1515:7:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
    ::InitializeCriticalSection(&m_critical_section);
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h:1530:7:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
    ::InitializeCriticalSection(&m_critical_section);
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h:1564:9:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
      ::EnterCriticalSection(&m_critical_section);
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h:1663:11:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
        ::InitializeCriticalSection(&m_critical_section);
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h:1679:11:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
        ::InitializeCriticalSection(&m_critical_section);
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h:1717:15:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
            ::EnterCriticalSection(&m_critical_section);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:714:63:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  initial_weights(weight initial, weight initial_random, bool random, uint32_t lda, uint32_t stride)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:715:67:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    : _initial(initial), _initial_random(initial_random), _random(random), _lda(lda), _stride(stride) {}
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:879:30:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    const std::string PATH = getenv( "PATH" );
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parser.cc:65:5:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
  ::InitializeCriticalSection(pm);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parser.cc:92:5:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
  ::EnterCriticalSection(pm);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:651:8:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
size_t random(uint64_t& v, size_t max) { return (size_t)(merand48(v) * (float)max); }
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:992:53:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    a = ( oracle_actions_cnt > 0) ?  oracle_actions[random(priv.all->random_state, oracle_actions_cnt )] :
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:993:53:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        (allowed_actions_cnt > 0) ? allowed_actions[random(priv.all->random_state, allowed_actions_cnt)] :
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:994:31:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        priv.is_ldf ? (action)random(priv.all->random_state, ec_cnt) :
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:995:22:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        (action)(1 + random(priv.all->random_state, priv.A));
data/vg-1.27.1+ds/deps/xg/deps/BBHash/bootest.cpp:33:22:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
#define srandomdev() srand((unsigned) time(NULL))
data/vg-1.27.1+ds/deps/xg/deps/BBHash/bootest.cpp:45:8:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	low = random();
data/vg-1.27.1+ds/deps/xg/deps/BBHash/bootest.cpp:46:9:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
	high = random();
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:7242:18:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            std::srand( config.rngSeed() );
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/main.cpp:183:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hvnpl:", long_options, &option_index);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/main.cpp:250:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hpv", long_options, &option_index);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/main.cpp:331:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hm:i:f:S:v:", long_options, &option_index);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/main.cpp:396:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hbf:S:v", long_options, &option_index);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/main.cpp:490:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hv", long_options, &option_index);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/main.cpp:575:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hvfbpwS:", long_options, &option_index);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/main.cpp:675:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hvbS:s:", long_options, &option_index);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/main.cpp:762:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hvS:", long_options, &option_index);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/main.cpp:841:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hvS:", long_options, &option_index);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/main.cpp:924:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "hpaAnel", long_options, &option_index);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/main.cpp:1069:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "vs:e:hS:b", long_options, &option_index);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp:39:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(17);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-matchers_test.cc:5203:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(static_cast<int>(seed));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/gtest.h:925:39:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  void ShuffleTests(internal::Random* random);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2426:27:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  const char* const env = getenv(name);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2429:10:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  return getenv(name);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:312:37:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void ShuffleRange(internal::Random* random, int begin, int end,
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:333:39:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
inline void Shuffle(internal::Random* random, std::vector<E>* v) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:334:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random, 0, static_cast<int>(v->size()), v);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-internal-inl.h:792:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  internal::Random* random() { return &random_; }
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:243:5:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
  ::InitializeCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:261:5:  [3] (misc) EnterCriticalSection:
  On some versions of Windows, exceptions can be thrown in low-memory
  situations. Use InitializeCriticalSectionAndSpinCount instead.
  ::EnterCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:293:11:  [3] (misc) InitializeCriticalSection:
  Exceptions can be thrown in low-memory situations. Use
  InitializeCriticalSectionAndSpinCount instead.
        ::InitializeCriticalSection(critical_section_);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:194:44:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  const char* const testbridge_test_only = getenv(GTEST_TEST_FILTER_ENV_VAR_);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2790:47:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
void TestCase::ShuffleTests(internal::Random* random) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:2791:11:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  Shuffle(random, &test_indices_);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4626:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random()->Reseed(random_seed_);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4940:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random(), 0, last_death_test_case_ + 1, &test_case_indices_);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4943:16:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  ShuffleRange(random(), last_death_test_case_ + 1,
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:4948:34:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    test_cases_[i]->ShuffleTests(random());
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:425:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv("TZ"))
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:426:26:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
      saved_tz_ = strdup(getenv("TZ"));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:713:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(42);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:715:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random.Generate(0),
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:718:7:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      random.Generate(testing::internal::Random::kMaxRange + 1),
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:725:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(12345);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:727:15:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    EXPECT_LT(random.Generate(kRange), kRange) << " for iteration " << i;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:742:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(kSeed);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:744:17:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    values[i] = random.Generate(kRange);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:747:3:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  random.Reseed(kSeed);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:749:26:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    EXPECT_EQ(values[i], random.Generate(kRange)) << " for iteration " << i;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:814:29:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
  testing::internal::Random random(1);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:817:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, -1, 1, &a),
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:820:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 4, 4, &a),
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:823:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 3, 2, &a),
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:826:21:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      ShuffleRange(&random, 3, 4, &a),
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:347:24:  [3] (tmpfile) GetTempFileName:
  Temporary file race condition in certain cases (e.g., if run as SYSTEM in
  many versions of Windows) (CWE-377).
            auto ret = GetTempFileName(dir.c_str(),"tmp_mapper_file_", 0 ,tmp_file_name);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:38:15:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        this->setstate(std::ios_base::failbit);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:71:21:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    if (fail) this->setstate(std::ios::failbit);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:98:23:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                this->setstate(err);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:103:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:125:23:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                this->setstate(err);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:130:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:168:15:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        this->setstate(std::ios_base::failbit);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:201:21:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    if (fail) this->setstate(std::ios::failbit);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:223:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:249:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:274:19:  [3] (random) setstate:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            this->setstate(err);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/bit_vector_generator.cpp:52:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(4711);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_generator.cpp:43:9:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        srand(seed);
data/vg-1.27.1+ds/deps/xg/src/xg.cpp:2586:35:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
                system_temp_dir = getenv(var_name);
data/vg-1.27.1+ds/src/colors.hpp:36:12:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    string random(void) {
data/vg-1.27.1+ds/src/crash.cpp:198:9:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
    if (getenv(var) != nullptr) {
data/vg-1.27.1+ds/src/crash.cpp:199:20:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
        if (strcmp(getenv(var), "1") == 0) {
data/vg-1.27.1+ds/src/option.cpp:263:17:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        int c = getopt_long (argc, argv, short_options.c_str(), &long_options[0], &option_index);
data/vg-1.27.1+ds/src/pictographs.hpp:35:12:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    string random(void) {
data/vg-1.27.1+ds/src/readfilter.cpp:697:45:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        ++counts.counts[Counts::FilterName::random];
data/vg-1.27.1+ds/src/readfilter.cpp:785:94:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
       << "Random Filter:                 " << counts.counts[ReadFilter::Counts::FilterName::random] << endl
data/vg-1.27.1+ds/src/readfilter.hpp:88:89:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                          min_end_matches, min_mapq, split, repeat, defray, defray_all, random, min_base_qual, filtered,
data/vg-1.27.1+ds/src/subcommand/add_main.cpp:78:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "v:n:r:f:ipt:h?",
data/vg-1.27.1+ds/src/subcommand/align_main.cpp:99:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "s:jhQ:m:M:g:e:Dr:F:O:bT:pL",
data/vg-1.27.1+ds/src/subcommand/annotate_main.cpp:123:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hx:a:pml:b:f:gs:nt:h",
data/vg-1.27.1+ds/src/subcommand/benchmark_main.cpp:55:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "ph?",
data/vg-1.27.1+ds/src/subcommand/bugs_main.cpp:39:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "n",
data/vg-1.27.1+ds/src/subcommand/call_main.cpp:121:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "k:Be:b:m:v:af:i:s:r:g:p:o:l:d:GTLM:t:h",
data/vg-1.27.1+ds/src/subcommand/chunk_main.cpp:146:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hx:G:a:gp:P:s:o:e:E:b:c:r:R:Tft:n:l:m:CMO:",
data/vg-1.27.1+ds/src/subcommand/circularize_main.cpp:67:9:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
    c = getopt_long (argc, argv, "hdp:P:a:z:",
data/vg-1.27.1+ds/src/subcommand/cluster_main.cpp:84:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hx:g:m:d:c:t:",
data/vg-1.27.1+ds/src/subcommand/combine_main.cpp:50:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "h",
data/vg-1.27.1+ds/src/subcommand/compare_main.cpp:56:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hd:e:t:",
data/vg-1.27.1+ds/src/subcommand/concat_main.cpp:58:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hp",
data/vg-1.27.1+ds/src/subcommand/construct_main.cpp:99:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "v:r:n:ph?z:t:R:m:as:CfSI:M:dF:i",
data/vg-1.27.1+ds/src/subcommand/convert_main.cpp:69:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hgvxapxoG:F:t:",
data/vg-1.27.1+ds/src/subcommand/crash_main.cpp:61:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "ht:",
data/vg-1.27.1+ds/src/subcommand/deconstruct_main.cpp:75:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hp:P:A:r:ed:t:v",
data/vg-1.27.1+ds/src/subcommand/depth_main.cpp:88:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hk:p:c:b:dg:a:n:s:m:t:",
data/vg-1.27.1+ds/src/subcommand/dotplot_main.cpp:54:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hx:",
data/vg-1.27.1+ds/src/subcommand/explode_main.cpp:50:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "ht:",
data/vg-1.27.1+ds/src/subcommand/filter_main.cpp:109:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "n:N:X:F:s:r:Od:e:fauo:m:Sx:AvVq:E:D:C:d:iIb:Ut:",
data/vg-1.27.1+ds/src/subcommand/filter_main.cpp:220:25:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                        srand(seed);
data/vg-1.27.1+ds/src/subcommand/find_main.cpp:170:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "d:x:n:e:s:o:k:hc:LS:z:j:CTp:P:r:l:amg:M:B:fDG:N:A:Y:Z:IQ:ER:W:K:H:",
data/vg-1.27.1+ds/src/subcommand/gamcompare_main.cpp:60:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hr:Ta:st:",
data/vg-1.27.1+ds/src/subcommand/gampcompare_main.cpp:65:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hr:a:t:Gd",
data/vg-1.27.1+ds/src/subcommand/gamsort_main.cpp:55:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "i:dhr:apt:",
data/vg-1.27.1+ds/src/subcommand/gbwt_main.cpp:167:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "x:o:pmfR:alPn:k:b:i:g:r:t:MCHSLTce:h?", long_options, &option_index);
data/vg-1.27.1+ds/src/subcommand/genotype_main.cpp:125:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hjvr:c:s:o:l:a:QAd:P:pt:V:I:G:F:zET:",
data/vg-1.27.1+ds/src/subcommand/giraffe_main.cpp:507:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hx:g:H:m:s:d:pG:f:iM:N:R:o:nb:c:C:D:F:e:a:S:u:v:w:Ot:r:A:",
data/vg-1.27.1+ds/src/subcommand/ids_main.cpp:75:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hci:d:jm:s",
data/vg-1.27.1+ds/src/subcommand/index_main.cpp:226:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "b:t:px:Lv:We:TM:F:G:zPoB:u:n:R:r:I:E:g:i:f:k:X:Z:Vld:maANDCs:j:w:h",
data/vg-1.27.1+ds/src/subcommand/inject_main.cpp:53:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hx:t:",
data/vg-1.27.1+ds/src/subcommand/join_main.cpp:45:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "h",
data/vg-1.27.1+ds/src/subcommand/kmers_main.cpp:85:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "k:t:pgBH:T:e:Fh",
data/vg-1.27.1+ds/src/subcommand/locify_main.cpp:73:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hl:x:g:nfo:b:s:",
data/vg-1.27.1+ds/src/subcommand/map_main.cpp:266:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "s:J:Q:d:x:g:1:T:N:R:c:M:t:G:jb:Kf:iw:P:Dk:Y:r:W:6H:Z:q:z:o:y:Au:B:I:S:l:e:C:V:O:L:a:n:E:X:UpF:m:7:v5:824:3:9:0:%",
data/vg-1.27.1+ds/src/subcommand/mcmc_main.cpp:78:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hi:s:p:o:l:r:v:",
data/vg-1.27.1+ds/src/subcommand/minimizer_main.cpp:119:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "g:i:k:w:d:l:Gpt:h", long_options, &option_index);
data/vg-1.27.1+ds/src/subcommand/mod_main.cpp:178:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hk:oi:q:Q:cpl:e:mt:SX:KPsunzNAf:Cg:x:RTU:Bbd:Ow:L:y:Z:Eav:G:M:Dr:I",
data/vg-1.27.1+ds/src/subcommand/mpmap_main.cpp:400:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hx:g:H:d:f:G:N:R:iSs:vX:u:b:I:D:BP:Q:UpM:r:W:K:F:c:C:R:En:l:e:q:z:w:o:y:L:mAt:Z:a",
data/vg-1.27.1+ds/src/subcommand/msga_main.cpp:203:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hf:n:s:g:b:K:X:w:DAc:P:E:Q:NY:H:t:m:M:q:O:I:i:o:y:ZW:z:k:L:e:r:u:l:C:F:J:B:a8R:T:",
data/vg-1.27.1+ds/src/subcommand/pack_main.cpp:86:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hx:o:i:g:a:dDut:eb:n:N:Q:c:",
data/vg-1.27.1+ds/src/subcommand/paths_main.cpp:132:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hLXv:x:g:Q:VEFAS:Tq:drap:",
data/vg-1.27.1+ds/src/subcommand/prune_main.cpp:186:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "k:e:s:M:Pruvx:g:m:apt:dh", long_options, &option_index);
data/vg-1.27.1+ds/src/subcommand/recalibrate_main.cpp:94:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hTm:t:",
data/vg-1.27.1+ds/src/subcommand/rna_main.cpp:117:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "n:m:y:s:l:ercdoraub:gw:f:i:t:ph?", long_options, &option_index);
data/vg-1.27.1+ds/src/subcommand/sift_main.cpp:119:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hut:vgG:pRo:I:W:OCDc:s:q:d:i:aw:r1",
data/vg-1.27.1+ds/src/subcommand/sim_main.cpp:215:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hrl:n:s:e:i:fax:Jp:v:Nud:F:P:Am:R:g:T:H:S:It:E:",
data/vg-1.27.1+ds/src/subcommand/simplify_main.cpp:83:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "a:pt:b:B:m:i:v:f:c:h?",
data/vg-1.27.1+ds/src/subcommand/snarls_main.cpp:94:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "A:sr:laTopm:v:f:i:eh?t:",
data/vg-1.27.1+ds/src/subcommand/sort_main.cpp:65:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "a:gr:wI:",
data/vg-1.27.1+ds/src/subcommand/srpe_main.cpp:102:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hzx:g:m:S:RI:r:t:a:wp:",
data/vg-1.27.1+ds/src/subcommand/stats_main.cpp:132:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hzlsHTcdtn:NEa:vAro:ORFD",
data/vg-1.27.1+ds/src/subcommand/surject_main.cpp:98:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hx:p:F:licbsN:R:f:C:t:SA",
data/vg-1.27.1+ds/src/subcommand/trace_main.cpp:66:9:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
    c = getopt_long (argc, argv, "x:G:a:n:d:jh",
data/vg-1.27.1+ds/src/subcommand/translate_main.cpp:66:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hp:m:P:a:o:l:",
data/vg-1.27.1+ds/src/subcommand/validate_main.cpp:70:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hneopa:x:",
data/vg-1.27.1+ds/src/subcommand/vectorize_main.cpp:96:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "AaihwM:fmpx:g:l:H:",
data/vg-1.27.1+ds/src/subcommand/version_main.cpp:42:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long(argc, argv, "sh",
data/vg-1.27.1+ds/src/subcommand/view_main.cpp:203:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "dgFjJhvVpaGbifA:s:wnlLIMcTtr:SuCZYmqQ:zXBREDx:kKe7:",
data/vg-1.27.1+ds/src/subcommand/viz_main.cpp:66:13:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
        c = getopt_long (argc, argv, "hx:i:n:o:X:Y:s:CDP",
data/vg-1.27.1+ds/src/unittest/catch.hpp:8480:18:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            std::srand( config.rngSeed() );
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:94:12:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        VG random;
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:95:35:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        random_graph(300, 3, 30, &random);
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:98:9:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        random.id_sort();
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:101:9:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        random.serialize_to_file(filename, 10);
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:110:13:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            random.for_each_handle([&](const handle_t& node) {
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:114:54:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                handle_t handle = indexed.get_handle(random.get_id(node));
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:120:51:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                REQUIRE(indexed.get_id(handle) == random.get_id(node));
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:127:52:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                REQUIRE(indexed.get_id(flipped) == random.get_id(node));
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:132:55:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                REQUIRE(indexed.get_length(handle) == random.get_length(node));
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:135:57:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                REQUIRE(indexed.get_sequence(handle) == random.get_sequence(node));
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:136:71:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                REQUIRE(indexed.get_sequence(indexed.flip(handle)) == random.get_sequence(random.flip(node)));
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:136:91:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                REQUIRE(indexed.get_sequence(indexed.flip(handle)) == random.get_sequence(random.flip(node)));
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:139:62:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                REQUIRE(indexed.get_degree(handle, false) == random.get_degree(node, false));
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:140:61:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                REQUIRE(indexed.get_degree(handle, true) == random.get_degree(node, true));
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:147:25:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                        random.follow_edges(flip_it ? random.flip(node) : node, go_left, [&](const handle_t& other) {
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:147:55:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                        random.follow_edges(flip_it ? random.flip(node) : node, go_left, [&](const handle_t& other) {
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:153:54:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
                            handle_t random_handle = random.get_handle(indexed.get_id(other), indexed.get_is_reverse(other));
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:169:49:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            REQUIRE(indexed.get_node_count() == random.get_node_count());
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:170:46:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            REQUIRE(indexed.min_node_id() == random.min_node_id());
data/vg-1.27.1+ds/src/unittest/indexed_vg.cpp:171:46:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            REQUIRE(indexed.max_node_id() == random.max_node_id());
data/vg-1.27.1+ds/src/unittest/source_sink_overlay.cpp:257:12:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        VG random;
data/vg-1.27.1+ds/src/unittest/source_sink_overlay.cpp:258:35:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        random_graph(100, 3, 30, &random);
data/vg-1.27.1+ds/src/unittest/source_sink_overlay.cpp:261:54:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        cerr << "Trial " << trial << ": " << pb2json(random.graph) << endl;
data/vg-1.27.1+ds/src/unittest/source_sink_overlay.cpp:264:27:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        id_t highest_id = random.max_node_id();
data/vg-1.27.1+ds/src/unittest/source_sink_overlay.cpp:271:19:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        VG copy = random;
data/vg-1.27.1+ds/src/unittest/source_sink_overlay.cpp:274:36:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        SourceSinkOverlay overlay(&random, 10, start_id, end_id);
data/vg-1.27.1+ds/src/unittest/source_sink_overlay.cpp:280:125:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
        vector<pair<unordered_set<id_t>, vector<handle_t>>> components = algorithms::weakly_connected_components_with_tips(&random);
data/vg-1.27.1+ds/src/utility.cpp:112:29:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
        const char* value = getenv("OMP_NUM_THREADS");
data/vg-1.27.1+ds/src/utility.cpp:360:35:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
                system_temp_dir = getenv(var_name);
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:61:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			 memcpy(_buffer,cr._buffer,_buffsize*sizeof(basetype) );
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:142:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
			_is = fopen(filename, "rb");
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:586:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			 memcpy(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) );
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:600:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				memcpy(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) );
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:1376:4:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
			char fname_old[1000];
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:1377:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(fname_old,"temp_p%i_level_%i",_pid,i-2);
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:1379:4:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
			char fname_curr[1000];
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:1380:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(fname_curr,"temp_p%i_level_%i",_pid,i);
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:1382:4:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
			char fname_prev[1000];
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:1383:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(fname_prev,"temp_p%i_level_%i",_pid,i-1);
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:1396:23:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
					_currlevelFile = fopen(fname_curr,"w");
data/vg-1.27.1+ds/deps/BBHash/bootest.cpp:75:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		 memcpy(_buffer,cr._buffer,_buffsize*sizeof(u_int64_t) );
data/vg-1.27.1+ds/deps/BBHash/bootest.cpp:148:9:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		_is = fopen(filename, "rb");
data/vg-1.27.1+ds/deps/BBHash/bootest.cpp:481:14:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		nthreads = atoi(argv[2]);
data/vg-1.27.1+ds/deps/BBHash/bootest.cpp:482:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		gammaFactor = atoi(argv[3]);
data/vg-1.27.1+ds/deps/BBHash/bootest.cpp:526:14:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		key_file = fopen("keyfile","w+");
data/vg-1.27.1+ds/deps/BBHash/bootest.cpp:572:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
				bench_file = fopen("benchfile","w+");
data/vg-1.27.1+ds/deps/BBHash/bootest.cpp:604:14:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
			vFiles[i]=fopen(("bucket"+to_string(i)).c_str(),"w+");
data/vg-1.27.1+ds/deps/BBHash/example.cpp:30:14:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		nthreads = atoi(argv[2]);
data/vg-1.27.1+ds/deps/BBHash/example_custom_hash.cpp:57:14:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		nthreads = atoi(argv[2]);
data/vg-1.27.1+ds/deps/DYNAMIC/benchmark.cpp:159:12:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	ulint n = atoi(argv[2]);
data/vg-1.27.1+ds/deps/DYNAMIC/cw-bwt.cpp:61:36:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		cwbwt = cw_bwt(path,cw_bwt::path,atoi(argv[3]),true);
data/vg-1.27.1+ds/deps/DYNAMIC/h0_lz77.cpp:57:48:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	ulint sa_rate = argc == 3 ? DEFAULT_SA_RATE : atoi(argv[1]);
data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/cw_bwt.hpp:197:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		if ((fp = fopen(path.c_str(), "wb")) == NULL) {
data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/BackwardFileIterator.h:34:8:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		fp = fopen(path.c_str(), "rb");
data/vg-1.27.1+ds/deps/dozeu/dozeu.h:117:41:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
#define dz_static_assert(expr)		typedef char dz_pp_cat(_st_, __LINE__)[(expr) ? 1 : -1]
data/vg-1.27.1+ds/deps/dozeu/dozeu.h:1642:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char revcomp[dz_unittest_query_length];
data/vg-1.27.1+ds/deps/dozeu/log.h:73:11:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			len += sprintf(str+len, "-oo,"); \
data/vg-1.27.1+ds/deps/dozeu/log.h:75:11:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			len += sprintf(str+len, "oo,"); \
data/vg-1.27.1+ds/deps/dozeu/log.h:77:11:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			len += sprintf(str+len, "%d,", *t); \
data/vg-1.27.1+ds/deps/dozeu/log.h:100:8:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
	_s += sprintf(_s, "                   "); \
data/vg-1.27.1+ds/deps/dozeu/log.h:102:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
		_s += sprintf(_s, " %02x", (uint8_t)i); \
data/vg-1.27.1+ds/deps/dozeu/log.h:106:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
		_s += sprintf(_s, "0x%016" PRIx64 ":", (uint64_t)_ptr); \
data/vg-1.27.1+ds/deps/dozeu/log.h:108:10:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			_s += sprintf(_s, " %02x", (uint8_t)_ptr[j]); \
data/vg-1.27.1+ds/deps/dozeu/log.h:110:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
		_s += sprintf(_s, "  "); \
data/vg-1.27.1+ds/deps/dozeu/log.h:112:10:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			_s += sprintf(_s, "%c", isprint(_ptr[j]) ? _ptr[j] : ' '); \
data/vg-1.27.1+ds/deps/dozeu/simde/hedley.h:1691:25:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
             ((struct { char v[sizeof(void) * 2]; } *) 1) \
data/vg-1.27.1+ds/deps/dozeu/simde/simde-common.h:643:42:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      #define simde_memcpy(dest, src, n) memcpy(dest, src, n)
data/vg-1.27.1+ds/deps/dozeu/unittest.h:92:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy((v1).a, (v0).a, sizeof(*(v).a) * (v0).n);	\
data/vg-1.27.1+ds/deps/dozeu/unittest.h:190:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char const *depends_on[16];
data/vg-1.27.1+ds/deps/dozeu/unittest.h:224:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char const *depends_on[16];
data/vg-1.27.1+ds/deps/dozeu/unittest.h:539:8:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
	_s += sprintf(_s, "                   "); \
data/vg-1.27.1+ds/deps/dozeu/unittest.h:541:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
		_s += sprintf(_s, " %02x", (uint8_t)i); \
data/vg-1.27.1+ds/deps/dozeu/unittest.h:545:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
		_s += sprintf(_s, "0x%016" PRIx64 ":", (uint64_t)_ptr); \
data/vg-1.27.1+ds/deps/dozeu/unittest.h:547:10:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			_s += sprintf(_s, " %02x", (uint8_t)_ptr[j]); \
data/vg-1.27.1+ds/deps/dozeu/unittest.h:549:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
		_s += sprintf(_s, "  "); \
data/vg-1.27.1+ds/deps/dozeu/unittest.h:551:10:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			_s += sprintf(_s, "%c", isprint(_ptr[j]) ? _ptr[j] : ' '); \
data/vg-1.27.1+ds/deps/dozeu/unittest.h:585:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char name[255];
data/vg-1.27.1+ds/deps/dozeu/unittest.h:1307:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char buf[p - b + 1];
data/vg-1.27.1+ds/deps/dozeu/unittest.h:1308:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(buf, b, p - b);
data/vg-1.27.1+ds/deps/dozeu/unittest.h:1400:34:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
			case 's': srand((unsigned int)atol(optarg)); break;
data/vg-1.27.1+ds/deps/gbwt/bwtmerge.cpp:85:12:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      std::memcpy(static_cast<void*>(this->data[i]), static_cast<void*>(source.data[i]), BLOCK_SIZE);
data/vg-1.27.1+ds/deps/gbwt/bwtmerge.cpp:315:1:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
open(GapArray<sdsl::int_vector_buffer<8>>& array, const std::string filename, size_type values)
data/vg-1.27.1+ds/deps/gbwt/bwtmerge.cpp:369:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
RankArray::open()
data/vg-1.27.1+ds/deps/gbwt/bwtmerge.cpp:378:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    gbwt::open(this->inputs[i], this->filenames[i], this->value_counts[i]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/query_idx.cpp:13:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char   buffer[buf_size];
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/word_pat2char_pat.cpp:12:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char   buffer[buf_size];
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:126:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    m = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:134:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    J = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:146:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifile = fopen(argv[1], "r");
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:167:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofile = fopen(argv[4], "w");
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:66:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    m = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:73:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    J = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:79:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifile = fopen(argv[1],"r");
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:100:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofile = fopen(argv[4],"w");
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/k2_trees/src/gen_k2t.cpp:63:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	fs.open(argv[3]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp:36:30:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    const uint64_t density = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/rrr_vector/src/rrr_time_and_space.cpp:63:22:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        uint16_t k = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/fm-index.cpp:26:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        max_locations = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/fm-index.cpp:29:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        post_context = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/fm-index.cpp:32:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        pre_context = atoi(argv[4]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/fm-rmq-index.cpp:52:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        max_locations = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/fm-rmq-index.cpp:55:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        post_context = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/examples/fm-rmq-index.cpp:58:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        pre_context = atoi(argv[4]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/test/gmock-internal-utils_test.cc:459:20:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int skip_count = atoi(log.substr(expected_message.size()).c_str());
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/test/gmock-more-actions_test.cc:631:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char ch[4] = {};
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2399:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  return fopen(path, mode);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/samples/sample2.cc:44:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(clone, a_c_string, len + 1);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:325:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[256];
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:741:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char executable_path[_MAX_PATH + 1];  // NOLINT
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:1026:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  const int cwd_fd = open(".", O_RDONLY);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc:105:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc:108:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:139:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  const int fd = open("/proc/self/as", O_RDONLY);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:865:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(buffer, regex, len);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:938:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp_dir_path[MAX_PATH + 1] = { '\0' };  // NOLINT
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:939:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp_file_path[MAX_PATH + 1] = { '\0' };  // NOLINT
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:976:29:  [2] (tmpfile) mkstemp:
  Potential for temporary file vulnerability in some circumstances. Some
  older Unix-like systems create temp files with permission to write by all
  by default, so be sure to set the umask to override this. Also, some older
  Unix systems might fail to use O_EXCL when opening the file, so make sure
  that O_EXCL is used by the library (CWE-377).
    const int captured_fd = mkstemp(name_template);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:65:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char text[5] = "";
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:859:7:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
      MultiByteToWideChar(CP_ACP, 0, ansi, length,
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:862:3:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
  MultiByteToWideChar(CP_ACP, 0, ansi, length,
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1677:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char error_text[kBufSize] = { '\0' };
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1761:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char str[5];  // Big enough for the largest valid code point.
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc:371:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char current_drive[_MAX_PATH];  // NOLINT
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc:388:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char non_drive[_MAX_PATH];  // NOLINT
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:131:32:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  UnprintableInFoo() : z_(0) { memcpy(xy_, "\xEF\x12\x0\x0\x34\xAB\x0\x0", 8); }
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:134:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char xy_[8];
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:1135:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char array[257];
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:7591:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  const char a[3] = "hi";
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:7675:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  const char a[2][3] = { "hi", "lo" };
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget_test.cc:58:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[max_size];
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/bwt.c:61:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char c[4];
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/bwt.c:98:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    blocksize = atoi(argv[i + 1]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/unbwt.c:61:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char c[4];
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector.hpp:1272:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        if (memcpy(m_data, v.data() ,v.capacity()/8)==nullptr) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector.hpp:1285:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            if (memcpy(m_data, v.data() ,v.capacity()/8)==nullptr) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:156:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, mode|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:158:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:188:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:189:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:215:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:216:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:298:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:300:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:380:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:382:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:384:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                ivb.m_ifile.open(ivb.m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:386:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                ivb.m_ofile.open(ivb.m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:345:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char tmp_file_name[1024] = {0};
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:365:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char tmp_dir_name[1024] = {0};
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/memory_management.hpp:397:52:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            if (!(mode&std::ios_base::out)) return open(filename.c_str(), O_RDONLY);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/memory_management.hpp:398:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            else return open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/ram_filebuf.hpp:24:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string s, std::ios_base::openmode mode);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/sfstream.hpp:32:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string& file, std::ios_base::openmode mode = std::ios_base::out);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/sfstream.hpp:62:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string& file, std::ios_base::openmode mode = std::ios_base::in);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/construct_lcp.cpp:124:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char alphabet[257] = {0};
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/construct_lcp.cpp:435:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char alphabet[257] = {0};
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/construct_lcp_helper.cpp:72:26:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_stream.open(m_file_name, std::ios::in | std::ios::out | std::ios::binary | std::ios::trunc);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/construct_lcp_helper.cpp:94:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(m_read_buf, m_write_buf, m_widx+1);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/memory_management.cpp:577:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(newptr,ptr,size);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/ram_filebuf.cpp:26:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
ram_filebuf::open(const std::string name, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:18:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(file, mode);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:22:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
osfstream::open(const std::string& file, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:30:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((ram_filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:33:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((std::filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:148:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(file, mode);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:152:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
isfstream::open(const std::string& file, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:160:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((ram_filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:163:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((std::filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/util.cpp:45:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char file_name[_MAX_FNAME] = { 0 };
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/util.cpp:62:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char dir_name[_MAX_DIR] = { 0 };
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/util.cpp:63:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char drive[_MAX_DRIVE] = {0};
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/util.cpp:110:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[4096];
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/csa_int_test.cpp:237:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    num_bytes = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/cst_int_test.cpp:478:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    num_bytes = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/replace_int_vector_value.cpp:17:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    uint64_t x = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/replace_int_vector_value.cpp:18:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    uint64_t y = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/csx-printf.cpp:10:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char line[BUF_SIZE];
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/tutorial/document_listing/doc_list_index.cpp:43:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char   buffer[64];
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/bwtmerge.h:240:6:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
void open(GapArray<sdsl::int_vector_buffer<8>>& array, const std::string filename, size_type values);
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/bwtmerge.h:284:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  void open() {}
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/bwtmerge.h:357:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    this->producer.open();
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/bwtmerge.h:498:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  void open();
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/variants.h:306:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  void open();
data/vg-1.27.1+ds/deps/gbwt/tests/test_bwtmerge.cpp:312:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    gbwt::open(input, filename, values.size());
data/vg-1.27.1+ds/deps/gbwt/tests/test_bwtmerge.cpp:398:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(part, filenames[file], value_counts[file]);
data/vg-1.27.1+ds/deps/gbwt/tests/test_bwtmerge.cpp:478:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    array.open();
data/vg-1.27.1+ds/deps/gbwt/tests/test_variants.cpp:120:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  phasings.open();
data/vg-1.27.1+ds/deps/gbwt/tests/test_variants.cpp:168:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  phasings.open();
data/vg-1.27.1+ds/deps/gbwt/utils.cpp:218:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char hostname[32];
data/vg-1.27.1+ds/deps/gbwt/variants.cpp:692:27:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if(open_file) { this->open(); }
data/vg-1.27.1+ds/deps/gbwt/variants.cpp:702:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
PhasingInformation::open()
data/vg-1.27.1+ds/deps/gbwt/variants.cpp:791:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  phasings.open();
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/bwtmerge.cpp:85:12:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      std::memcpy(static_cast<void*>(this->data[i]), static_cast<void*>(source.data[i]), BLOCK_SIZE);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/bwtmerge.cpp:315:1:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
open(GapArray<sdsl::int_vector_buffer<8>>& array, const std::string filename, size_type values)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/bwtmerge.cpp:369:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
RankArray::open()
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/bwtmerge.cpp:378:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    gbwt::open(this->inputs[i], this->filenames[i], this->value_counts[i]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/query_idx.cpp:13:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char   buffer[buf_size];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/document_retrieval/src/word_pat2char_pat.cpp:12:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char   buffer[buf_size];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:126:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    m = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:134:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    J = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:146:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifile = fopen(argv[1], "r");
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:167:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofile = fopen(argv[4], "w");
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:66:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    m = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:73:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    J = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:79:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifile = fopen(argv[1],"r");
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:100:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofile = fopen(argv[4],"w");
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/k2_trees/src/gen_k2t.cpp:63:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	fs.open(argv[3]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp:36:30:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    const uint64_t density = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/rrr_vector/src/rrr_time_and_space.cpp:63:22:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        uint16_t k = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/fm-index.cpp:26:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        max_locations = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/fm-index.cpp:29:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        post_context = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/fm-index.cpp:32:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        pre_context = atoi(argv[4]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/fm-rmq-index.cpp:52:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        max_locations = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/fm-rmq-index.cpp:55:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        post_context = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/examples/fm-rmq-index.cpp:58:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        pre_context = atoi(argv[4]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/test/gmock-internal-utils_test.cc:459:20:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int skip_count = atoi(log.substr(expected_message.size()).c_str());
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/test/gmock-more-actions_test.cc:631:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char ch[4] = {};
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2399:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  return fopen(path, mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/samples/sample2.cc:44:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(clone, a_c_string, len + 1);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:325:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[256];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:741:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char executable_path[_MAX_PATH + 1];  // NOLINT
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:1026:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  const int cwd_fd = open(".", O_RDONLY);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc:105:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc:108:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:139:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  const int fd = open("/proc/self/as", O_RDONLY);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:865:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(buffer, regex, len);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:938:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp_dir_path[MAX_PATH + 1] = { '\0' };  // NOLINT
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:939:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp_file_path[MAX_PATH + 1] = { '\0' };  // NOLINT
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:976:29:  [2] (tmpfile) mkstemp:
  Potential for temporary file vulnerability in some circumstances. Some
  older Unix-like systems create temp files with permission to write by all
  by default, so be sure to set the umask to override this. Also, some older
  Unix systems might fail to use O_EXCL when opening the file, so make sure
  that O_EXCL is used by the library (CWE-377).
    const int captured_fd = mkstemp(name_template);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:65:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char text[5] = "";
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:859:7:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
      MultiByteToWideChar(CP_ACP, 0, ansi, length,
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:862:3:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
  MultiByteToWideChar(CP_ACP, 0, ansi, length,
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1677:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char error_text[kBufSize] = { '\0' };
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1761:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char str[5];  // Big enough for the largest valid code point.
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc:371:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char current_drive[_MAX_PATH];  // NOLINT
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc:388:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char non_drive[_MAX_PATH];  // NOLINT
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:131:32:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  UnprintableInFoo() : z_(0) { memcpy(xy_, "\xEF\x12\x0\x0\x34\xAB\x0\x0", 8); }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:134:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char xy_[8];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:1135:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char array[257];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:7591:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  const char a[3] = "hi";
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:7675:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  const char a[2][3] = { "hi", "lo" };
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget_test.cc:58:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[max_size];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/bwt.c:61:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char c[4];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/bwt.c:98:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    blocksize = atoi(argv[i + 1]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/unbwt.c:61:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char c[4];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector.hpp:1272:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        if (memcpy(m_data, v.data() ,v.capacity()/8)==nullptr) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector.hpp:1285:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            if (memcpy(m_data, v.data() ,v.capacity()/8)==nullptr) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:156:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, mode|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:158:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:188:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:189:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:215:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:216:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:298:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:300:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:380:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:382:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:384:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                ivb.m_ifile.open(ivb.m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:386:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                ivb.m_ofile.open(ivb.m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:345:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char tmp_file_name[1024] = {0};
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:365:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char tmp_dir_name[1024] = {0};
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/memory_management.hpp:397:52:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            if (!(mode&std::ios_base::out)) return open(filename.c_str(), O_RDONLY);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/memory_management.hpp:398:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            else return open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/ram_filebuf.hpp:24:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string s, std::ios_base::openmode mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/sfstream.hpp:32:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string& file, std::ios_base::openmode mode = std::ios_base::out);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/sfstream.hpp:62:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string& file, std::ios_base::openmode mode = std::ios_base::in);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/construct_lcp.cpp:124:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char alphabet[257] = {0};
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/construct_lcp.cpp:435:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char alphabet[257] = {0};
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/construct_lcp_helper.cpp:72:26:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_stream.open(m_file_name, std::ios::in | std::ios::out | std::ios::binary | std::ios::trunc);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/construct_lcp_helper.cpp:94:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(m_read_buf, m_write_buf, m_widx+1);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/memory_management.cpp:577:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(newptr,ptr,size);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/ram_filebuf.cpp:26:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
ram_filebuf::open(const std::string name, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:18:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(file, mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:22:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
osfstream::open(const std::string& file, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:30:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((ram_filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:33:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((std::filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:148:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(file, mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:152:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
isfstream::open(const std::string& file, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:160:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((ram_filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/sfstream.cpp:163:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((std::filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/util.cpp:45:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char file_name[_MAX_FNAME] = { 0 };
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/util.cpp:62:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char dir_name[_MAX_DIR] = { 0 };
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/util.cpp:63:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char drive[_MAX_DRIVE] = {0};
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/util.cpp:110:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[4096];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/csa_int_test.cpp:237:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    num_bytes = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/cst_int_test.cpp:478:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    num_bytes = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/replace_int_vector_value.cpp:17:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    uint64_t x = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/replace_int_vector_value.cpp:18:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    uint64_t y = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/csx-printf.cpp:10:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char line[BUF_SIZE];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/tutorial/document_listing/doc_list_index.cpp:43:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char   buffer[64];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/bwtmerge.h:240:6:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
void open(GapArray<sdsl::int_vector_buffer<8>>& array, const std::string filename, size_type values);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/bwtmerge.h:284:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  void open() {}
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/bwtmerge.h:357:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    this->producer.open();
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/bwtmerge.h:498:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  void open();
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/variants.h:306:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  void open();
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/tests/test_bwtmerge.cpp:312:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    gbwt::open(input, filename, values.size());
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/tests/test_bwtmerge.cpp:398:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(part, filenames[file], value_counts[file]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/tests/test_bwtmerge.cpp:478:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    array.open();
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/tests/test_variants.cpp:120:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  phasings.open();
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/tests/test_variants.cpp:168:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  phasings.open();
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/utils.cpp:207:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char hostname[32];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/variants.cpp:692:27:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if(open_file) { this->open(); }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/variants.cpp:702:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
PhasingInformation::open()
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/variants.cpp:791:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  phasings.open();
data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp:81:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char magic_bytes[4];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/types.hpp:34:19:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct handle_t { char data[sizeof(nid_t)]; };
data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/types.hpp:40:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct path_handle_t { char data[sizeof(int64_t)]; };
data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/types.hpp:43:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct step_handle_t { char data[2 * sizeof(int64_t)]; };
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/document_retrieval/src/query_idx.cpp:13:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char   buffer[buf_size];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/document_retrieval/src/word_pat2char_pat.cpp:12:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char   buffer[buf_size];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:126:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    m = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:134:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    J = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:146:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifile = fopen(argv[1], "r");
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:167:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofile = fopen(argv[4], "w");
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:66:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    m = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:73:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    J = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:79:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifile = fopen(argv[1],"r");
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:100:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofile = fopen(argv[4],"w");
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/k2_trees/src/gen_k2t.cpp:63:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	fs.open(argv[3]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp:36:30:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    const uint64_t density = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/rrr_vector/src/rrr_time_and_space.cpp:63:22:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        uint16_t k = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/fm-index.cpp:26:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        max_locations = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/fm-index.cpp:29:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        post_context = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/fm-index.cpp:32:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        pre_context = atoi(argv[4]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/fm-rmq-index.cpp:52:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        max_locations = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/fm-rmq-index.cpp:55:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        post_context = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/examples/fm-rmq-index.cpp:58:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        pre_context = atoi(argv[4]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googlemock/test/gmock-internal-utils_test.cc:459:20:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int skip_count = atoi(log.substr(expected_message.size()).c_str());
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googlemock/test/gmock-more-actions_test.cc:631:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char ch[4] = {};
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2399:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  return fopen(path, mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/samples/sample2.cc:44:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(clone, a_c_string, len + 1);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:325:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[256];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:741:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char executable_path[_MAX_PATH + 1];  // NOLINT
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:1026:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  const int cwd_fd = open(".", O_RDONLY);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc:105:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc:108:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:139:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  const int fd = open("/proc/self/as", O_RDONLY);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:865:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(buffer, regex, len);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:938:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp_dir_path[MAX_PATH + 1] = { '\0' };  // NOLINT
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:939:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp_file_path[MAX_PATH + 1] = { '\0' };  // NOLINT
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:976:29:  [2] (tmpfile) mkstemp:
  Potential for temporary file vulnerability in some circumstances. Some
  older Unix-like systems create temp files with permission to write by all
  by default, so be sure to set the umask to override this. Also, some older
  Unix systems might fail to use O_EXCL when opening the file, so make sure
  that O_EXCL is used by the library (CWE-377).
    const int captured_fd = mkstemp(name_template);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:65:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char text[5] = "";
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:859:7:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
      MultiByteToWideChar(CP_ACP, 0, ansi, length,
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:862:3:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
  MultiByteToWideChar(CP_ACP, 0, ansi, length,
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1677:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char error_text[kBufSize] = { '\0' };
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1761:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char str[5];  // Big enough for the largest valid code point.
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc:371:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char current_drive[_MAX_PATH];  // NOLINT
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc:388:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char non_drive[_MAX_PATH];  // NOLINT
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:131:32:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  UnprintableInFoo() : z_(0) { memcpy(xy_, "\xEF\x12\x0\x0\x34\xAB\x0\x0", 8); }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:134:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char xy_[8];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:1135:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char array[257];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:7591:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  const char a[3] = "hi";
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:7675:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  const char a[2][3] = { "hi", "lo" };
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget_test.cc:58:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[max_size];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/libdivsufsort/examples/bwt.c:61:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char c[4];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/libdivsufsort/examples/bwt.c:98:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    blocksize = atoi(argv[i + 1]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/libdivsufsort/examples/unbwt.c:61:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char c[4];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector.hpp:1272:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        if (memcpy(m_data, v.data() ,v.capacity()/8)==nullptr) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector.hpp:1285:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            if (memcpy(m_data, v.data() ,v.capacity()/8)==nullptr) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:156:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, mode|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:158:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:188:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:189:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:215:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:216:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:298:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:300:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:380:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:382:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:384:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                ivb.m_ifile.open(ivb.m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:386:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                ivb.m_ofile.open(ivb.m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:345:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char tmp_file_name[1024] = {0};
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:365:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char tmp_dir_name[1024] = {0};
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/memory_management.hpp:397:52:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            if (!(mode&std::ios_base::out)) return open(filename.c_str(), O_RDONLY);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/memory_management.hpp:398:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            else return open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/ram_filebuf.hpp:24:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string s, std::ios_base::openmode mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/sfstream.hpp:32:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string& file, std::ios_base::openmode mode = std::ios_base::out);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/sfstream.hpp:62:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string& file, std::ios_base::openmode mode = std::ios_base::in);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/construct_lcp.cpp:124:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char alphabet[257] = {0};
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/construct_lcp.cpp:435:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char alphabet[257] = {0};
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/construct_lcp_helper.cpp:72:26:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_stream.open(m_file_name, std::ios::in | std::ios::out | std::ios::binary | std::ios::trunc);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/construct_lcp_helper.cpp:94:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(m_read_buf, m_write_buf, m_widx+1);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/memory_management.cpp:577:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(newptr,ptr,size);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/ram_filebuf.cpp:26:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
ram_filebuf::open(const std::string name, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:18:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(file, mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:22:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
osfstream::open(const std::string& file, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:30:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((ram_filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:33:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((std::filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:148:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(file, mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:152:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
isfstream::open(const std::string& file, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:160:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((ram_filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/sfstream.cpp:163:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((std::filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/util.cpp:45:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char file_name[_MAX_FNAME] = { 0 };
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/util.cpp:62:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char dir_name[_MAX_DIR] = { 0 };
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/util.cpp:63:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char drive[_MAX_DRIVE] = {0};
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/util.cpp:110:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[4096];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/csa_int_test.cpp:237:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    num_bytes = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/cst_int_test.cpp:478:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    num_bytes = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/replace_int_vector_value.cpp:17:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    uint64_t x = atoi(argv[2]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/replace_int_vector_value.cpp:18:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    uint64_t y = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/tutorial/csx-printf.cpp:10:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char line[BUF_SIZE];
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/tutorial/document_listing/doc_list_index.cpp:43:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char   buffer[64];
data/vg-1.27.1+ds/deps/gbwtgraph/gfa.cpp:52:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    this->fd = ::open(filename.c_str(), O_RDONLY);
data/vg-1.27.1+ds/deps/gcsa2/algorithms.cpp:567:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    left_output.open(left_name.c_str(), std::ios_base::binary);
data/vg-1.27.1+ds/deps/gcsa2/algorithms.cpp:574:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    right_output.open(right_name.c_str(), std::ios_base::binary);
data/vg-1.27.1+ds/deps/gcsa2/files.cpp:316:32:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    std::ifstream input; this->open(input, file);
data/vg-1.27.1+ds/deps/gcsa2/files.cpp:365:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
InputGraph::open(std::ifstream& input, size_type file) const
data/vg-1.27.1+ds/deps/gcsa2/files.cpp:373:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  input.open(this->filenames[file].c_str(), std::ios_base::binary);
data/vg-1.27.1+ds/deps/gcsa2/files.cpp:425:30:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  std::ifstream input; this->open(input, file);
data/vg-1.27.1+ds/deps/gcsa2/gcsa.cpp:299:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  this->paths.open(graph.path_name);
data/vg-1.27.1+ds/deps/gcsa2/gcsa.cpp:300:16:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  this->labels.open(graph.rank_name);
data/vg-1.27.1+ds/deps/gcsa2/gcsa.cpp:301:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  this->from_nodes.open(graph.from_name);
data/vg-1.27.1+ds/deps/gcsa2/gcsa.cpp:313:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  this->paths.open(graph.path_name);
data/vg-1.27.1+ds/deps/gcsa2/gcsa.cpp:314:16:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  this->labels.open(graph.rank_name);
data/vg-1.27.1+ds/deps/gcsa2/gcsa.cpp:315:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  this->from_nodes.open(graph.from_name);
data/vg-1.27.1+ds/deps/gcsa2/gcsa.cpp:558:44:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  ReadBuffer<uint8_t> lcp_array; lcp_array.open(merged_graph.lcp_name);
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/files.h:91:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  void open(std::ifstream& input, size_type file) const;
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/internal.h:386:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  void open(const std::string& filename);
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/internal.h:435:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
ReadBuffer<Element>::open(const std::string& filename)
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/internal.h:443:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  this->file.open(filename.c_str(), std::ios_base::binary);
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/internal.h:566:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  void open(const std::string& filename, size_type _buffer_size = MEGABYTE);
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/internal.h:598:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  this->open(filename, _buffer_size);
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/internal.h:609:23:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
WriteBuffer<Element>::open(const std::string& filename, size_type _buffer_size)
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/internal.h:611:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  this->file.open(filename.c_str(), std::ios_base::binary);
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/path_graph.h:316:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  void open(std::ifstream& path_file, std::ifstream& rank_file, size_type file) const;
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:333:28:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    this->path_files[file].open(this->graph.path_names[file]);
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:334:28:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    this->rank_files[file].open(this->graph.rank_names[file]);
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:410:26:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  this->path_files[file].open(this->graph.path_names[file]);
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:411:26:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  this->rank_files[file].open(this->graph.rank_names[file]);
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:514:28:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    this->path_files[file].open(path_graph.path_names[file]);
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:515:28:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    this->rank_files[file].open(path_graph.rank_names[file]);
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:827:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
PathGraph::open(std::ifstream& path_file, std::ifstream& rank_file, size_type file) const
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:835:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  path_file.open(this->path_names[file].c_str(), std::ios_base::binary);
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:842:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  rank_file.open(this->rank_names[file].c_str(), std::ios_base::binary);
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:1082:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  this->open(path_file, rank_file, file);
data/vg-1.27.1+ds/deps/gcsa2/utils.cpp:195:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char hostname[32];
data/vg-1.27.1+ds/deps/gfakluge/src/gfa_builder.hpp:183:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifi.open(vcf_file);
data/vg-1.27.1+ds/deps/gfakluge/src/gfa_builder.hpp:345:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(dummy_name, contig_name.c_str(), contig_name.size() + 1);
data/vg-1.27.1+ds/deps/gfakluge/src/gfakluge.hpp:87:24:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                return atol(lhs.c_str()) < atol(rhs.c_str());
data/vg-1.27.1+ds/deps/gfakluge/src/gfakluge.hpp:87:44:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                return atol(lhs.c_str()) < atol(rhs.c_str());
data/vg-1.27.1+ds/deps/gfakluge/src/gfakluge.hpp:567:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            fd = open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/gfakluge/src/gfakluge.hpp:728:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                gfi.open(filename, std::ifstream::in);
data/vg-1.27.1+ds/deps/gfakluge/src/gfakluge.hpp:1024:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                gfi.open(filename, std::ifstream::in);
data/vg-1.27.1+ds/deps/gfakluge/src/gfakluge.hpp:1082:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                gfi.open(filename, std::ifstream::in);
data/vg-1.27.1+ds/deps/gfakluge/src/gfakluge.hpp:2267:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                gfi.open(filename.c_str(), std::ifstream::in);
data/vg-1.27.1+ds/deps/gfakluge/src/gfakluge.hpp:2564:36:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                            rank = atoi(tokens[3].c_str());
data/vg-1.27.1+ds/deps/gfakluge/src/gfakluge.hpp:2621:40:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                                rank = atoi(tokens[3].c_str());
data/vg-1.27.1+ds/deps/gfakluge/src/gfakluge.hpp:2641:38:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                        a.position = atoi(tokens[2].c_str());
data/vg-1.27.1+ds/deps/gfakluge/src/gfakluge.hpp:2644:36:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                        a.length = atoi(tokens[5].c_str());
data/vg-1.27.1+ds/deps/gfakluge/src/main.cpp:197:26:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                minlen = atoi(optarg);
data/vg-1.27.1+ds/deps/gfakluge/src/main.cpp:354:33:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                max_node_size = atoi(optarg);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/examples/getseq.cpp:36:21:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        int start = atoi(argv[3]);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/examples/getseq.cpp:37:19:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        int end = atoi(argv[4]);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/pliib.hpp:35:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static char complement_array [26] = {
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/pliib.hpp:225:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(ret, s, d_index * sizeof(char));
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/pliib.hpp:247:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(ret, s + start, rsz * sizeof(char));
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/pliib.hpp:257:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(t, s.c_str(), slen);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/pliib.hpp:353:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(contig, bend + first_bracket_index + 1, colon_index - first_bracket_index - 1);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/pliib.hpp:357:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(pstr, bend + colon_index + 1, last_bracket_index - colon_index - 1);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/pliib.hpp:358:20:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        position = atoi(pstr);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:72:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(this->name, splits[0].c_str(), splits[0].length() * sizeof(char));
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:140:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        ofi.open(filename);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:159:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    faFile.open(fastaName);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:161:23:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (!(fai.fasta = fopen(fastaName, "r"))){
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:248:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifi.open((const char*) ifn);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:250:23:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (!(fai.fasta = fopen(fastaFileName, "r"))){
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:326:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(ret, seq + start, (end - start) * sizeof(char) );
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:235:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(scratch, to_swizzle, size);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:277:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(scratch, to_unswizzle, size);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:400:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(pvEStore, seed->pvE, padded_read_length);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:401:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(pvHStore, seed->pvHStore, padded_read_length);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:502:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(alignment->seed.pvE,      pvEStore, padded_read_length);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:503:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(alignment->seed.pvHStore, pvHStore, padded_read_length);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:621:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(pvE, seed->pvE, segLen*sizeof(__m128i));
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:622:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(pvHStore, seed->pvHStore, segLen*sizeof(__m128i));
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:914:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(alignment->seed.pvE,      pvE,      segLen*sizeof(__m128i));
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:915:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(alignment->seed.pvHStore, pvHStore, segLen*sizeof(__m128i));
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1076:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(scratch, to_swizzle, size * sizeof(int16_t));
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1117:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(scratch, to_unswizzle, size * sizeof(int16_t));
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1244:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(pvEStore, seed->pvE, padded_read_length * sizeof(int16_t));
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1245:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(pvHStore, seed->pvHStore, padded_read_length * sizeof(int16_t));
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1349:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(alignment->seed.pvE,      pvEStore, padded_read_length * sizeof(int16_t));
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1350:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(alignment->seed.pvHStore, pvHStore, padded_read_length * sizeof(int16_t));
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1439:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(pvE, seed->pvE, segLen*sizeof(__m128i));
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1440:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(pvHStore, seed->pvHStore, segLen*sizeof(__m128i));
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1669:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(alignment->seed.pvE,      pvE,      segLen*sizeof(__m128i));
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1670:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(alignment->seed.pvHStore, pvHStore, segLen*sizeof(__m128i));
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:5501:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(ret_nt_table, nt_table, 128*sizeof(int8_t));
data/vg-1.27.1+ds/deps/gssw/src/kseq.h:123:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
data/vg-1.27.1+ds/deps/gssw/src/main.c:221:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char mat_name[16];
data/vg-1.27.1+ds/deps/gssw/src/main.c:284:22:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
			case 'm': match = atoi(optarg); break;
data/vg-1.27.1+ds/deps/gssw/src/main.c:285:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
			case 'x': mismatch = atoi(optarg); break;
data/vg-1.27.1+ds/deps/gssw/src/main.c:286:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
			case 'o': gap_open = atoi(optarg); break;
data/vg-1.27.1+ds/deps/gssw/src/main.c:287:30:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
			case 'e': gap_extension = atoi(optarg); break;
data/vg-1.27.1+ds/deps/gssw/src/main.c:289:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
			case 'f': filter = atoi(optarg); break;
data/vg-1.27.1+ds/deps/gssw/src/main.c:329:17:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		FILE *f_mat = fopen(mat_name, "r");
data/vg-1.27.1+ds/deps/gssw/src/main.c:330:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char line[128];
data/vg-1.27.1+ds/deps/gssw/src/main.c:337:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
				char str[4], *s = str;
data/vg-1.27.1+ds/deps/gssw/src/main.c:344:27:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
						mata[k++] = (int8_t)atoi(str);
data/vg-1.27.1+ds/deps/gssw/src/main.c:352:26:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
					mata[k++] = (int8_t)atoi(str);
data/vg-1.27.1+ds/deps/gssw/src/simde/hedley.h:1691:25:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
             ((struct { char v[sizeof(void) * 2]; } *) 1) \
data/vg-1.27.1+ds/deps/gssw/src/simde/simde-common.h:643:42:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      #define simde_memcpy(dest, src, n) memcpy(dest, src, n)
data/vg-1.27.1+ds/deps/gssw/src/ssw_cpp.cpp:193:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(score_matrix_, score_matrix, sizeof(int8_t) * score_matrix_size_ * score_matrix_size_);
data/vg-1.27.1+ds/deps/gssw/src/ssw_cpp.cpp:195:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(translation_matrix_, translation_matrix, sizeof(int8_t) * translation_matrix_size);
data/vg-1.27.1+ds/deps/gssw/src/ssw_cpp.cpp:386:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(score_matrix_, score_matrix, sizeof(int8_t) * score_matrix_size_ * score_matrix_size_);
data/vg-1.27.1+ds/deps/gssw/src/ssw_cpp.cpp:388:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(translation_matrix_, translation_matrix, sizeof(int8_t) * translation_matrix_size);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:61:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			 memcpy(_buffer,cr._buffer,_buffsize*sizeof(basetype) );
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:142:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
			_is = fopen(filename, "rb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:586:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			 memcpy(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) );
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:600:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				memcpy(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) );
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:1376:4:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
			char fname_old[1000];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:1377:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(fname_old,"temp_p%i_level_%i",_pid,i-2);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:1379:4:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
			char fname_curr[1000];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:1380:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(fname_curr,"temp_p%i_level_%i",_pid,i);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:1382:4:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
			char fname_prev[1000];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:1383:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(fname_prev,"temp_p%i_level_%i",_pid,i-1);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:1396:23:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
					_currlevelFile = fopen(fname_curr,"w");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/bootest.cpp:75:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		 memcpy(_buffer,cr._buffer,_buffsize*sizeof(u_int64_t) );
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/bootest.cpp:148:9:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		_is = fopen(filename, "rb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/bootest.cpp:481:14:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		nthreads = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/bootest.cpp:482:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		gammaFactor = atoi(argv[3]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/bootest.cpp:526:14:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		key_file = fopen("keyfile","w+");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/bootest.cpp:572:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
				bench_file = fopen("benchfile","w+");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/bootest.cpp:604:14:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
			vFiles[i]=fopen(("bucket"+to_string(i)).c_str(),"w+");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/example.cpp:30:14:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		nthreads = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/example_custom_hash.cpp:57:14:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		nthreads = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/benchmark.cpp:157:12:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	ulint n = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/cw-bwt.cpp:61:36:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		cwbwt = cw_bwt(path,cw_bwt::path,atoi(argv[3]),true);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/h0_lz77.cpp:57:48:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	ulint sa_rate = argc == 3 ? DEFAULT_SA_RATE : atoi(argv[1]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/algorithms/cw_bwt.hpp:197:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		if ((fp = fopen(path.c_str(), "wb")) == NULL) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/BackwardFileIterator.h:34:8:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		fp = fopen(path.c_str(), "rb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp:81:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char magic_bytes[4];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/types.hpp:34:19:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct handle_t { char data[sizeof(nid_t)]; };
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/types.hpp:40:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct path_handle_t { char data[sizeof(int64_t)]; };
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/types.hpp:43:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct step_handle_t { char data[2 * sizeof(int64_t)]; };
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/complex.h:24:28:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static constexpr const char value[3] = { 'Z', c, '\0' };
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/detail/class.h:563:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy((void *) tp_doc, rec.doc, size);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/detail/common.h:714:28:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static constexpr const char value[2] = { c, '\0' };
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/detail/descr.h:26:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char text[N + 1];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_buffers.cpp:26:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(m_data, s.m_data, sizeof(float) * (size_t) (m_rows * m_cols));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_buffers.cpp:47:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(m_data, s.m_data, sizeof(float) * (size_t) (m_rows * m_cols));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_buffers.cpp:87:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(v->data(), info.ptr, sizeof(float) * (size_t) (v->rows() * v->cols()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_embed/test_interpreter.cpp:275:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    test_module.open(module_file);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_numpy_dtypes.cpp:76:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char a[3];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_numpy_dtypes.cpp:90:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char a[3][4];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_sequences_and_iterators.cpp:105:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(m_data, &value[0], sizeof(float) * m_size);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_sequences_and_iterators.cpp:110:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(m_data, s.m_data, sizeof(float)*m_size);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_sequences_and_iterators.cpp:125:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
                memcpy(m_data, s.m_data, sizeof(float)*m_size);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/document_retrieval/src/query_idx.cpp:13:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char   buffer[buf_size];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/document_retrieval/src/word_pat2char_pat.cpp:12:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char   buffer[buf_size];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:126:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    m = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:134:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    J = atoi(argv[3]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:146:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifile = fopen(argv[1], "r");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:167:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofile = fopen(argv[4], "w");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:66:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    m = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:73:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    J = atoi(argv[3]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:79:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifile = fopen(argv[1],"r");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:100:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofile = fopen(argv[4],"w");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/k2_trees/src/gen_k2t.cpp:63:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	fs.open(argv[3]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp:36:30:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    const uint64_t density = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/rrr_vector/src/rrr_time_and_space.cpp:63:22:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        uint16_t k = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/fm-index.cpp:26:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        max_locations = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/fm-index.cpp:29:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        post_context = atoi(argv[3]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/fm-index.cpp:32:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        pre_context = atoi(argv[4]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/fm-rmq-index.cpp:52:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        max_locations = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/fm-rmq-index.cpp:55:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        post_context = atoi(argv[3]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/examples/fm-rmq-index.cpp:58:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        pre_context = atoi(argv[4]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-internal-utils_test.cc:459:20:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int skip_count = atoi(log.substr(expected_message.size()).c_str());
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-more-actions_test.cc:631:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char ch[4] = {};
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2399:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  return fopen(path, mode);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample2.cc:44:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(clone, a_c_string, len + 1);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:325:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[256];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:741:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char executable_path[_MAX_PATH + 1];  // NOLINT
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:1026:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  const int cwd_fd = open(".", O_RDONLY);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc:105:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc:108:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:139:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  const int fd = open("/proc/self/as", O_RDONLY);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:865:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(buffer, regex, len);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:938:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp_dir_path[MAX_PATH + 1] = { '\0' };  // NOLINT
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:939:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp_file_path[MAX_PATH + 1] = { '\0' };  // NOLINT
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:976:29:  [2] (tmpfile) mkstemp:
  Potential for temporary file vulnerability in some circumstances. Some
  older Unix-like systems create temp files with permission to write by all
  by default, so be sure to set the umask to override this. Also, some older
  Unix systems might fail to use O_EXCL when opening the file, so make sure
  that O_EXCL is used by the library (CWE-377).
    const int captured_fd = mkstemp(name_template);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:65:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char text[5] = "";
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:859:7:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
      MultiByteToWideChar(CP_ACP, 0, ansi, length,
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:862:3:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
  MultiByteToWideChar(CP_ACP, 0, ansi, length,
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1677:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char error_text[kBufSize] = { '\0' };
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1761:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char str[5];  // Big enough for the largest valid code point.
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc:371:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char current_drive[_MAX_PATH];  // NOLINT
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc:388:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char non_drive[_MAX_PATH];  // NOLINT
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:131:32:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  UnprintableInFoo() : z_(0) { memcpy(xy_, "\xEF\x12\x0\x0\x34\xAB\x0\x0", 8); }
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:134:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char xy_[8];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:1135:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char array[257];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:7591:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  const char a[3] = "hi";
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:7675:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  const char a[2][3] = { "hi", "lo" };
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget_test.cc:58:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[max_size];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/libdivsufsort/examples/bwt.c:61:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char c[4];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/libdivsufsort/examples/bwt.c:98:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    blocksize = atoi(argv[i + 1]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/libdivsufsort/examples/unbwt.c:61:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char c[4];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector.hpp:1272:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        if (memcpy(m_data, v.data() ,v.capacity()/8)==nullptr) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector.hpp:1285:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            if (memcpy(m_data, v.data() ,v.capacity()/8)==nullptr) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:156:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, mode|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:158:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:188:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:189:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:215:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:216:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:298:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:300:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:380:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:382:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:384:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                ivb.m_ifile.open(ivb.m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:386:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                ivb.m_ofile.open(ivb.m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:345:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char tmp_file_name[1024] = {0};
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:365:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char tmp_dir_name[1024] = {0};
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/memory_management.hpp:397:52:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            if (!(mode&std::ios_base::out)) return open(filename.c_str(), O_RDONLY);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/memory_management.hpp:398:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            else return open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/ram_filebuf.hpp:24:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string s, std::ios_base::openmode mode);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/sfstream.hpp:32:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string& file, std::ios_base::openmode mode = std::ios_base::out);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/sfstream.hpp:62:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string& file, std::ios_base::openmode mode = std::ios_base::in);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/construct_lcp.cpp:124:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char alphabet[257] = {0};
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/construct_lcp.cpp:435:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char alphabet[257] = {0};
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/construct_lcp_helper.cpp:72:26:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_stream.open(m_file_name, std::ios::in | std::ios::out | std::ios::binary | std::ios::trunc);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/construct_lcp_helper.cpp:94:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(m_read_buf, m_write_buf, m_widx+1);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/memory_management.cpp:577:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(newptr,ptr,size);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/ram_filebuf.cpp:26:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
ram_filebuf::open(const std::string name, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:18:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(file, mode);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:22:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
osfstream::open(const std::string& file, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:30:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((ram_filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:33:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((std::filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:148:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(file, mode);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:152:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
isfstream::open(const std::string& file, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:160:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((ram_filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/sfstream.cpp:163:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((std::filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/util.cpp:45:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char file_name[_MAX_FNAME] = { 0 };
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/util.cpp:62:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char dir_name[_MAX_DIR] = { 0 };
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/util.cpp:63:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char drive[_MAX_DRIVE] = {0};
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/util.cpp:110:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[4096];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/csa_int_test.cpp:237:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    num_bytes = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/cst_int_test.cpp:478:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    num_bytes = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/replace_int_vector_value.cpp:17:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    uint64_t x = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/replace_int_vector_value.cpp:18:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    uint64_t y = atoi(argv[3]);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/tutorial/csx-printf.cpp:10:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char line[BUF_SIZE];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/tutorial/document_listing/doc_list_index.cpp:43:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char   buffer[64];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/insert_rvalue.cc:25:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[10], buf2[10];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/insert_rvalue.cc:29:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buf, "%d", i); 
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/insert_rvalue.cc:30:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buf2, "val%d", i);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/insert_rvalue.cc:37:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buf, "%d", i); 
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/insert_rvalue.cc:38:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buf2, "val%d", i);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/insert_rvalue.cc:45:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buf, "%d", i); 
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/insert_rvalue.cc:46:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buf2, "val%d", i);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/serialize_file.cc:117:17:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *out = fopen("ages.dmp", "wb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/serialize_file.cc:124:19:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *input = fopen("ages.dmp", "rb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/serialize_large.cc:76:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buff[20];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/serialize_large.cc:77:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buff, "%zu", i);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/serialize_large.cc:83:17:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *out = fopen("ages.dmp", "wb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/serialize_large.cc:93:19:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *input = fopen("ages.dmp", "rb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp.h:1384:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(static_cast<void *>(_group + i), _group + i-1, sizeof(*_group));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp.h:1488:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(static_cast<void *>(_group + i), _group + i + 1, sizeof(*_group));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp.h:2086:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
                memcpy(static_cast<void *>(first), _first_group, sizeof(*first) * (std::min)(sz, old_sz));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_dlalloc.h:543:31:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                dev_zero_fd = open("/dev/zero", O_RDWR);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_dlalloc.h:1643:22:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            unsigned char buf[sizeof(size_t)];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_dlalloc.h:1645:23:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            if ((fd = open("/dev/urandom", O_RDONLY)) >= 0 &&
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_dlalloc.h:3812:21:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
                    memcpy(mem, oldmem, (oc < bytes) ? oc : bytes);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_memory.h:130:21:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                i = atoi(line);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_memory.h:134:21:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        auto file = fopen("/proc/self/status", "r");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_memory.h:136:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char line[128];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:88:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char tmppath_buffer[1024];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:108:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(result, str, len + 1);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:1177:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buffer[64];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:1193:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buffer[64];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:1258:28:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        return (*this)(fp, atoi(value));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:1522:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buff[20];
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:1525:13:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
            sprintf(buff, "%d", j);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:2396:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE* fp = fopen(file.c_str(), "wb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:2406:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fp = fopen(file.c_str(), "rb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:2440:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE* fp = fopen(file.c_str(), "wb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:2460:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fp = fopen(file.c_str(), "rb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:2505:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE* fp = fopen(file.c_str(), "wb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:2514:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fp = fopen(file.c_str(), "rb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:2544:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE* fp = fopen(file.c_str(), "wb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:2553:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fp = fopen(file.c_str(), "rb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:2582:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(reinterpret_cast<char*>(buf), s_->data(), len);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:2665:20:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        FILE* fp = fopen(file.c_str(), "wb");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:2677:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char contents[24] = {0};
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:2678:14:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        fp = fopen(file.c_str(), "rb");
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:61:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			 memcpy(_buffer,cr._buffer,_buffsize*sizeof(basetype) );
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:142:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
			_is = fopen(filename, "rb");
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:586:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			 memcpy(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) );
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:600:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				memcpy(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) );
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:1376:4:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
			char fname_old[1000];
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:1377:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(fname_old,"temp_p%i_level_%i",_pid,i-2);
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:1379:4:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
			char fname_curr[1000];
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:1380:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(fname_curr,"temp_p%i_level_%i",_pid,i);
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:1382:4:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
			char fname_prev[1000];
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:1383:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(fname_prev,"temp_p%i_level_%i",_pid,i-1);
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:1396:23:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
					_currlevelFile = fopen(fname_curr,"w");
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/bootest.cpp:75:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		 memcpy(_buffer,cr._buffer,_buffsize*sizeof(u_int64_t) );
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/bootest.cpp:148:9:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		_is = fopen(filename, "rb");
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/bootest.cpp:481:14:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		nthreads = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/bootest.cpp:482:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		gammaFactor = atoi(argv[3]);
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/bootest.cpp:526:14:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		key_file = fopen("keyfile","w+");
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/bootest.cpp:572:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
				bench_file = fopen("benchfile","w+");
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/bootest.cpp:604:14:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
			vFiles[i]=fopen(("bucket"+to_string(i)).c_str(),"w+");
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/example.cpp:30:14:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		nthreads = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/example_custom_hash.cpp:57:14:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		nthreads = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/benchmark.cpp:159:12:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	ulint n = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/cw-bwt.cpp:61:36:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		cwbwt = cw_bwt(path,cw_bwt::path,atoi(argv[3]),true);
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/h0_lz77.cpp:57:48:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	ulint sa_rate = argc == 3 ? DEFAULT_SA_RATE : atoi(argv[1]);
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/cw_bwt.hpp:197:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		if ((fp = fopen(path.c_str(), "wb")) == NULL) {
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/structures/BackwardFileIterator.h:34:8:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		fp = fopen(path.c_str(), "rb");
data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp:81:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char magic_bytes[4];
data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/types.hpp:34:19:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct handle_t { char data[sizeof(nid_t)]; };
data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/types.hpp:40:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct path_handle_t { char data[sizeof(int64_t)]; };
data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/types.hpp:43:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct step_handle_t { char data[2 * sizeof(int64_t)]; };
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/complex.h:24:28:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static constexpr const char value[3] = { 'Z', c, '\0' };
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/detail/class.h:563:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy((void *) tp_doc, rec.doc, size);
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/detail/common.h:714:28:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static constexpr const char value[2] = { c, '\0' };
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/detail/descr.h:26:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char text[N + 1];
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_buffers.cpp:26:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(m_data, s.m_data, sizeof(float) * (size_t) (m_rows * m_cols));
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_buffers.cpp:47:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(m_data, s.m_data, sizeof(float) * (size_t) (m_rows * m_cols));
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_buffers.cpp:87:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(v->data(), info.ptr, sizeof(float) * (size_t) (v->rows() * v->cols()));
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_embed/test_interpreter.cpp:275:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    test_module.open(module_file);
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_numpy_dtypes.cpp:76:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char a[3];
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_numpy_dtypes.cpp:90:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char a[3][4];
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_sequences_and_iterators.cpp:105:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(m_data, &value[0], sizeof(float) * m_size);
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_sequences_and_iterators.cpp:110:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(m_data, s.m_data, sizeof(float)*m_size);
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_sequences_and_iterators.cpp:125:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
                memcpy(m_data, s.m_data, sizeof(float)*m_size);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/document_retrieval/src/query_idx.cpp:13:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char   buffer[buf_size];
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/document_retrieval/src/word_pat2char_pat.cpp:12:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char   buffer[buf_size];
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:126:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    m = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:134:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    J = atoi(argv[3]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:146:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifile = fopen(argv[1], "r");
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:167:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofile = fopen(argv[4], "w");
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:66:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    m = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:73:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    J = atoi(argv[3]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:79:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifile = fopen(argv[1],"r");
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:100:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofile = fopen(argv[4],"w");
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/k2_trees/src/gen_k2t.cpp:63:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	fs.open(argv[3]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp:36:30:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    const uint64_t density = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/rrr_vector/src/rrr_time_and_space.cpp:63:22:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        uint16_t k = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/fm-index.cpp:26:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        max_locations = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/fm-index.cpp:29:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        post_context = atoi(argv[3]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/fm-index.cpp:32:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        pre_context = atoi(argv[4]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/fm-rmq-index.cpp:52:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        max_locations = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/fm-rmq-index.cpp:55:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        post_context = atoi(argv[3]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/examples/fm-rmq-index.cpp:58:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        pre_context = atoi(argv[4]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-internal-utils_test.cc:459:20:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int skip_count = atoi(log.substr(expected_message.size()).c_str());
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-more-actions_test.cc:631:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char ch[4] = {};
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2399:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  return fopen(path, mode);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample2.cc:44:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(clone, a_c_string, len + 1);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:325:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[256];
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:741:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char executable_path[_MAX_PATH + 1];  // NOLINT
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:1026:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  const int cwd_fd = open(".", O_RDONLY);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc:105:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc:108:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:139:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  const int fd = open("/proc/self/as", O_RDONLY);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:865:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(buffer, regex, len);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:938:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp_dir_path[MAX_PATH + 1] = { '\0' };  // NOLINT
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:939:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp_file_path[MAX_PATH + 1] = { '\0' };  // NOLINT
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:976:29:  [2] (tmpfile) mkstemp:
  Potential for temporary file vulnerability in some circumstances. Some
  older Unix-like systems create temp files with permission to write by all
  by default, so be sure to set the umask to override this. Also, some older
  Unix systems might fail to use O_EXCL when opening the file, so make sure
  that O_EXCL is used by the library (CWE-377).
    const int captured_fd = mkstemp(name_template);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:65:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char text[5] = "";
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:859:7:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
      MultiByteToWideChar(CP_ACP, 0, ansi, length,
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:862:3:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
  MultiByteToWideChar(CP_ACP, 0, ansi, length,
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1677:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char error_text[kBufSize] = { '\0' };
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1761:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char str[5];  // Big enough for the largest valid code point.
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc:371:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char current_drive[_MAX_PATH];  // NOLINT
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc:388:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char non_drive[_MAX_PATH];  // NOLINT
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:131:32:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  UnprintableInFoo() : z_(0) { memcpy(xy_, "\xEF\x12\x0\x0\x34\xAB\x0\x0", 8); }
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:134:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char xy_[8];
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:1135:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char array[257];
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:7591:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  const char a[3] = "hi";
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:7675:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  const char a[2][3] = { "hi", "lo" };
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget_test.cc:58:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[max_size];
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/libdivsufsort/examples/bwt.c:61:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char c[4];
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/libdivsufsort/examples/bwt.c:98:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    blocksize = atoi(argv[i + 1]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/libdivsufsort/examples/unbwt.c:61:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char c[4];
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector.hpp:1272:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        if (memcpy(m_data, v.data() ,v.capacity()/8)==nullptr) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector.hpp:1285:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            if (memcpy(m_data, v.data() ,v.capacity()/8)==nullptr) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:156:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, mode|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:158:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:188:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:189:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:215:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:216:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:298:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:300:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:380:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:382:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:384:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                ivb.m_ifile.open(ivb.m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:386:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                ivb.m_ofile.open(ivb.m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:345:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char tmp_file_name[1024] = {0};
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:365:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char tmp_dir_name[1024] = {0};
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/memory_management.hpp:397:52:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            if (!(mode&std::ios_base::out)) return open(filename.c_str(), O_RDONLY);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/memory_management.hpp:398:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            else return open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/ram_filebuf.hpp:24:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string s, std::ios_base::openmode mode);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/sfstream.hpp:32:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string& file, std::ios_base::openmode mode = std::ios_base::out);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/sfstream.hpp:62:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string& file, std::ios_base::openmode mode = std::ios_base::in);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/construct_lcp.cpp:124:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char alphabet[257] = {0};
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/construct_lcp.cpp:435:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char alphabet[257] = {0};
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/construct_lcp_helper.cpp:72:26:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_stream.open(m_file_name, std::ios::in | std::ios::out | std::ios::binary | std::ios::trunc);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/construct_lcp_helper.cpp:94:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(m_read_buf, m_write_buf, m_widx+1);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/memory_management.cpp:577:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(newptr,ptr,size);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/ram_filebuf.cpp:26:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
ram_filebuf::open(const std::string name, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:18:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(file, mode);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:22:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
osfstream::open(const std::string& file, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:30:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((ram_filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:33:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((std::filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:148:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(file, mode);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:152:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
isfstream::open(const std::string& file, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:160:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((ram_filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/sfstream.cpp:163:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((std::filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/util.cpp:45:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char file_name[_MAX_FNAME] = { 0 };
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/util.cpp:62:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char dir_name[_MAX_DIR] = { 0 };
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/util.cpp:63:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char drive[_MAX_DRIVE] = {0};
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/util.cpp:110:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[4096];
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/csa_int_test.cpp:237:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    num_bytes = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/cst_int_test.cpp:478:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    num_bytes = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/replace_int_vector_value.cpp:17:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    uint64_t x = atoi(argv[2]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/replace_int_vector_value.cpp:18:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    uint64_t y = atoi(argv[3]);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/csx-printf.cpp:10:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char line[BUF_SIZE];
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/tutorial/document_listing/doc_list_index.cpp:43:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char   buffer[64];
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/insert_rvalue.cc:25:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[10], buf2[10];
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/insert_rvalue.cc:29:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buf, "%d", i); 
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/insert_rvalue.cc:30:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buf2, "val%d", i);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/insert_rvalue.cc:37:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buf, "%d", i); 
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/insert_rvalue.cc:38:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buf2, "val%d", i);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/insert_rvalue.cc:45:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buf, "%d", i); 
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/insert_rvalue.cc:46:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buf2, "val%d", i);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/serialize_file.cc:117:17:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *out = fopen("ages.dmp", "wb");
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/serialize_file.cc:124:19:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *input = fopen("ages.dmp", "rb");
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/serialize_large.cc:76:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buff[20];
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/serialize_large.cc:77:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buff, "%zu", i);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/serialize_large.cc:83:17:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *out = fopen("ages.dmp", "wb");
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/serialize_large.cc:93:19:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *input = fopen("ages.dmp", "rb");
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp.h:1384:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(static_cast<void *>(_group + i), _group + i-1, sizeof(*_group));
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp.h:1488:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(static_cast<void *>(_group + i), _group + i + 1, sizeof(*_group));
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp.h:2086:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
                memcpy(static_cast<void *>(first), _first_group, sizeof(*first) * (std::min)(sz, old_sz));
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_dlalloc.h:543:31:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                dev_zero_fd = open("/dev/zero", O_RDWR);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_dlalloc.h:1643:22:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            unsigned char buf[sizeof(size_t)];
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_dlalloc.h:1645:23:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            if ((fd = open("/dev/urandom", O_RDONLY)) >= 0 &&
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_dlalloc.h:3812:21:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
                    memcpy(mem, oldmem, (oc < bytes) ? oc : bytes);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_memory.h:130:21:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                i = atoi(line);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_memory.h:134:21:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        auto file = fopen("/proc/self/status", "r");
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_memory.h:136:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char line[128];
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:88:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char tmppath_buffer[1024];
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:108:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(result, str, len + 1);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:1177:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buffer[64];
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:1193:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buffer[64];
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:1258:28:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        return (*this)(fp, atoi(value));
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:1522:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buff[20];
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:1525:13:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
            sprintf(buff, "%d", j);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:2396:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE* fp = fopen(file.c_str(), "wb");
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:2406:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fp = fopen(file.c_str(), "rb");
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:2440:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE* fp = fopen(file.c_str(), "wb");
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:2460:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fp = fopen(file.c_str(), "rb");
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:2505:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE* fp = fopen(file.c_str(), "wb");
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:2514:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fp = fopen(file.c_str(), "rb");
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:2544:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE* fp = fopen(file.c_str(), "wb");
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:2553:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fp = fopen(file.c_str(), "rb");
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:2582:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(reinterpret_cast<char*>(buf), s_->data(), len);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:2665:20:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        FILE* fp = fopen(file.c_str(), "wb");
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:2677:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char contents[24] = {0};
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:2678:14:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        fp = fopen(file.c_str(), "rb");
data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/internal/varint.hpp:50:8:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  std::memcpy(&x, p, 8);
data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/internal/varint.hpp:58:10:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    std::memcpy(&x, p, s);
data/vg-1.27.1+ds/deps/libbdsg/include/bdsg/internal/varint.hpp:68:8:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  std::memcpy(&x, p, 2);
data/vg-1.27.1+ds/deps/libbdsg/src/node.cpp:25:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(bytes.data()+seq_start(), seq.c_str(), seq.size());
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1797:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char n[s+1]; n[s] = '\0';
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1806:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char k[s+1]; k[s] = '\0';
data/vg-1.27.1+ds/deps/libbdsg/src/utility.cpp:11:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static const char complement[256] = {'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 8
data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp:81:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char magic_bytes[4];
data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/types.hpp:34:19:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct handle_t { char data[sizeof(nid_t)]; };
data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/types.hpp:40:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct path_handle_t { char data[sizeof(int64_t)]; };
data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/types.hpp:43:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct step_handle_t { char data[2 * sizeof(int64_t)]; };
data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp:81:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char magic_bytes[4];
data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/types.hpp:34:19:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct handle_t { char data[sizeof(nid_t)]; };
data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/types.hpp:40:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct path_handle_t { char data[sizeof(int64_t)]; };
data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/types.hpp:43:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct step_handle_t { char data[2 * sizeof(int64_t)]; };
data/vg-1.27.1+ds/deps/libvgio/include/vg/io/fdstream.hpp:113:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buffer[bufSize+pbSize];        // data buffer
data/vg-1.27.1+ds/deps/libvgio/src/edit.cpp:92:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static const char complement[256] = {'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 8
data/vg-1.27.1+ds/deps/libvgio/src/json2pb.cpp:238:56:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		_CONVERT_WITH_STRING(CPPTYPE_INT32, json_int_t, "I", atoi, SetInt32, AddInt32);
data/vg-1.27.1+ds/deps/libvgio/src/message_iterator.cpp:33:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buffer[to_sniff];
data/vg-1.27.1+ds/deps/libvgio/src/vpkg.cpp:42:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buffer[to_sniff];
data/vg-1.27.1+ds/deps/mmmultimap/src/mmiitree.hpp:75:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        buffer->fd = open(path, O_RDWR);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmiitree.hpp:195:16:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        writer.open(filename.c_str(), std::ios::binary | std::ios::trunc);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmiitree.hpp:213:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            writer.open(writer_filename(i), std::ios::binary | std::ios::app);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmiitree.hpp:230:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        reader_fd = open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmiitree.hpp:320:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        int fd = open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmiitree.hpp:352:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(&v, &reader[i*sizeof(Interval)], sizeof(Interval));
data/vg-1.27.1+ds/deps/mmmultimap/src/mmmultimap.hpp:52:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        buffer->fd = open(path, O_RDWR);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmmultimap.hpp:206:16:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        writer.open(filename.c_str(), std::ios::binary | std::ios::trunc);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmmultimap.hpp:224:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            writer.open(writer_filename(i), std::ios::binary | std::ios::app);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmmultimap.hpp:241:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        reader_fd = open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmmultimap.hpp:323:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        int fd = open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmmultimap.hpp:353:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(&e, &reader[i*record_size], sizeof(Entry));
data/vg-1.27.1+ds/deps/mmmultimap/src/mmmultiset.hpp:45:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        buffer->fd = open(path, O_RDWR);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmmultiset.hpp:140:16:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        writer.open(filename.c_str(), std::ios::binary | std::ios::trunc);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmmultiset.hpp:158:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            writer.open(writer_filename(i), std::ios::binary | std::ios::app);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmmultiset.hpp:175:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        reader_fd = open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmmultiset.hpp:276:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        int fd = open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmmultiset.hpp:308:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(&v, &reader[i*sizeof(Value)], sizeof(Value));
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/document_retrieval/src/query_idx.cpp:13:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char   buffer[buf_size];
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/document_retrieval/src/word_pat2char_pat.cpp:12:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char   buffer[buf_size];
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:126:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    m = atoi(argv[2]);
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:134:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    J = atoi(argv[3]);
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:146:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifile = fopen(argv[1], "r");
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:167:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofile = fopen(argv[4], "w");
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:66:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    m = atoi(argv[2]);
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:73:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    J = atoi(argv[3]);
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:79:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifile = fopen(argv[1],"r");
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:100:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofile = fopen(argv[4],"w");
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/k2_trees/src/gen_k2t.cpp:63:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	fs.open(argv[3]);
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp:36:30:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    const uint64_t density = atoi(argv[2]);
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/rrr_vector/src/rrr_time_and_space.cpp:63:22:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        uint16_t k = atoi(argv[2]);
data/vg-1.27.1+ds/deps/sdsl-lite/examples/fm-index.cpp:26:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        max_locations = atoi(argv[2]);
data/vg-1.27.1+ds/deps/sdsl-lite/examples/fm-index.cpp:29:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        post_context = atoi(argv[3]);
data/vg-1.27.1+ds/deps/sdsl-lite/examples/fm-index.cpp:32:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        pre_context = atoi(argv[4]);
data/vg-1.27.1+ds/deps/sdsl-lite/examples/fm-rmq-index.cpp:52:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        max_locations = atoi(argv[2]);
data/vg-1.27.1+ds/deps/sdsl-lite/examples/fm-rmq-index.cpp:55:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        post_context = atoi(argv[3]);
data/vg-1.27.1+ds/deps/sdsl-lite/examples/fm-rmq-index.cpp:58:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        pre_context = atoi(argv[4]);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector.hpp:1272:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        if (memcpy(m_data, v.data() ,v.capacity()/8)==nullptr) {
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector.hpp:1285:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            if (memcpy(m_data, v.data() ,v.capacity()/8)==nullptr) {
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:156:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, mode|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:158:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:188:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:189:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:215:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:216:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:298:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:300:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:380:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:382:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:384:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                ivb.m_ifile.open(ivb.m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:386:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                ivb.m_ofile.open(ivb.m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:345:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char tmp_file_name[1024] = {0};
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:365:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char tmp_dir_name[1024] = {0};
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/memory_management.hpp:397:52:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            if (!(mode&std::ios_base::out)) return open(filename.c_str(), O_RDONLY);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/memory_management.hpp:398:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            else return open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/ram_filebuf.hpp:24:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string s, std::ios_base::openmode mode);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/sfstream.hpp:32:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string& file, std::ios_base::openmode mode = std::ios_base::out);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/sfstream.hpp:62:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string& file, std::ios_base::openmode mode = std::ios_base::in);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_lcp.cpp:124:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char alphabet[257] = {0};
data/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_lcp.cpp:435:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char alphabet[257] = {0};
data/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:72:26:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_stream.open(m_file_name, std::ios::in | std::ios::out | std::ios::binary | std::ios::trunc);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:94:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(m_read_buf, m_write_buf, m_widx+1);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/memory_management.cpp:577:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(newptr,ptr,size);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/ram_filebuf.cpp:26:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
ram_filebuf::open(const std::string name, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:18:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(file, mode);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:22:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
osfstream::open(const std::string& file, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:30:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((ram_filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:33:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((std::filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:148:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(file, mode);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:152:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
isfstream::open(const std::string& file, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:160:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((ram_filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/sfstream.cpp:163:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((std::filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/util.cpp:45:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char file_name[_MAX_FNAME] = { 0 };
data/vg-1.27.1+ds/deps/sdsl-lite/lib/util.cpp:62:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char dir_name[_MAX_DIR] = { 0 };
data/vg-1.27.1+ds/deps/sdsl-lite/lib/util.cpp:63:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char drive[_MAX_DRIVE] = {0};
data/vg-1.27.1+ds/deps/sdsl-lite/lib/util.cpp:110:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[4096];
data/vg-1.27.1+ds/deps/sdsl-lite/test/csa_int_test.cpp:237:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    num_bytes = atoi(argv[2]);
data/vg-1.27.1+ds/deps/sdsl-lite/test/cst_int_test.cpp:478:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    num_bytes = atoi(argv[2]);
data/vg-1.27.1+ds/deps/sdsl-lite/test/replace_int_vector_value.cpp:17:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    uint64_t x = atoi(argv[2]);
data/vg-1.27.1+ds/deps/sdsl-lite/test/replace_int_vector_value.cpp:18:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    uint64_t y = atoi(argv[3]);
data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/csx-printf.cpp:10:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char line[BUF_SIZE];
data/vg-1.27.1+ds/deps/sdsl-lite/tutorial/document_listing/doc_list_index.cpp:43:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char   buffer[64];
data/vg-1.27.1+ds/deps/sha1/sha1.cpp:237:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char sbuf[BLOCK_BYTES];
data/vg-1.27.1+ds/deps/sonLib/C/impl/avl.c:191:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char da[AVL_MAX_HEIGHT]; /* Cached comparison results. */
data/vg-1.27.1+ds/deps/sonLib/C/impl/avl.c:313:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char da[AVL_MAX_HEIGHT]; /* |avl_link[]| indexes. */
data/vg-1.27.1+ds/deps/sonLib/C/impl/avl.c:610:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(trav->avl_stack, (const void *) src->avl_stack,
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:57:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fileHandle = fopen(tempFile, "w");
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:60:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fileHandle = fopen(tempFile, "r");
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:129:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char line[lineLength+1];
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:133:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(line, sequence+i, sizeof(char)*l);
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:160:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char cA[STRING_ARRAY_SIZE];
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:334:20:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    (*newString) = memcpy(st_malloc((string-i + 1)*sizeof(char)), i, (string-i)*sizeof(char));
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:504:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fileHandle = fopen(fastaFile, "r");
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:89:11:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    new = memcpy(st_malloc(((int64_t) base) * newSize), current,
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:351:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(i->list, list, j);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:870:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        int fd = open(pattern, O_CREAT|O_EXCL, 0600);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:947:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char cA[1000];
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:1012:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fileHandle = fopen(cA4, "w");
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:137:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static char cA[BIG_STRING_ARRAY_SIZE+1]; //STRING_ARRAY_SIZE];
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:140:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static char cA2[STRING_ARRAY_SIZE];
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:141:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static char cA3[STRING_ARRAY_SIZE];
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCache.c:64:35:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    record->record = copyMemory ? memcpy(st_malloc(size), value, size)
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCache.c:122:15:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    char *j = memcpy(st_malloc(i), record1->record, record1->size);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCache.c:123:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(j + record1->size, record2->record, record2->size);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCache.c:159:28:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            char *newMem = memcpy(st_malloc(newSize),
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCache.c:204:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(record->record + start - record->start, value, size);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCache.c:268:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(cA, record->record + j, i);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCommon.c:119:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static char cA[100000];
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase.c:267:27:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    buildRequest->value = memcpy(st_malloc(sizeOfRecord), value, sizeOfRecord);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabaseConf.c:117:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char *toReplace[5] = { "</", "<", "/>", ">", "=" };
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_BigRecordFile.c:71:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char filePathBuffer[MAXIMUM_PATH_LENGTH];
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_BigRecordFile.c:103:16:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	int64_t key = atol(keyString);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_BigRecordFile.c:183:20:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	FILE* recHandle = fopen(recordPath, "wb");
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_BigRecordFile.c:227:20:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	FILE* recHandle = fopen(recordPath, "rb");
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_BigRecordFile.c:266:20:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	FILE* recHandle = fopen(recordPath, "rb");
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_KyotoTycoon.cpp:65:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (!rdb->open(dbRemote_Host, dbRemote_Port, timeout)) {
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_KyotoTycoon.cpp:381:19:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		record = (char*)memcpy(st_malloc(*recordSize), newRecord, *recordSize);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_KyotoTycoon.cpp:400:27:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    char* record = (char*)memcpy(st_malloc( sizeof(int64_t)), newRecord,  sizeof(int64_t));
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_KyotoTycoon.cpp:433:25:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		void *partialRecord = memcpy(st_malloc(sizeInBytes), record + zeroBasedByteOffset, sizeInBytes);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_KyotoTycoon.cpp:486:6:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
					memcpy(record, curRecord.value.data(), recordSize);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_KyotoTycoon.cpp:540:6:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
					memcpy(record, mapIt->second.data(), recordSize);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_MySql.c:146:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char *warnings[maxToReport];
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_TokyoCabinet.c:240:27:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    void *partialRecord = memcpy(st_malloc(sizeInBytes), record + zeroBasedByteOffset, sizeInBytes);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibList.c:88:11:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    new = memcpy(st_malloc(((int64_t)base)*newSize), current, ((int64_t)base)*(*currentSize));
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:74:20:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        char *cA = memcpy(st_malloc(((*string)-i + 1)*sizeof(char)), i, ((*string)-i)*sizeof(char));
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:138:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(cA + j, cA2, k);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:141:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(cA + j, pad, padLength);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:181:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    char *cA2 = memcpy(st_malloc(sizeof(char) * (length + 1)), cA + start, length);
data/vg-1.27.1+ds/deps/sonLib/C/impl/stJson.c:18:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	return atoi(tokStr);
data/vg-1.27.1+ds/deps/sonLib/C/impl/stPhylogeny.c:43:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(ret, info, sizeof(stIndexedTreeInfo));
data/vg-1.27.1+ds/deps/sonLib/C/impl/stPhylogeny.c:45:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(ret->leavesBelow, info->leavesBelow, ret->totalNumLeaves * sizeof(char));
data/vg-1.27.1+ds/deps/sonLib/C/impl/stSafeC.c:21:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[256];
data/vg-1.27.1+ds/deps/sonLib/C/impl/stSafeC.c:60:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(mem2, mem, size);
data/vg-1.27.1+ds/deps/sonLib/C/tests/cigarsTest.c:35:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fileHandle = fopen(argv[1], "r");
data/vg-1.27.1+ds/deps/sonLib/C/tests/cigarsTest.c:43:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fileHandle = fopen(argv[1], "w");
data/vg-1.27.1+ds/deps/sonLib/C/tests/fastaCTest.c:29:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fileHandle = fopen(argv[1], "r");
data/vg-1.27.1+ds/deps/sonLib/C/tests/fastaCTest.c:33:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fileHandle = fopen(argv[2], "w");
data/vg-1.27.1+ds/deps/sonLib/C/tests/kt_connect_test.cpp:17:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if (!rdb->open("kolossus-10.kilokluster.ucsc.edu", 1978, -1)) {
data/vg-1.27.1+ds/deps/sonLib/C/tests/sonLibExceptTest.c:123:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    int fn = open(errFile, O_WRONLY|O_CREAT|O_TRUNC, 0666);
data/vg-1.27.1+ds/deps/sonLib/C/tests/sonLibFileTest.c:29:24:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *fileHandle = fopen(tempFileName1, "w");
data/vg-1.27.1+ds/deps/sonLib/C/tests/sonLibFileTest.c:39:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fileHandle = fopen(tempFileName2, "w");
data/vg-1.27.1+ds/deps/sonLib/C/tests/sonLibFileTest.c:45:24:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *fileHandle = fopen(tempFileName1, "r");
data/vg-1.27.1+ds/deps/sonLib/C/tests/sonLibListTest.c:18:8:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static char *strings[5] = { "one", "two", "three", "four", "five" };
data/vg-1.27.1+ds/deps/sonLib/C/tests/sonLibStringTest.c:17:11:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    const char *test[3] = { "hello this is a test", "", "BOO\nTOO\n" };
data/vg-1.27.1+ds/deps/sonLib/C/tests/sonLibStringTest.c:69:11:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    const char *cA[3] = { "Hello world wo", "wo", " foo " };
data/vg-1.27.1+ds/deps/sonLib/C/tests/sonLibTreeTest.c:127:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char *testNewickStrings[4] =  { "(((a,b,(c,))d),e)f;",  ";", "f;", "();" };
data/vg-1.27.1+ds/deps/sonLib/C/tests/stPhylogenyTest.c:1085:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char labelStr[2];
data/vg-1.27.1+ds/deps/sonLib/C/tests/stPhylogenyTest.c:1107:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char labelStr[2];
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:80:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char text[2];
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:89:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buf[HUGE_STRING_LEN];
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:105:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(str->buffer + pos, text, length);
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:150:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buf[HUGE_STRING_LEN];
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:208:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buf[STRING_MAX];
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:210:2:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
	sprintf(buf, "expected <%d> but was <%d>", expected, actual);
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:217:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buf[STRING_MAX];
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:219:2:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
	sprintf(buf, "expected <%f> but was <%f>", expected, actual); 
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:227:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char buf[STRING_MAX];
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:229:2:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
	sprintf(buf, "expected pointer <0x%p> but was <0x%p>", expected, actual);
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:211:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char expected_message[STRING_MAX];
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:216:2:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
	sprintf(expected_message, "expected pointer <0x%p> but was <0x%p>", nullPtr, &x);
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:639:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char expected[STRING_MAX];
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:640:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char expectedMsg[STRING_MAX];
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:641:2:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
	sprintf(expected, "expected <%lf> but was <%lf>", x, y);
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:642:2:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
	sprintf(expectedMsg, "some text: expected <%lf> but was <%lf>", x, y);
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/align.c:64:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char tempname[MAX_NAME_LENGTH];
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/aln2dist.c:105:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if ((input = fopen( fname, "r" )) == NULL)
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/aln2tree.c:130:63:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    else if (strcmp(optname, "-boot") == 0) calc_bootstraps = atoi( optarg );
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/aln2tree.c:143:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if ((input = fopen( fname, "r" )) == NULL)
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/dist2tree.c:72:23:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if ((matrixfile = fopen( argv[1], "r" )) == NULL)
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/distancemat.c:371:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char identifier[11];
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/distancemat_merops.c:381:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char identifier[11];
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/quicktree.c:160:63:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    else if (strcmp(optname, "-boot") == 0) calc_bootstraps = atoi( optarg );
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/quicktree.c:201:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if ((input = fopen( fname, "r" )) == NULL)
data/vg-1.27.1+ds/deps/sparsepp/examples/serialize_file.cc:68:17:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *out = fopen("ages.dmp", "wb");
data/vg-1.27.1+ds/deps/sparsepp/examples/serialize_file.cc:75:19:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *input = fopen("ages.dmp", "rb");
data/vg-1.27.1+ds/deps/sparsepp/examples/serialize_large.cc:76:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buff[20];
data/vg-1.27.1+ds/deps/sparsepp/examples/serialize_large.cc:77:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buff, "%zu", i);
data/vg-1.27.1+ds/deps/sparsepp/examples/serialize_large.cc:83:17:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *out = fopen("ages.dmp", "wb");
data/vg-1.27.1+ds/deps/sparsepp/examples/serialize_large.cc:93:19:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE *input = fopen("ages.dmp", "rb");
data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp.h:1384:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(_group + i, _group + i-1, sizeof(*_group));
data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp.h:1488:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(_group + i, _group + i + 1, sizeof(*_group));
data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp.h:2090:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
                memcpy(first, _first_group, sizeof(*first) * (std::min)(sz, old_sz));
data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_dlalloc.h:543:31:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                dev_zero_fd = open("/dev/zero", O_RDWR);
data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_dlalloc.h:1643:22:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            unsigned char buf[sizeof(size_t)];
data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_dlalloc.h:1645:23:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            if ((fd = open("/dev/urandom", O_RDONLY)) >= 0 &&
data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_dlalloc.h:3812:21:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
                    memcpy(mem, oldmem, (oc < bytes) ? oc : bytes);
data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_memory.h:130:21:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                i = atoi(line);
data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_memory.h:134:21:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        auto file = fopen("/proc/self/status", "r");
data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_memory.h:136:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char line[128];
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:89:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char tmppath_buffer[1024];
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:1169:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buffer[64];
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:1185:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buffer[64];
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:1250:28:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        return (*this)(fp, atoi(value));
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:1514:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buff[20];
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:1517:13:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
            sprintf(buff, "%d", j);
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:2388:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE* fp = fopen(file.c_str(), "wb");
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:2398:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fp = fopen(file.c_str(), "rb");
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:2432:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE* fp = fopen(file.c_str(), "wb");
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:2452:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fp = fopen(file.c_str(), "rb");
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:2497:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE* fp = fopen(file.c_str(), "wb");
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:2506:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fp = fopen(file.c_str(), "rb");
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:2536:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    FILE* fp = fopen(file.c_str(), "wb");
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:2545:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fp = fopen(file.c_str(), "rb");
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:2574:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(reinterpret_cast<char*>(buf), s_->data(), len);
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:2657:20:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        FILE* fp = fopen(file.c_str(), "wb");
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:2669:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char contents[24] = {0};
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:2670:14:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        fp = fopen(file.c_str(), "rb");
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/interface.cpp:420:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(to_return, &temp[0], sizeof(size_t)*N);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/serialize_index.cpp:17:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  slls_out.open(slls_path, ios::out | ios::trunc);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:1587:23:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    struct TrueType { char sizer[1]; };
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:1588:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    struct FalseType { char sizer[2]; };
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:3178:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char storage[sizeof(T)];
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:6136:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        void open() {
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:6230:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                open();
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:6276:26:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                tracker->open();
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:6465:16:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        static char altStackMem[SIGSTKSZ];
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:7059:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char **utf8Argv = new char *[ argc ];
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:7559:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char data[bufferSize];
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:7596:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        m_ofs.open( filename.c_str() );
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:8816:21:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
                    char asChar[sizeof (int)];
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:9454:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char buffer[maxDoubleSize];
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:9461:13:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
            sprintf(buffer, "%.3f", duration);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:9687:16:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        static char line[CATCH_CONFIG_CONSOLE_WIDTH] = {0};
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:10281:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char timeStamp[timeStampSize];
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/profiler.cpp:184:33:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
          size_t par_max_size = atol(argv[command_pos + 2]);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/profiler.cpp:185:35:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
          size_t par_size_steps = atol(argv[command_pos + 3]);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/profiler.cpp:202:35:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
          size_t par_min_length = atol(argv[command_pos + 2]);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/profiler.cpp:203:35:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
          size_t par_max_length = atol(argv[command_pos + 3]);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/profiler.cpp:204:37:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
          size_t par_length_steps = atol(argv[command_pos + 4]);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/profiler.cpp:213:24:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
          replicates = atol(argv[command_pos + 1]);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/profiler.cpp:320:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      expt_pars_out.open(experiment_path, ios::out | ios::trunc);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/profiler.cpp:330:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  expt_in.open(experiment_path, ios::in);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/profiler.cpp:358:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  slls_in.open(slls_path, ios::in);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/profiler.cpp:386:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  file_output.open(out_path, ios::out | ios::trunc);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/test.cpp:70:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    testout.open("testout.linref", ios::out | ios::trunc);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/test.cpp:74:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    testin.open("testout.linref", ios::in);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/test.cpp:159:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    testout.open("testout.cohort", ios::out | ios::trunc);
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/test.cpp:175:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    testin.open("testout.cohort", ios::in);
data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractfeatures.cpp:33:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char buf[rc];
data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractpixels.cpp:33:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char buf[rc];
data/vg-1.27.1+ds/deps/vowpal_wabbit/cluster/spanning_tree_main.cc:47:16:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      pid_file.open(argv[1]);
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h:293:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char prob_str[10] = { 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h:347:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char feature_str[strlen] = { 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h:1050:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char prob_str[10] = { 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h:1104:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char feature_str[strlen] = { 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h:1693:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
          ::memcpy(chosen_actions, actions, num_actions * sizeof(u32));
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h:1702:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      ::memcpy(actions, chosen_actions, num_actions * sizeof(u32));
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h:297:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char prob_str[10] = { 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h:357:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char feature_str[strlen] = { 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h:1131:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char prob_str[10] = { 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h:1191:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char feature_str[strlen] = { 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h:1864:23:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
                    ::memcpy(chosen_actions, actions, num_actions * sizeof(u32));
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h:1873:15:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            ::memcpy(actions, chosen_actions, num_actions * sizeof(u32));
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/utility.h:190:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char values[10];
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/utility.h:247:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buff[buf_size];
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/utility.h:254:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buff[buf_size];
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/test/unit/MWTExploreTests.cpp:609:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char expected_log[100] = { 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/test/unit/MWTExploreTestsMultiAction.cpp:643:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char expected_log[100] = { 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/utility.h:186:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char values[10];
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/utility.h:237:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buff[buf_size];
data/vg-1.27.1+ds/deps/vowpal_wabbit/library/ezexample_predict_threaded.cc:83:21:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int threadcount = atoi(argv[1]);
data/vg-1.27.1+ds/deps/vowpal_wabbit/library/ezexample_predict_threaded.cc:84:14:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  runcount = atoi(argv[2]);
data/vg-1.27.1+ds/deps/vowpal_wabbit/library/gd_mf_weights.cc:56:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  size_t rank = atoi(location);
data/vg-1.27.1+ds/deps/vowpal_wabbit/library/gd_mf_weights.cc:64:16:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  FILE* file = fopen(infile.c_str(), "r");
data/vg-1.27.1+ds/deps/vowpal_wabbit/library/recommend.cc:125:12:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if((fB = fopen(blacklistfilename.c_str(), "r")) == NULL)
data/vg-1.27.1+ds/deps/vowpal_wabbit/library/recommend.cc:130:12:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if((fU = fopen(userfilename.c_str(), "r")) == NULL )
data/vg-1.27.1+ds/deps/vowpal_wabbit/library/recommend.cc:135:12:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if((fI = fopen(itemfilename.c_str(), "r")) == NULL )
data/vg-1.27.1+ds/deps/vowpal_wabbit/python/pylibvw.cc:243:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char ns_str[2] = { (char)ns, 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/active.cc:91:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp[30];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/active.cc:92:5:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
    sprintf(temp, "%f", res);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/active.cc:98:7:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
      sprintf(temp, " %f", weight);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/active_interactor.cc:77:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[256];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/active_interactor.cc:92:10:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    port=atoi(argv[2]);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/allreduce.h:206:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char child_read_buf[2][ar_buf_size + sizeof(T) - 1];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/allreduce_sockets.cc:49:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char dotted_quad[INET_ADDRSTRLEN];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/allreduce_sockets.cc:53:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char hostname[NI_MAXHOST];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/allreduce_sockets.cc:54:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char servInfo[NI_MAXSERV];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/allreduce_sockets.cc:198:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char dotted_quad[INET_ADDRSTRLEN];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/array_parameters.h:138:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(default_value, input.default_value, stride());
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/array_parameters_dense.h:128:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(dest, _begin, float_count * sizeof(float));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bs.cc:135:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp[30];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bs.cc:136:5:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
    sprintf(temp, "%f", res);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bs.cc:141:5:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
    sprintf(temp, "%f", lb);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bs.cc:144:5:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
    sprintf(temp, "%f", ub);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cache.cc:183:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(c, &f.value(), sizeof(feature_value));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cache.cc:198:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(c, tag.begin(), tag.size());
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb_adf.cc:194:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char temp[1];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb_explore.cc:294:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char temp_str[20];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb_explore.cc:300:5:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
    sprintf(temp_str,"%f ", ec.pred.a_s[i].score);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb_explore.cc:309:3:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
  sprintf(temp_str, "%d:%f", maxid, maxprob);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/confidence.cc:33:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp[30];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/confidence.cc:34:5:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
    sprintf(temp, "%f %f", res, confidence);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/csoaa.cc:530:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char temp[1];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/example.cc:156:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(fec.tag,ec->tag.begin(), fec.tag_len);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/ezexample.h:20:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char str[2];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/global_data.cc:97:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp[30];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/global_data.cc:99:7:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
      sprintf(temp, "%f", res);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/global_data.cc:101:7:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
      sprintf(temp, "%.0f", res);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/global_data.cc:156:15:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      int n = atoi(ngram.c_str());
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/global_data.cc:166:15:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      int n = atoi(ngram.c_str()+1);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/global_data.cc:181:15:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      int n = atoi(limit.c_str());
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/global_data.cc:191:15:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      int n = atoi(limit.c_str()+1);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/global_data.h:107:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  { char v_str[128];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/global_data.h:150:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(temp, label_list.c_str(), strlen(label_list.c_str()));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/global_data.h:166:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(l_copy.begin, l.begin, len * sizeof(char));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/global_data.h:506:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char redefine[256]; // keeps new chars for amespaces
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/interactions.cc:222:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(oi.data, v.begin(), size);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/io_buf.h:95:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
          ret = open(name, O_RDONLY|O_LARGEFILE);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/io_buf.h:112:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        ret = open(name, O_CREAT|O_WRONLY|O_LARGEFILE|O_TRUNC,0666);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/io_buf.h:225:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(data,p,len);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/io_buf.h:249:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy (p, data, len);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc:605:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(queries + prev_sum, b->space.begin(), b->head - b->space.begin());
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:115:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(&mx, &x, sizeof(uint32_t));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:119:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(&mx_f, &mx, sizeof(float));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:122:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(&vx, &x, sizeof(uint32_t));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:141:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(&v, &approx, sizeof(uint32_t));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:199:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(&ret, &val, sizeof(uint32_t));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:656:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(v, new_gamma.begin(), sizeof(float) * l.topics);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:659:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(old_gamma.begin(), new_gamma.begin(), sizeof(float) * l.topics);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:687:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(ec->pred.scalars.begin(), new_gamma.begin(), l.topics * sizeof(float));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:352:8:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  fp = fopen("atxm_debug.csv", "wt");
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lrq.cc:94:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      unsigned int k = atoi (i.c_str () + 2);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lrq.cc:211:22:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    unsigned int k = atoi (i.c_str () + 2);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lrqfa.cc:149:12:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  lrq->k = atoi(lrqopt.substr(last_index+1).c_str());
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/multiclass.cc:45:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(c, &ld->label, sizeof(ld->label));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/multiclass.cc:47:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(c, &ld->weight, sizeof(ld->weight));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/multiclass.cc:112:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char temp_str[10];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/multiclass.cc:115:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char label_str[512];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/multiclass.cc:124:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char temp_str[10];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/multiclass.cc:127:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char label_str[512];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/multilabel.cc:113:20:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      uint32_t n = atoi(p->parse_name[i].begin);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/network.cc:43:12:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    port = atoi(colon+1);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/nn.cc:142:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy (&sd, n.all->sd, sizeof(shared_data));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/oaa.cc:171:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char temp_str[10];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/oaa.cc:183:5:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
    sprintf(temp_str, "%f", ec.pred.scalars[i]); // 0.123 -> 0.123000
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:97:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char buf[1024];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:230:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(word, c, d-c);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:1002:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      f = open(fstr, O_CREAT|O_WRONLY|O_LARGEFILE|O_TRUNC,0666);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:1027:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      f = open(t, O_CREAT|O_WRONLY|O_LARGEFILE|O_TRUNC,0666);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_example.cc:66:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char (*redefine)[256];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:174:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(__dest, __src, __n);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:191:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(buff2, version.to_string().c_str(), min(v_length, buf2_size));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:211:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(buff2, all.id.c_str(), min(v_length, default_buf_size));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:270:11:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
          char pair[3] = { 0, 0, 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:274:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(pair, all.pairs[i].c_str(), 2);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:302:11:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
          char triple[4] = { 0, 0, 0, 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:307:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(triple, all.triples[i].c_str(), 3);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:408:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char ngram[4] = { 0, 0, 0, 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:412:11:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
          memcpy(ngram, all.ngram_strings[i].c_str(), min(3, all.ngram_strings[i].size()));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:438:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char skip[4] = { 0, 0, 0, 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:442:11:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
          memcpy(skip, all.skip_strings[i].c_str(), min(3, all.skip_strings[i].size()));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parser.cc:476:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      port_file.open(all.opts_n_args.vm["port_file"].as<string>().c_str());
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parser.cc:495:16:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      pid_file.open(all.opts_n_args.vm["pid_file"].as<string>().c_str());
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parser.cc:515:7:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      memcpy(sd, all.sd, sizeof(shared_data));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:420:30:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
  if      (big > 9999999999) sprintf(c, "%dg", (int)(big / 1000000000));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:421:30:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
  else if (big >    9999999) sprintf(c, "%dm", (int)(big /    1000000));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:422:30:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
  else if (big >       9999) sprintf(c, "%dk", (int)(big /       1000));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:423:30:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
  else                       sprintf(c, "%d",  (int)(big));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:444:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char true_label[21];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:445:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char pred_label[21];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:466:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char inst_cntr[9];  number_to_natural((size_t)all.sd->example_number, inst_cntr);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:467:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char total_pred[8]; number_to_natural(priv.total_predictions_made, total_pred);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:468:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char total_cach[8]; number_to_natural(priv.total_cache_hits, total_cach);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:469:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char total_exge[8]; number_to_natural(priv.total_examples_generated, total_exge);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:1532:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(priv.learn_condition_on.begin(), condition_on, condition_on_cnt * sizeof(ptag));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:1554:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(priv.learn_allowed_actions.begin(), allowed_actions, allowed_actions_cnt*sizeof(action));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:1677:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(priv.learn_allowed_actions.begin(), allowed_actions, allowed_actions_cnt * sizeof(action));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:1737:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(B, A+lo, N*sizeof(size_t));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:2385:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  FILE *f = fopen(filename, "r");
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:2936:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(A.begin(), old_pointer, old_size * sizeof(T));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:2975:25:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
      if (a != nullptr) memcpy(A.begin() + old_size, a, count * sizeof(T));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_entityrelationtask.cc:122:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  id1 = atoi(s1.c_str());
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search_entityrelationtask.cc:130:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  id2 = atoi(s2.c_str());
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/simple_label.cc:46:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(c, &ld->label, sizeof(ld->label));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/simple_label.cc:48:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(c, &ld->weight, sizeof(ld->weight));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/simple_label.cc:50:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(c, &ld->initial, sizeof(ld->initial));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/spanning_tree.cc:161:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char dotted_quad[INET_ADDRSTRLEN];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/spanning_tree.cc:165:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char hostname[NI_MAXHOST];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/spanning_tree.cc:166:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char servInfo[NI_MAXSERV];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/topk.cc:32:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp[30];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/topk.cc:39:7:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
      sprintf(temp, "%f", tmp_example.first);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/v_array.h:193:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(v._end, _begin, num * sizeof(T));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/vw_exception.cc:55:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[4 * 1024];
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/vw_exception.h:79:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char __errmsg[256]; \
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/vw_exception.h:91:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char __errmsg[256]; \
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:61:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			 memcpy(_buffer,cr._buffer,_buffsize*sizeof(basetype) );
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:142:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
			_is = fopen(filename, "rb");
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:586:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			 memcpy(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) );
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:600:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				memcpy(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) );
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:1376:4:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
			char fname_old[1000];
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:1377:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(fname_old,"temp_p%i_level_%i",_pid,i-2);
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:1379:4:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
			char fname_curr[1000];
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:1380:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(fname_curr,"temp_p%i_level_%i",_pid,i);
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:1382:4:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
			char fname_prev[1000];
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:1383:4:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
			sprintf(fname_prev,"temp_p%i_level_%i",_pid,i-1);
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:1396:23:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
					_currlevelFile = fopen(fname_curr,"w");
data/vg-1.27.1+ds/deps/xg/deps/BBHash/bootest.cpp:75:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		 memcpy(_buffer,cr._buffer,_buffsize*sizeof(u_int64_t) );
data/vg-1.27.1+ds/deps/xg/deps/BBHash/bootest.cpp:148:9:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		_is = fopen(filename, "rb");
data/vg-1.27.1+ds/deps/xg/deps/BBHash/bootest.cpp:481:14:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		nthreads = atoi(argv[2]);
data/vg-1.27.1+ds/deps/xg/deps/BBHash/bootest.cpp:482:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		gammaFactor = atoi(argv[3]);
data/vg-1.27.1+ds/deps/xg/deps/BBHash/bootest.cpp:526:14:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		key_file = fopen("keyfile","w+");
data/vg-1.27.1+ds/deps/xg/deps/BBHash/bootest.cpp:572:18:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
				bench_file = fopen("benchfile","w+");
data/vg-1.27.1+ds/deps/xg/deps/BBHash/bootest.cpp:604:14:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
			vFiles[i]=fopen(("bucket"+to_string(i)).c_str(),"w+");
data/vg-1.27.1+ds/deps/xg/deps/BBHash/example.cpp:30:14:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		nthreads = atoi(argv[2]);
data/vg-1.27.1+ds/deps/xg/deps/BBHash/example_custom_hash.cpp:57:14:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
		nthreads = atoi(argv[2]);
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:956:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char timeStamp[timeStampSize];
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:3187:29:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        alignas(alignof(T)) char storage[sizeof(T)];
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:3644:16:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        static char line[CATCH_CONFIG_CONSOLE_WIDTH] = {0};
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:3917:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        void open();
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:8281:31:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char **utf8Argv = new char *[ argc ];
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:8388:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char data[bufferSize];
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:8427:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        m_ofs.open( filename.c_str() );
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:8644:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy( m_data, m_start, m_size );
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:9156:23:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    void TrackerBase::open() {
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:9245:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            open();
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:9284:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            tracker->open();
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:9557:21:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
                    char asChar[sizeof (int)];
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:10175:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buffer[maxDoubleSize];
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:10182:9:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        sprintf(buffer, "%.3f", duration);
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:10547:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            void open() {
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:10576:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                tp.open();
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:11155:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char timeStamp[timeStampSize];
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfa_builder.hpp:183:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifi.open(vcf_file);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfa_builder.hpp:345:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(dummy_name, contig_name.c_str(), contig_name.size() + 1);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfakluge.hpp:87:24:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                return atol(lhs.c_str()) < atol(rhs.c_str());
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfakluge.hpp:87:44:  [2] (integer) atol:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                return atol(lhs.c_str()) < atol(rhs.c_str());
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfakluge.hpp:567:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            fd = open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfakluge.hpp:728:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                gfi.open(filename, std::ifstream::in);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfakluge.hpp:1023:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                gfi.open(filename, std::ifstream::in);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfakluge.hpp:1081:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                gfi.open(filename, std::ifstream::in);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfakluge.hpp:2266:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                gfi.open(filename.c_str(), std::ifstream::in);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfakluge.hpp:2563:36:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                            rank = atoi(tokens[3].c_str());
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfakluge.hpp:2620:40:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                                rank = atoi(tokens[3].c_str());
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfakluge.hpp:2640:38:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                        a.position = atoi(tokens[2].c_str());
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/gfakluge.hpp:2643:36:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                        a.length = atoi(tokens[5].c_str());
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/main.cpp:197:26:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                minlen = atoi(optarg);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/main.cpp:354:33:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                max_node_size = atoi(optarg);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/examples/getseq.cpp:36:21:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        int start = atoi(argv[3]);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/examples/getseq.cpp:37:19:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        int end = atoi(argv[4]);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/pliib.hpp:35:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static char complement_array [26] = {
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/pliib.hpp:225:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(ret, s, d_index * sizeof(char));
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/pliib.hpp:247:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(ret, s + start, rsz * sizeof(char));
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/pliib.hpp:257:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(t, s.c_str(), slen);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/pliib.hpp:353:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(contig, bend + first_bracket_index + 1, colon_index - first_bracket_index - 1);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/pliib.hpp:357:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(pstr, bend + colon_index + 1, last_bracket_index - colon_index - 1);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/pliib.hpp:358:20:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        position = atoi(pstr);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:72:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(this->name, splits[0].c_str(), splits[0].length() * sizeof(char));
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:140:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        ofi.open(filename);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:159:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    faFile.open(fastaName);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:161:23:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (!(fai.fasta = fopen(fastaName, "r"))){
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:248:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifi.open((const char*) ifn);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:250:23:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    if (!(fai.fasta = fopen(fastaFileName, "r"))){
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:326:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(ret, seq + start, (end - start) * sizeof(char) );
data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp:81:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char magic_bytes[4];
data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/types.hpp:34:19:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct handle_t { char data[sizeof(nid_t)]; };
data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/types.hpp:40:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct path_handle_t { char data[sizeof(int64_t)]; };
data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/types.hpp:43:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
struct step_handle_t { char data[2 * sizeof(int64_t)]; };
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmiitree.hpp:84:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        buffer->fd = open(path, O_RDWR);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmiitree.hpp:204:16:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        writer.open(filename.c_str(), std::ios::binary | std::ios::trunc);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmiitree.hpp:222:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            writer.open(writer_filename(i), std::ios::binary | std::ios::app);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmiitree.hpp:239:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        reader_fd = open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmiitree.hpp:351:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        int fd = open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmiitree.hpp:388:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(&v, &reader[i*sizeof(Interval)], sizeof(Interval));
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmmultimap.hpp:52:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        buffer->fd = open(path, O_RDWR);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmmultimap.hpp:206:16:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        writer.open(filename.c_str(), std::ios::binary | std::ios::trunc);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmmultimap.hpp:224:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            writer.open(writer_filename(i), std::ios::binary | std::ios::app);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmmultimap.hpp:241:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        reader_fd = open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmmultimap.hpp:345:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        int fd = open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmmultimap.hpp:380:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(&e, &reader[i*record_size], sizeof(Entry));
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmmultiset.hpp:45:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        buffer->fd = open(path, O_RDWR);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmmultiset.hpp:140:16:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        writer.open(filename.c_str(), std::ios::binary | std::ios::trunc);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmmultiset.hpp:158:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            writer.open(writer_filename(i), std::ios::binary | std::ios::app);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmmultiset.hpp:175:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        reader_fd = open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmmultiset.hpp:298:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        int fd = open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmmultiset.hpp:335:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(&v, &reader[i*sizeof(Value)], sizeof(Value));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/document_retrieval/src/query_idx.cpp:13:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char   buffer[buf_size];
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/document_retrieval/src/word_pat2char_pat.cpp:12:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char   buffer[buf_size];
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:126:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    m = atoi(argv[2]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:134:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    J = atoi(argv[3]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:146:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifile = fopen(argv[1], "r");
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:167:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofile = fopen(argv[4], "w");
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:66:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    m = atoi(argv[2]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:73:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    J = atoi(argv[3]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:79:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ifile = fopen(argv[1],"r");
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_extract/src/genintervals.c:100:13:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ofile = fopen(argv[4],"w");
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/k2_trees/src/gen_k2t.cpp:63:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	fs.open(argv[3]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/rrr_vector/src/generate_rnd_bitvector.cpp:36:30:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    const uint64_t density = atoi(argv[2]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/rrr_vector/src/rrr_time_and_space.cpp:63:22:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        uint16_t k = atoi(argv[2]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/fm-index.cpp:26:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        max_locations = atoi(argv[2]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/fm-index.cpp:29:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        post_context = atoi(argv[3]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/fm-index.cpp:32:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        pre_context = atoi(argv[4]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/fm-rmq-index.cpp:52:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        max_locations = atoi(argv[2]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/fm-rmq-index.cpp:55:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        post_context = atoi(argv[3]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/examples/fm-rmq-index.cpp:58:23:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        pre_context = atoi(argv[4]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-internal-utils_test.cc:459:20:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
  int skip_count = atoi(log.substr(expected_message.size()).c_str());
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-more-actions_test.cc:631:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char ch[4] = {};
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2399:10:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  return fopen(path, mode);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample2.cc:44:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(clone, a_c_string, len + 1);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:325:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[256];
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:741:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char executable_path[_MAX_PATH + 1];  // NOLINT
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-death-test.cc:1026:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  const int cwd_fd = open(".", O_RDONLY);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc:105:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-filepath.cc:108:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:139:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  const int fd = open("/proc/self/as", O_RDONLY);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:865:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  memcpy(buffer, regex, len);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:938:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp_dir_path[MAX_PATH + 1] = { '\0' };  // NOLINT
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:939:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char temp_file_path[MAX_PATH + 1] = { '\0' };  // NOLINT
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:976:29:  [2] (tmpfile) mkstemp:
  Potential for temporary file vulnerability in some circumstances. Some
  older Unix-like systems create temp files with permission to write by all
  by default, so be sure to set the umask to override this. Also, some older
  Unix systems might fail to use O_EXCL when opening the file, so make sure
  that O_EXCL is used by the library (CWE-377).
    const int captured_fd = mkstemp(name_template);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:65:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char text[5] = "";
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:859:7:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
      MultiByteToWideChar(CP_ACP, 0, ansi, length,
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:862:3:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
  MultiByteToWideChar(CP_ACP, 0, ansi, length,
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1677:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char error_text[kBufSize] = { '\0' };
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1761:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char str[5];  // Big enough for the largest valid code point.
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc:371:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char current_drive[_MAX_PATH];  // NOLINT
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-filepath_test.cc:388:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char non_drive[_MAX_PATH];  // NOLINT
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:131:32:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  UnprintableInFoo() : z_(0) { memcpy(xy_, "\xEF\x12\x0\x0\x34\xAB\x0\x0", 8); }
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:134:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char xy_[8];
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:1135:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char array[257];
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:7591:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  const char a[3] = "hi";
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest_unittest.cc:7675:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  const char a[2][3] = { "hi", "lo" };
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget_test.cc:58:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[max_size];
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/libdivsufsort/examples/bwt.c:61:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char c[4];
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/libdivsufsort/examples/bwt.c:98:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    blocksize = atoi(argv[i + 1]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/libdivsufsort/examples/unbwt.c:61:12:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  unsigned char c[4];
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector.hpp:1272:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        if (memcpy(m_data, v.data() ,v.capacity()/8)==nullptr) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector.hpp:1285:17:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            if (memcpy(m_data, v.data() ,v.capacity()/8)==nullptr) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:156:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, mode|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:158:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:188:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:189:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:215:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:216:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:298:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ofile.open(m_filename, std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:300:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:380:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_ifile.open(m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:382:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_ofile.open(m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:384:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                ivb.m_ifile.open(ivb.m_filename, std::ios::in|std::ios::binary);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:386:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                ivb.m_ofile.open(ivb.m_filename, std::ios::in|std::ios::out|std::ios::binary);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:345:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char tmp_file_name[1024] = {0};
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:365:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char tmp_dir_name[1024] = {0};
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/memory_management.hpp:397:52:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            if (!(mode&std::ios_base::out)) return open(filename.c_str(), O_RDONLY);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/memory_management.hpp:398:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            else return open(filename.c_str(), O_RDWR);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/ram_filebuf.hpp:24:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string s, std::ios_base::openmode mode);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/sfstream.hpp:32:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string& file, std::ios_base::openmode mode = std::ios_base::out);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/sfstream.hpp:62:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(const std::string& file, std::ios_base::openmode mode = std::ios_base::in);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/construct_lcp.cpp:124:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char alphabet[257] = {0};
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/construct_lcp.cpp:435:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    unsigned char alphabet[257] = {0};
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/construct_lcp_helper.cpp:72:26:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                m_stream.open(m_file_name, std::ios::in | std::ios::out | std::ios::binary | std::ios::trunc);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/construct_lcp_helper.cpp:94:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(m_read_buf, m_write_buf, m_widx+1);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/memory_management.cpp:577:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(newptr,ptr,size);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/ram_filebuf.cpp:26:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
ram_filebuf::open(const std::string name, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:18:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(file, mode);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:22:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
osfstream::open(const std::string& file, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:30:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((ram_filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:33:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((std::filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:148:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(file, mode);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:152:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
isfstream::open(const std::string& file, std::ios_base::openmode mode)
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:160:48:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((ram_filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/sfstream.cpp:163:49:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        success = ((std::filebuf*)m_streambuf)->open(m_file, mode);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/util.cpp:45:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char file_name[_MAX_FNAME] = { 0 };
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/util.cpp:62:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char dir_name[_MAX_DIR] = { 0 };
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/util.cpp:63:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char drive[_MAX_DRIVE] = {0};
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/util.cpp:110:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[4096];
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/csa_int_test.cpp:237:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    num_bytes = atoi(argv[2]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/cst_int_test.cpp:478:17:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    num_bytes = atoi(argv[2]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/replace_int_vector_value.cpp:17:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    uint64_t x = atoi(argv[2]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/replace_int_vector_value.cpp:18:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
    uint64_t y = atoi(argv[3]);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/csx-printf.cpp:10:1:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
char line[BUF_SIZE];
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/tutorial/document_listing/doc_list_index.cpp:43:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char   buffer[64];
data/vg-1.27.1+ds/deps/xg/src/xg.cpp:2547:14:  [2] (tmpfile) mkstemp:
  Potential for temporary file vulnerability in some circumstances. Some
  older Unix-like systems create temp files with permission to write by all
  by default, so be sure to set the umask to override this. Also, some older
  Unix systems might fail to use O_EXCL when opening the file, so make sure
  that O_EXCL is used by the library (CWE-377).
    int fd = mkstemp(&tmpname[0]);
data/vg-1.27.1+ds/deps/xg/src/xg.hpp:107:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static const char complement[256] = {'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 8
data/vg-1.27.1+ds/src/alignment.cpp:538:18:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static const char nt_encoding[256] = {
data/vg-1.27.1+ds/src/alignment.cpp:1842:16:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        sbuf = atoi(buf.c_str()) - 1;
data/vg-1.27.1+ds/src/alignment.cpp:1845:16:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        ebuf = atoi(buf.c_str());
data/vg-1.27.1+ds/src/build_index.cpp:30:36:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
    gcsa::InputGraph input_graph({ tmpfile }, true);
data/vg-1.27.1+ds/src/build_index.cpp:36:23:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
    temp_file::remove(tmpfile);
data/vg-1.27.1+ds/src/constructor.cpp:2207:24:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            reference->open(fasta_filename);
data/vg-1.27.1+ds/src/constructor.cpp:2227:27:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            variant_file->open(mutable_filename);
data/vg-1.27.1+ds/src/constructor.cpp:2239:24:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            insertion->open(insertion_filename);
data/vg-1.27.1+ds/src/crash.cpp:148:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        tempStream.open(dirName+ "/stacktrace.txt");
data/vg-1.27.1+ds/src/gapless_extender.cpp:190:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        std::memcpy(&a, seq.data() + match.read_interval.second, len);
data/vg-1.27.1+ds/src/gapless_extender.cpp:191:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        std::memcpy(&b, target.first + node_offset, len);
data/vg-1.27.1+ds/src/gapless_extender.cpp:218:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        std::memcpy(&a, seq.data() + match.read_interval.second, len);
data/vg-1.27.1+ds/src/gapless_extender.cpp:219:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        std::memcpy(&b, target.first + node_offset, len);
data/vg-1.27.1+ds/src/gapless_extender.cpp:248:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        std::memcpy(&a, seq.data() + match.read_interval.first - len, len);
data/vg-1.27.1+ds/src/gapless_extender.cpp:249:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        std::memcpy(&b, target.first + match.offset - len, len);
data/vg-1.27.1+ds/src/haplotype_indexer.cpp:292:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    variant_file.open(vcf_filename);
data/vg-1.27.1+ds/src/hts_alignment_emitter.cpp:70:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char out_mode[5];
data/vg-1.27.1+ds/src/hts_alignment_emitter.cpp:84:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char tmp[2];
data/vg-1.27.1+ds/src/index.cpp:97:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
void Index::open(const std::string& dir, bool read_only) {
data/vg-1.27.1+ds/src/index.cpp:150:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(dir, true);
data/vg-1.27.1+ds/src/index.cpp:155:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(dir, false);
data/vg-1.27.1+ds/src/index.cpp:160:5:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    open(dir, false);
data/vg-1.27.1+ds/src/index.cpp:223:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3, &id, sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:239:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3, &node, sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:243:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*6 + sizeof(nid_t), &other, sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:259:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3, &node, sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:263:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*6 + sizeof(nid_t), &other, sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:277:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3, kmer.c_str(), kmer.size());
data/vg-1.27.1+ds/src/index.cpp:279:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*4 + kmer.size(), &id, sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:293:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3, &node_id, sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:297:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*6 + sizeof(nid_t), &path_id, sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:299:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*7 + sizeof(nid_t) + sizeof(int64_t), &path_pos, sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:314:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3, &node_id, sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:318:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*6 + sizeof(nid_t), &path_id, sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:332:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3, &path_id, sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:334:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*4 + sizeof(int64_t), &path_pos, sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:338:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*7 + 2*sizeof(int64_t), &node_id, sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:349:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3, kmer.c_str(), kmer.size());
data/vg-1.27.1+ds/src/index.cpp:360:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3, tag.c_str(), tag.size());
data/vg-1.27.1+ds/src/index.cpp:372:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3, &node_id, sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:399:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3, &node_id, sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:439:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3, &aln_id, sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:451:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3, &node_id, sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:464:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3, &node_id, sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:466:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3+sizeof(nid_t), &aln_id, sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:468:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(k + sizeof(char)*3+sizeof(nid_t) + sizeof(int64_t), &rank, sizeof(int16_t));
data/vg-1.27.1+ds/src/index.cpp:522:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&id, (k + 3*sizeof(char)), sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:535:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&node_id, (k + 3*sizeof(char)), sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:536:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&other_id, (k + 6*sizeof(char)) + sizeof(nid_t), sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:542:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&backward_char, (k + 7*sizeof(char)) + 2*sizeof(nid_t), sizeof(char));
data/vg-1.27.1+ds/src/index.cpp:638:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&id, k+4*sizeof(char)+kmer.size(), sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:640:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&pos, (char*)value.c_str(), sizeof(int32_t));
data/vg-1.27.1+ds/src/index.cpp:656:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&node_id, (k + 3*sizeof(char)), sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:657:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&path_id, (k + 6*sizeof(char) + sizeof(nid_t)), sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:658:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&path_pos, (k + 7*sizeof(char) + sizeof(nid_t) + sizeof(int64_t)), sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:669:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&path_id, (k + 3*sizeof(char)), sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:670:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&path_pos, (k + 4*sizeof(char)+sizeof(int64_t)), sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:672:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&node_id, (k + 7*sizeof(char)+2*sizeof(int64_t)), sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:681:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&node_id, (k + 3*sizeof(char)), sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:692:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&node_id, (k + 3*sizeof(char)), sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:703:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&aln_id, (k + 3*sizeof(char)), sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:710:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&node_id, (k + 3*sizeof(char)), sizeof(nid_t));
data/vg-1.27.1+ds/src/index.cpp:712:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&aln_id, (k + 3*sizeof(char)+sizeof(nid_t)), sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:714:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy(&rank, (k + 3*sizeof(char) + sizeof(nid_t) + sizeof(int64_t)), sizeof(int16_t));
data/vg-1.27.1+ds/src/index.cpp:751:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(&id, (char*)value.c_str(), sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:757:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(&id, ((char*)prefix.c_str())+7, sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:979:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(&id, data.c_str(), sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:988:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy((char*)data.c_str(), &id, sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:1010:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy((char*)prefix.c_str() + prefix_size, &id, sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:1022:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy((char*)data.c_str(), &id, sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:1042:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(&id, (char*)data.c_str(), sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:1516:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy(&id, (void*)(key.c_str() + 10*sizeof(char)), sizeof(int64_t));
data/vg-1.27.1+ds/src/index.cpp:2035:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy((char*)data.c_str(), &pos, sizeof(int32_t));
data/vg-1.27.1+ds/src/index.cpp:2046:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
    memcpy((char*) data.c_str(), &pos, sizeof(int32_t));
data/vg-1.27.1+ds/src/index.cpp:2110:22:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        sizes.insert(atoi(key.substr(5).c_str()));
data/vg-1.27.1+ds/src/index.hpp:94:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    void open(const std::string& dir, bool read_only = false);
data/vg-1.27.1+ds/src/index_manager.cpp:170:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            out.open(temp_filename);
data/vg-1.27.1+ds/src/io/json_stream_helper.hpp:45:15:  [2] (misc) fopen:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        _fp = fopen(file_name.c_str(), "r");
data/vg-1.27.1+ds/src/kmer.cpp:280:18:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
    ofstream out(tmpfile);
data/vg-1.27.1+ds/src/kmer.cpp:284:12:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
    return tmpfile;
data/vg-1.27.1+ds/src/packer.cpp:431:29:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            tmpfstreams[i]->open(edit_tmpfile_names[i], std::ios_base::binary);
data/vg-1.27.1+ds/src/region.cpp:19:21:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
            start = atoi(target.substr(foundFirstColon + 1).c_str());
data/vg-1.27.1+ds/src/region.cpp:22:21:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
            start = atoi(target.substr(foundFirstColon + 1, foundRangeDash - foundRangeDash - 1).c_str());
data/vg-1.27.1+ds/src/region.cpp:23:19:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
            end = atoi(target.substr(foundRangeDash + 1).c_str());
data/vg-1.27.1+ds/src/sampler.cpp:856:19:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    position_file.open(filename);
data/vg-1.27.1+ds/src/srpe.cpp:32:19:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        gamstream.open(gamfile);
data/vg-1.27.1+ds/src/stream_sorter.hpp:372:24:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        streams.back().open(filename);
data/vg-1.27.1+ds/src/subcommand/add_main.cpp:160:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        vcf.open(vcf_filename);
data/vg-1.27.1+ds/src/subcommand/align_main.cpp:191:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      matrix_stream.open(matrix_file_name);
data/vg-1.27.1+ds/src/subcommand/annotate_main.cpp:207:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        snarl_stream.open(snarls_name);
data/vg-1.27.1+ds/src/subcommand/call_main.cpp:435:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        variant_file.open(vcf_filename);
data/vg-1.27.1+ds/src/subcommand/call_main.cpp:444:24:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            ref_fasta->open(ref_fasta_filename);
data/vg-1.27.1+ds/src/subcommand/call_main.cpp:448:24:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            ins_fasta->open(ins_fasta_filename);
data/vg-1.27.1+ds/src/subcommand/chunk_main.cpp:543:24:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            gam_stream.open(gam_file);
data/vg-1.27.1+ds/src/subcommand/chunk_main.cpp:678:26:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                out_file.open(name);
data/vg-1.27.1+ds/src/subcommand/chunk_main.cpp:869:26:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                out_file.open(out_name.str());
data/vg-1.27.1+ds/src/subcommand/circularize_main.cpp:109:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        pfi.open(pathfile);
data/vg-1.27.1+ds/src/subcommand/find_main.cpp:323:26:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
            subgraph_k = atoi(optarg);
data/vg-1.27.1+ds/src/subcommand/find_main.cpp:363:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        nli.open(node_list_file);
data/vg-1.27.1+ds/src/subcommand/find_main.cpp:818:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                in.open(gam_file.c_str());
data/vg-1.27.1+ds/src/subcommand/genotype_main.cpp:272:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        vars->open(recall_vcf);
data/vg-1.27.1+ds/src/subcommand/genotype_main.cpp:274:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        lin_ref->open(fasta);
data/vg-1.27.1+ds/src/subcommand/genotype_main.cpp:280:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            ins->open(insertions_file);
data/vg-1.27.1+ds/src/subcommand/giraffe_main.cpp:1008:16:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        report.open(report_name);
data/vg-1.27.1+ds/src/subcommand/index_main.cpp:573:30:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                variant_file.open(vcf_name);
data/vg-1.27.1+ds/src/subcommand/locify_main.cpp:282:62:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
                if (locus_to_keep[aln.locus(i).name()].count(atoi(allele.name().c_str()))) {
data/vg-1.27.1+ds/src/subcommand/map_main.cpp:572:30:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
            max_gap_length = atoi(optarg);     // fall through
data/vg-1.27.1+ds/src/subcommand/map_main.cpp:709:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      matrix_stream.open(matrix_file_name);
data/vg-1.27.1+ds/src/subcommand/map_main.cpp:939:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        ref.open(fasta_file);
data/vg-1.27.1+ds/src/subcommand/mcmc_main.cpp:170:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        vcf_file_out.open(vcf_out, ios::out);
data/vg-1.27.1+ds/src/subcommand/mod_main.cpp:386:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        variant_file.open(vcf_filename);
data/vg-1.27.1+ds/src/subcommand/mpmap_main.cpp:1353:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      matrix_stream.open(matrix_file_name);
data/vg-1.27.1+ds/src/subcommand/mpmap_main.cpp:1362:31:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        distance_index_stream.open(distance_index_name);
data/vg-1.27.1+ds/src/subcommand/mpmap_main.cpp:1372:26:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            snarl_stream.open(snarls_name);
data/vg-1.27.1+ds/src/subcommand/mpmap_main.cpp:1386:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        gbwt_stream.open(gbwt_name);
data/vg-1.27.1+ds/src/subcommand/mpmap_main.cpp:1394:19:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        ls_stream.open(sublinearLS_name);
data/vg-1.27.1+ds/src/subcommand/mpmap_main.cpp:1733:33:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    multipath_mapper._mem_stats.open(MEM_STATS_FILE);
data/vg-1.27.1+ds/src/subcommand/msga_main.cpp:383:30:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
            max_gap_length = atoi(optarg);     // fall through
data/vg-1.27.1+ds/src/subcommand/msga_main.cpp:454:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        ref.open(fasta_file_name);
data/vg-1.27.1+ds/src/subcommand/pack_main.cpp:187:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        nli.open(node_list_file);
data/vg-1.27.1+ds/src/subcommand/rna_main.cpp:377:23:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        fasta_ostream.open(fasta_out_filename);
data/vg-1.27.1+ds/src/subcommand/rna_main.cpp:391:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        info_ostream.open(info_out_filename);
data/vg-1.27.1+ds/src/subcommand/sift_main.cpp:294:26:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        reversing_stream.open(reversing_fn);
data/vg-1.27.1+ds/src/subcommand/sift_main.cpp:298:25:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        unmapped_stream.open(unmapped_fn);
data/vg-1.27.1+ds/src/subcommand/sift_main.cpp:302:27:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        discordant_stream.open(discordant_fn);
data/vg-1.27.1+ds/src/subcommand/sift_main.cpp:306:20:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        oea_stream.open(oea_fn);
data/vg-1.27.1+ds/src/subcommand/sift_main.cpp:310:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        split_stream.open(split_fn);
data/vg-1.27.1+ds/src/subcommand/sift_main.cpp:313:23:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        insert_stream.open(insert_fn);
data/vg-1.27.1+ds/src/subcommand/sift_main.cpp:316:24:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        clipped_stream.open(clipped_fn);
data/vg-1.27.1+ds/src/subcommand/sift_main.cpp:548:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    in.open(alignment_file);
data/vg-1.27.1+ds/src/subcommand/simplify_main.cpp:199:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        variant_file.open(vcf_filename);
data/vg-1.27.1+ds/src/subcommand/snarls_main.cpp:177:21:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        trav_stream.open(traversal_file);
data/vg-1.27.1+ds/src/subcommand/snarls_main.cpp:222:22:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        variant_file.open(vcf_filename);
data/vg-1.27.1+ds/src/subcommand/snarls_main.cpp:231:24:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            ref_fasta->open(ref_fasta_filename);
data/vg-1.27.1+ds/src/subcommand/snarls_main.cpp:235:24:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            ins_fasta->open(ins_fasta_filename);
data/vg-1.27.1+ds/src/subcommand/vectorize_main.cpp:311:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            ofi.open(wabbit_mapping_file);
data/vg-1.27.1+ds/src/subcommand/view_main.cpp:455:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        in.open(alignments.c_str());
data/vg-1.27.1+ds/src/subcommand/view_main.cpp:462:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        in.open(loci_file.c_str());
data/vg-1.27.1+ds/src/unittest/blocked_gzip_input_stream.cpp:241:19:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    int discard = open("/dev/null", O_WRONLY);
data/vg-1.27.1+ds/src/unittest/catch.hpp:1564:23:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    struct TrueType { char sizer[1]; };
data/vg-1.27.1+ds/src/unittest/catch.hpp:1565:24:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    struct FalseType { char sizer[2]; };
data/vg-1.27.1+ds/src/unittest/catch.hpp:3116:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char storage[sizeof(T)];
data/vg-1.27.1+ds/src/unittest/catch.hpp:6064:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        void open() {
data/vg-1.27.1+ds/src/unittest/catch.hpp:6158:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                open();
data/vg-1.27.1+ds/src/unittest/catch.hpp:6204:26:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                tracker->open();
data/vg-1.27.1+ds/src/unittest/catch.hpp:6391:16:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        static char altStackMem[SIGSTKSZ];
data/vg-1.27.1+ds/src/unittest/catch.hpp:7420:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char data[bufferSize];
data/vg-1.27.1+ds/src/unittest/catch.hpp:7457:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        m_ofs.open( filename.c_str() );
data/vg-1.27.1+ds/src/unittest/catch.hpp:8676:21:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
                    char asChar[sizeof (int)];
data/vg-1.27.1+ds/src/unittest/catch.hpp:9321:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char buffer[maxDoubleSize];
data/vg-1.27.1+ds/src/unittest/catch.hpp:9328:13:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
            sprintf(buffer, "%.3f", duration);
data/vg-1.27.1+ds/src/unittest/catch.hpp:9554:16:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        static char line[CATCH_CONFIG_CONSOLE_WIDTH] = {0};
data/vg-1.27.1+ds/src/unittest/catch.hpp:10148:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char timeStamp[timeStampSize];
data/vg-1.27.1+ds/src/unittest/constructor.cpp:213:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    vcf.open(vcf_stream);
data/vg-1.27.1+ds/src/unittest/constructor.cpp:247:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    vcf.open(vcf_stream);
data/vg-1.27.1+ds/src/unittest/constructor.cpp:260:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    reference.open(fasta_filename);
data/vg-1.27.1+ds/src/unittest/constructor.cpp:308:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    vcf.open(vcf_stream);
data/vg-1.27.1+ds/src/unittest/constructor.cpp:321:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    reference.open(fasta_filename);
data/vg-1.27.1+ds/src/unittest/constructor.cpp:858:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    vcf.open(vcf_stream);
data/vg-1.27.1+ds/src/unittest/haplotypes.cpp:178:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  slls_out.open(matching_test_file, ios::out | ios::trunc);
data/vg-1.27.1+ds/src/unittest/haplotypes.cpp:182:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  slls_in.open(matching_test_file, ios::in);
data/vg-1.27.1+ds/src/unittest/haplotypes.cpp:185:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  slls_in.open(matching_test_file, ios::in);
data/vg-1.27.1+ds/src/unittest/haplotypes.cpp:188:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  slls_in.open(matching_test_file, ios::in);
data/vg-1.27.1+ds/src/unittest/haplotypes.cpp:191:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  slls_in.open(matching_test_file, ios::in);
data/vg-1.27.1+ds/src/unittest/haplotypes.cpp:194:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  slls_in.open(matching_test_file, ios::in);
data/vg-1.27.1+ds/src/unittest/haplotypes.cpp:201:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  nslls_out.open(nonmatching_test_file, ios::out | ios::trunc);
data/vg-1.27.1+ds/src/unittest/haplotypes.cpp:205:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  nslls_in.open(nonmatching_test_file, ios::in);
data/vg-1.27.1+ds/src/unittest/min_distance.cpp:1444:17:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            buf.open("distanceIndex", ios::in);
data/vg-1.27.1+ds/src/unittest/variant_adder.cpp:43:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    vcf.open(vcf_stream);
data/vg-1.27.1+ds/src/unittest/variant_adder.cpp:90:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    vcf.open(vcf_stream);
data/vg-1.27.1+ds/src/unittest/variant_adder.cpp:144:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    vcf.open(vcf_stream);
data/vg-1.27.1+ds/src/unittest/variant_adder.cpp:198:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    vcf.open(vcf_stream);
data/vg-1.27.1+ds/src/unittest/variant_adder.cpp:284:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    vcf.open(vcf_stream);
data/vg-1.27.1+ds/src/unittest/vcf_buffer.cpp:46:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    vcf.open(vcf_stream);
data/vg-1.27.1+ds/src/utility.cpp:14:14:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
static const char complement[256] = {'N', 'N', 'N', 'N', 'N', 'N', 'N', 'N', // 8
data/vg-1.27.1+ds/src/utility.cpp:152:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char cchars [s.size()+1];
data/vg-1.27.1+ds/src/utility.cpp:321:14:  [2] (tmpfile) mkstemp:
  Potential for temporary file vulnerability in some circumstances. Some
  older Unix-like systems create temp files with permission to write by all
  by default, so be sure to set the umask to override this. Also, some older
  Unix systems might fail to use O_EXCL when opening the file, so make sure
  that O_EXCL is used by the library (CWE-377).
    int fd = mkstemp(&tmpname[0]);
data/vg-1.27.1+ds/src/utility.cpp:486:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        in.open(file_name.c_str());
data/vg-1.27.1+ds/src/variant_recall.cpp:37:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    gamstream.open(gamfile);
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:784:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_size), sizeof(_size));
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:785:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_nchar), sizeof(_nchar));
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:787:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char *>(_bitArray), (std::streamsize)(sizeof(uint64_t) * _nchar));
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:790:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char *>(&sizer),  sizeof(size_t));
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:792:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size()));
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:1201:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_gamma), sizeof(_gamma));
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:1202:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_nb_levels), sizeof(_nb_levels));
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:1203:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_lastbitsetrank), sizeof(_lastbitsetrank));
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:1204:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_nelem), sizeof(_nelem));
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:1236:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char *>(&final_hash_size), sizeof(size_t));
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:1243:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				is.read(reinterpret_cast<char *>(&key), sizeof(elem_t));
data/vg-1.27.1+ds/deps/BBHash/BooPHF.h:1244:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				is.read(reinterpret_cast<char *>(&value), sizeof(uint64_t));
data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/cw_bwt.hpp:343:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			s = ca.ASCIItoCode( bwIt->read() );//this symbol has as context the current state of the automaton
data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/cw_bwt.hpp:495:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			head = ca.ASCIItoCode( bwIt->read() );//this symbol has context corresponding to ca.currentState(). symbol entering from left in context
data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/BackwardFileIterator.h:84:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	symbol read(){
data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/BackwardIterator.h:27:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	virtual symbol read(){return 0;};
data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/BackwardStringIterator.h:45:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	symbol read(){
data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/ContextAutomata.h:156:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
							sampled_text.push_back( bfr->read() );
data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/ContextAutomata.h:171:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			bfr->read();//skip character on text
data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/ContextAutomata.h:310:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			symbol s = bwIt->read();
data/vg-1.27.1+ds/deps/DYNAMIC/include/algorithms/cw-bwt/structures/ContextAutomata.h:403:46:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			context = shift(context, ASCIItoCode(bfr->read()) );
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:276:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&encode_size,sizeof(encode_size));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:277:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&decode_size,sizeof(decode_size));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:282:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			in.read((char*)&c,sizeof(c));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:297:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			in.read((char*)&c,sizeof(c));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:303:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&sigma,sizeof(sigma));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:305:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&log_sigma,sizeof(log_sigma));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:307:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&enc_type,sizeof(enc_type));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:345:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&size,sizeof(size));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:352:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)w.data(),n_words*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/bwt.hpp:397:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&a_size,sizeof(a_size));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/bwt.hpp:398:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&terminator_position,sizeof(terminator_position));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/bwt.hpp:403:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			in.read((char*)&a,sizeof(a));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/fm_index.hpp:190:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&sample_rate,sizeof(sample_rate));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/gap_bitvector.hpp:346:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&size_,sizeof(size_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/gap_bitvector.hpp:347:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&bits_set_,sizeof(bits_set_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/hacked_vector.hpp:395:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&w_size,sizeof(w_size));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/hacked_vector.hpp:400:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)words.data(),sizeof(uint64_t)*w_size);
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/hacked_vector.hpp:404:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&MASK,sizeof(MASK));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/hacked_vector.hpp:406:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&size_,sizeof(size_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/hacked_vector.hpp:408:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&width_,sizeof(width_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/hacked_vector.hpp:410:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&int_per_word_,sizeof(int_per_word_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/lciv.hpp:1167:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&subtree_sizes_len,sizeof(subtree_sizes_len));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/lciv.hpp:1169:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&children_len,sizeof(children_len));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/lciv.hpp:1171:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&leaves_len,sizeof(leaves_len));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/lciv.hpp:1176:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)subtree_sizes.data(),sizeof(uint64_t)*subtree_sizes_len);
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/lciv.hpp:1178:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&has_leaves_,sizeof(has_leaves_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/lciv.hpp:1200:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&rank_,sizeof(rank_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/lciv.hpp:1202:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&nr_children,sizeof(nr_children));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/packed_vector.hpp:715:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&w_size,sizeof(w_size));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/packed_vector.hpp:720:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	    in.read((char*)words.data(),sizeof(uint64_t)*w_size);
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/packed_vector.hpp:724:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&psum_,sizeof(psum_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/packed_vector.hpp:726:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&MASK,sizeof(MASK));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/packed_vector.hpp:728:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&size_,sizeof(size_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/packed_vector.hpp:730:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&width_,sizeof(width_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/packed_vector.hpp:732:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&int_per_word_,sizeof(int_per_word_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/rle_string.hpp:607:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&rpl_size, sizeof(rpl_size));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/rle_string.hpp:612:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			in.read((char*)&key,sizeof(key));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/sparse_vector.hpp:339:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&NIL,sizeof(NIL));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/spsi.hpp:1338:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&subtree_sizes_len, sizeof(subtree_sizes_len));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/spsi.hpp:1340:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&subtree_psums_len, sizeof(subtree_psums_len));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/spsi.hpp:1342:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&children_len, sizeof(children_len));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/spsi.hpp:1344:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&leaves_len, sizeof(leaves_len));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/spsi.hpp:1353:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)subtree_sizes.data(), sizeof(uint64_t) * subtree_sizes.size());
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/spsi.hpp:1354:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)subtree_psums.data(), sizeof(uint64_t) * subtree_psums.size());
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/spsi.hpp:1356:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&has_leaves_, sizeof(has_leaves_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/spsi.hpp:1374:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&rank_, sizeof(rank_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/spsi.hpp:1376:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&nr_children, sizeof(nr_children));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/wm_string.hpp:234:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&n,sizeof(n));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/wm_string.hpp:580:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&l_,sizeof(l_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/wm_string.hpp:582:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&is_leaf_,sizeof(is_leaf_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/wm_string.hpp:589:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&has_child0,sizeof(has_child0));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/wm_string.hpp:590:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&has_child1,sizeof(has_child1));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/wt_string.hpp:223:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&n, sizeof(n));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/wt_string.hpp:655:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&l_, sizeof(l_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/wt_string.hpp:657:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&is_leaf_, sizeof(is_leaf_));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/wt_string.hpp:664:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&has_child0, sizeof(has_child0));
data/vg-1.27.1+ds/deps/DYNAMIC/include/internal/wt_string.hpp:665:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&has_child1, sizeof(has_child1));
data/vg-1.27.1+ds/deps/dozeu/example.c:57:6:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	    strlen(query)				/* length */
data/vg-1.27.1+ds/deps/dozeu/example.c:67:14:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	    "ACAC", strlen("ACAC"), 0	/* reference-side sequence, its length, and node id */
data/vg-1.27.1+ds/deps/dozeu/example.c:71:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[1] = dz_extend(dz, q, &ff[0], 1, "TTGT", strlen("TTGT"), 1);
data/vg-1.27.1+ds/deps/dozeu/example.c:72:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[2] = dz_extend(dz, q, &ff[0], 1, "ATCC", strlen("ATCC"), 2);
data/vg-1.27.1+ds/deps/dozeu/example.c:73:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[3] = dz_extend(dz, q, &ff[1], 2, "AGAC", strlen("AGAC"), 3);		/* "&ff[1], 2" indicates ff[1] and ff[2] are incoming nodes */
data/vg-1.27.1+ds/deps/dozeu/example.c:76:43:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[4] = dz_extend(dz, q, &ff[3], 1, "T", strlen("T"), 4);
data/vg-1.27.1+ds/deps/dozeu/example.c:77:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[5] = dz_extend(dz, q, &ff[3], 2, "TTCTA", strlen("TTCTA"), 5);	/* "&ff[3], 2" indicates ff[3] and ff[4] are incoming nodes */
data/vg-1.27.1+ds/deps/dozeu/example.c:80:43:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[6] = dz_extend(dz, q, &ff[5], 1, "A", strlen("A"), 6);
data/vg-1.27.1+ds/deps/dozeu/example.c:81:43:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[7] = dz_extend(dz, q, &ff[5], 1, "C", strlen("C"), 7);
data/vg-1.27.1+ds/deps/dozeu/example.c:82:43:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[8] = dz_extend(dz, q, &ff[5], 1, "G", strlen("G"), 8);
data/vg-1.27.1+ds/deps/dozeu/example.c:83:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[9] = dz_extend(dz, q, &ff[6], 3, "CACGG", strlen("CACGG"), 9);
data/vg-1.27.1+ds/deps/dozeu/example.protein.c:93:6:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	    strlen(query)				/* length */
data/vg-1.27.1+ds/deps/dozeu/example.protein.c:103:14:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	    "MSAL", strlen("MSAL"), 0   /* reference-side sequence, its length, and node id */
data/vg-1.27.1+ds/deps/dozeu/example.protein.c:107:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[1] = dz_extend(dz, q, &ff[0], 1, "LILA", strlen("LILA"), 1);
data/vg-1.27.1+ds/deps/dozeu/example.protein.c:108:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[2] = dz_extend(dz, q, &ff[0], 1, "KKLG", strlen("KKLG"), 2);
data/vg-1.27.1+ds/deps/dozeu/example.protein.c:109:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[3] = dz_extend(dz, q, &ff[1], 2, "LVGA", strlen("LVGA"), 3);		/* "&ff[1], 2" indicates ff[1] and ff[2] are incoming nodes */
data/vg-1.27.1+ds/deps/dozeu/example.protein.c:112:43:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[4] = dz_extend(dz, q, &ff[3], 1, "A", strlen("A"), 4);
data/vg-1.27.1+ds/deps/dozeu/example.protein.c:113:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[5] = dz_extend(dz, q, &ff[3], 2, "AVAFP", strlen("AVAFP"), 5);	/* "&ff[3], 2" indicates ff[3] and ff[4] are incoming nodes */
data/vg-1.27.1+ds/deps/dozeu/example.protein.c:116:43:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[6] = dz_extend(dz, q, &ff[5], 1, "A", strlen("A"), 6);
data/vg-1.27.1+ds/deps/dozeu/example.protein.c:117:43:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[7] = dz_extend(dz, q, &ff[5], 1, "E", strlen("E"), 7);
data/vg-1.27.1+ds/deps/dozeu/example.protein.c:118:43:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[8] = dz_extend(dz, q, &ff[5], 1, "M", strlen("M"), 8);
data/vg-1.27.1+ds/deps/dozeu/example.protein.c:119:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	ff[9] = dz_extend(dz, q, &ff[6], 3, "EDDCL", strlen("EDDCL"), 9);
data/vg-1.27.1+ds/deps/dozeu/log.h:70:9:  [1] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source is a constant character.
	len += sprintf(str+len, "["); \
data/vg-1.27.1+ds/deps/dozeu/log.h:93:4:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		(strlen("0x0123456789abcdef:") + 16 * strlen(" 00a") + strlen("  \n+ margin")) \
data/vg-1.27.1+ds/deps/dozeu/log.h:93:41:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		(strlen("0x0123456789abcdef:") + 16 * strlen(" 00a") + strlen("  \n+ margin")) \
data/vg-1.27.1+ds/deps/dozeu/log.h:93:58:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		(strlen("0x0123456789abcdef:") + 16 * strlen(" 00a") + strlen("  \n+ margin")) \
data/vg-1.27.1+ds/deps/dozeu/log.h:94:5:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		+ strlen(#ptr) + strlen("\n`' len: 100000000"); \
data/vg-1.27.1+ds/deps/dozeu/log.h:94:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		+ strlen(#ptr) + strlen("\n`' len: 100000000"); \
data/vg-1.27.1+ds/deps/dozeu/log.h:104:8:  [1] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source is a constant character.
	_s += sprintf(_s, "\n"); \
data/vg-1.27.1+ds/deps/dozeu/log.h:114:9:  [1] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source is a constant character.
		_s += sprintf(_s, "\n"); \
data/vg-1.27.1+ds/deps/dozeu/simde/x86/sse4.2.h:167:35:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    int64x2_t eq_hi = vshrq_n_s64(equal, 63);
data/vg-1.27.1+ds/deps/dozeu/unittest.h:334:5:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	if(strlen(fmt) != 0) {
data/vg-1.27.1+ds/deps/dozeu/unittest.h:390:5:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	if(strlen(fmt) != 0) {
data/vg-1.27.1+ds/deps/dozeu/unittest.h:532:4:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		(strlen("0x0123456789abcdef:") + 16 * strlen(" 00a") + strlen("  \n+ margin")) \
data/vg-1.27.1+ds/deps/dozeu/unittest.h:532:41:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		(strlen("0x0123456789abcdef:") + 16 * strlen(" 00a") + strlen("  \n+ margin")) \
data/vg-1.27.1+ds/deps/dozeu/unittest.h:532:58:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		(strlen("0x0123456789abcdef:") + 16 * strlen(" 00a") + strlen("  \n+ margin")) \
data/vg-1.27.1+ds/deps/dozeu/unittest.h:533:5:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		+ strlen(#ptr) + strlen("\n`' len: 100000000"); \
data/vg-1.27.1+ds/deps/dozeu/unittest.h:533:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		+ strlen(#ptr) + strlen("\n`' len: 100000000"); \
data/vg-1.27.1+ds/deps/dozeu/unittest.h:543:8:  [1] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source is a constant character.
	_s += sprintf(_s, "\n"); \
data/vg-1.27.1+ds/deps/dozeu/unittest.h:553:9:  [1] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source is a constant character.
		_s += sprintf(_s, "\n"); \
data/vg-1.27.1+ds/deps/dozeu/unittest.h:615:5:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	if(strlen(filename) > filename_len_limit) {
data/vg-1.27.1+ds/deps/dozeu/unittest.h:620:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	char *cmd = (char *)malloc(strlen(cmd_base) + strlen(filename) + 1);
data/vg-1.27.1+ds/deps/dozeu/unittest.h:620:48:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	char *cmd = (char *)malloc(strlen(cmd_base) + strlen(filename) + 1);
data/vg-1.27.1+ds/deps/dozeu/unittest.h:635:13:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	while((c = getc(fp)) != EOF) {
data/vg-1.27.1+ds/deps/gbwt/bwtmerge.cpp:172:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    DiskIO::read(in, this->data[i], block_bytes);
data/vg-1.27.1+ds/deps/gbwt/bwtmerge.cpp:335:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
GapIterator<BlockArray>::read()
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:47:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    len = strlen(forbid);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp:237:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:233:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:236:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/test/gmock-generated-matchers_test.cc:465:58:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    nested.push_back(list<char>(strings[i], strings[i] + strlen(strings[i])));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/test/gmock-matchers_test.cc:3933:59:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  int operator()(const char* s) { return static_cast<int>(strlen(s)); }
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2388:10:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  return strncpy(dest, src, n);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2410:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  return static_cast<int>(read(fd, buf, count));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/samples/sample2.cc:42:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t len = strlen(a_c_string);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/samples/sample2.h:77:36:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    return c_string_ == NULL ? 0 : strlen(c_string_);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:599:33:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t full_regex_len = strlen(regex) + 10;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:853:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t len = strlen(regex);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:325:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    PrintCharsAsStringTo(s, strlen(s), os);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:342:34:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    PrintCharsAsStringTo(s, std::wcslen(s), os);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:857:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const int length = strlen(ansi);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1822:34:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    num_chars = static_cast<int>(wcslen(str));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:3596:32:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      segment = next_segment + strlen("]]>");
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:3762:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  result.reserve(strlen(str) + 1);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:5001:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t prefix_len = strlen(prefix);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:5397:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  else if (temp_dir[strlen(temp_dir) - 1] == '\\')
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:876:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(a, a + kSize, numbers.begin()));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget.cc:60:3:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  strncpy(buffer, name_.c_str(), max_size-1);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/sasearch.c:83:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  Psize = strlen(P);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:340:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*data)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:341:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:343:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:380:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:381:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:388:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector.hpp:1590:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) p, conf::SDSL_BLOCK_SIZE*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector.hpp:1594:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*) p, ((capacity()>>6)-idx)*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:65:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                m_ifile.read((char*) m_buffer.data(), (m_buffersize*width())/8);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:96:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        uint64_t read(const uint64_t idx)
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:414:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    return m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:433:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t x = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:449:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t x = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:465:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t w = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:473:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t w = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp:94:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    in.read((char*)&w, sizeof(uint8_t));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:313:25:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            return std::equal(begin(), end(), v.begin());
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:359:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            return std::string(tmp_file_name,strlen(tmp_file_name));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/io.hpp:103:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&t, sizeof(t));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/io.hpp:214:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                in.read((char*)v.data(), file_size);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/io.hpp:224:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    in.read((char*)buf.data(), block_size);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/io.hpp:227:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint8_t* end   = begin+read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_treap.hpp:201:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                auto v = read<uint32_t,uint32_t,uint32_t>(bufs);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_treap.hpp:204:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                auto v = read<uint64_t,uint64_t,uint64_t>(bufs);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_treap.hpp:211:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                            read(std::vector<int_vector_buffer<>*>& bufs)
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_support_tree2.hpp:295:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        big_lcp_in.read((char*)&y, sizeof(y));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/select_support_mcl.hpp:469:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*) &m_arg_cnt, sizeof(size_type)/sizeof(char));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_helper.hpp:125:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) child, 2*sizeof(child[0]));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_helper.hpp:286:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) m_c_to_leaf, fixed_sigma*sizeof(m_c_to_leaf[0]));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_helper.hpp:287:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) m_path, fixed_sigma*sizeof(m_path[0]));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:20:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (n + read <= 64) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:21:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (((*d >> read)&bits::lo_set[n]) == bits::lo_set[n])
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:24:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:24:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:25:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            value = 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:27:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            n -= (64-read);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:47:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:48:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:50:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:91:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:92:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:94:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:101:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:102:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:104:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:117:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:118:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:120:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:127:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:128:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:130:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:143:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:144:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:146:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:153:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:154:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:156:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:20:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (n + read <= 64) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:21:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (((*d >> read)&bits::lo_set[n]) == bits::lo_set[n])
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:24:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:24:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:25:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            value = 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:27:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            n -= (64-read);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:47:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:48:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:50:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:76:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:77:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:79:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:86:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:87:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:89:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:102:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:103:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:105:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:112:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:113:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:115:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp:23:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    i = bits::cnt11(*d & ~bits::lo_set[read], carry);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp:31:89:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bits_to_decode += ((w-1)<<6) + bits::sel11(*(d+w), n-(i-temp), oldcarry) + 65 - read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp:34:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bits_to_decode = bits::sel11(*d >> read, n)+1;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp:44:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp:45:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp:47:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp:48:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                bits_to_decode -= (64-read);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/construct_lcp_helper.cpp:90:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            m_stream.read((char*) m_read_buf, m_buffer_size);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/io.cpp:19:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    uint64_t n = strlen((const char*)v);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/io.cpp:74:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(buf, size);
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/memory_management.cpp:630:28:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            auto ps = std::mismatch(ps_str.begin(),ps_str.end(), line.begin());
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/lib/memory_management.cpp:634:28:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            auto pf = std::mismatch(pf_str.begin(),pf_str.end(), line.begin());
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:59:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:81:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:105:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:141:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:165:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),stdvec.begin()));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:190:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),stdvec.begin()));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:208:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),ivmu.begin()));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:209:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:213:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmu.begin(),ivmu.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:215:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmu.begin(),ivmu.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:222:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),ivmu.begin()));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:240:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:248:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:254:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:277:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(tmp_buf.begin(),tmp_buf.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/bwtmerge.h:259:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->read();
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/bwtmerge.h:276:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void operator++() { this->pos++; this->read(); }
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/bwtmerge.h:293:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read()
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/bwtmerge.h:301:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    size_type node_diff = ByteCode::read(this->array->data, this->data_pointer);
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/bwtmerge.h:304:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->value.second += ByteCode::read(this->array->data, this->data_pointer);
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/bwtmerge.h:316:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
template<> void GapIterator<BlockArray>::read();
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/bwtmerge.h:359:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->read();
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/bwtmerge.h:395:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if(this->bufferEnd()) { this->read(); }
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/bwtmerge.h:431:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read()
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/internal.h:52:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static bool read(std::istream& in, Element* data, size_type n = 1)
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/internal.h:57:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      in.read(reinterpret_cast<char*>(data + offset), bytes);
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/internal.h:120:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    DiskIO::read(in, data.data(), data_size);
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/internal.h:149:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static value_type read(ByteArray& array, size_type& i)
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/internal.h:205:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  run_type read(ByteArray& array, size_type& i)
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/internal.h:210:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      run.first = ByteCode::read(array, i);
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/internal.h:211:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      run.second = ByteCode::read(array, i) + 1;
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/internal.h:216:71:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if(run.second >= this->run_continues) { run.second += ByteCode::read(array, i); }
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/internal.h:353:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->read();
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/internal.h:357:68:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void operator++() { this->curr_offset = this->next_offset; this->read(); }
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/internal.h:411:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read()
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/internal.h:421:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->run = this->decoder.read(this->record.body, this->next_offset);
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/variants.h:318:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void begin() { this->site = 0; this->data_offset = 0; this->read(); }
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/variants.h:319:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void operator++() { this->site++; this->read(); }
data/vg-1.27.1+ds/deps/gbwt/include/gbwt/variants.h:331:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read();
data/vg-1.27.1+ds/deps/gbwt/support.cpp:351:42:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  if(subtract_equal) { reverse_offset -= equal; }
data/vg-1.27.1+ds/deps/gbwt/support.cpp:471:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  this->outgoing.resize(ByteCode::read(source, start));
data/vg-1.27.1+ds/deps/gbwt/support.cpp:475:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    outedge.first = ByteCode::read(source, start) + prev;
data/vg-1.27.1+ds/deps/gbwt/support.cpp:477:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    outedge.second = ByteCode::read(source, start);
data/vg-1.27.1+ds/deps/gbwt/support.cpp:487:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  return (ByteCode::read(source, start) == 0);
data/vg-1.27.1+ds/deps/gbwt/support.cpp:1145:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if(this->data.size() > 0) { DiskIO::read(in, this->data.data(), this->data.size()); }
data/vg-1.27.1+ds/deps/gbwt/variants.cpp:754:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void PhasingInformation::read()
data/vg-1.27.1+ds/deps/gbwt/variants.cpp:763:36:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  size_type max_allele = ByteCode::read(this->data, this->data_offset);
data/vg-1.27.1+ds/deps/gbwt/variants.cpp:765:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  run_type run = decoder.read(this->data, this->data_offset);
data/vg-1.27.1+ds/deps/gbwt/variants.cpp:768:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if(run.second == 0) { run = decoder.read(this->data, this->data_offset); }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/bwtmerge.cpp:172:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    DiskIO::read(in, this->data[i], block_bytes);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/bwtmerge.cpp:335:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
GapIterator<BlockArray>::read()
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:47:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    len = strlen(forbid);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp:237:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:233:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:236:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/test/gmock-generated-matchers_test.cc:465:58:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    nested.push_back(list<char>(strings[i], strings[i] + strlen(strings[i])));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googlemock/test/gmock-matchers_test.cc:3933:59:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  int operator()(const char* s) { return static_cast<int>(strlen(s)); }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2388:10:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  return strncpy(dest, src, n);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2410:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  return static_cast<int>(read(fd, buf, count));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/samples/sample2.cc:42:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t len = strlen(a_c_string);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/samples/sample2.h:77:36:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    return c_string_ == NULL ? 0 : strlen(c_string_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:599:33:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t full_regex_len = strlen(regex) + 10;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:853:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t len = strlen(regex);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:325:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    PrintCharsAsStringTo(s, strlen(s), os);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:342:34:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    PrintCharsAsStringTo(s, std::wcslen(s), os);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:857:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const int length = strlen(ansi);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1822:34:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    num_chars = static_cast<int>(wcslen(str));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:3596:32:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      segment = next_segment + strlen("]]>");
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:3762:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  result.reserve(strlen(str) + 1);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:5001:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t prefix_len = strlen(prefix);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:5397:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  else if (temp_dir[strlen(temp_dir) - 1] == '\\')
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:876:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(a, a + kSize, numbers.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget.cc:60:3:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  strncpy(buffer, name_.c_str(), max_size-1);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/external/libdivsufsort/examples/sasearch.c:83:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  Psize = strlen(P);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:340:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*data)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:341:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:343:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:380:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:381:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:388:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector.hpp:1590:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) p, conf::SDSL_BLOCK_SIZE*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector.hpp:1594:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*) p, ((capacity()>>6)-idx)*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:65:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                m_ifile.read((char*) m_buffer.data(), (m_buffersize*width())/8);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:96:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        uint64_t read(const uint64_t idx)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:414:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    return m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:433:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t x = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:449:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t x = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:465:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t w = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:473:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t w = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp:94:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    in.read((char*)&w, sizeof(uint8_t));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:313:25:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            return std::equal(begin(), end(), v.begin());
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:359:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            return std::string(tmp_file_name,strlen(tmp_file_name));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/io.hpp:103:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&t, sizeof(t));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/io.hpp:214:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                in.read((char*)v.data(), file_size);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/io.hpp:224:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    in.read((char*)buf.data(), block_size);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/io.hpp:227:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint8_t* end   = begin+read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_treap.hpp:201:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                auto v = read<uint32_t,uint32_t,uint32_t>(bufs);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_treap.hpp:204:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                auto v = read<uint64_t,uint64_t,uint64_t>(bufs);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/k2_treap.hpp:211:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                            read(std::vector<int_vector_buffer<>*>& bufs)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/lcp_support_tree2.hpp:295:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        big_lcp_in.read((char*)&y, sizeof(y));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/select_support_mcl.hpp:469:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*) &m_arg_cnt, sizeof(size_type)/sizeof(char));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_helper.hpp:125:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) child, 2*sizeof(child[0]));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_helper.hpp:286:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) m_c_to_leaf, fixed_sigma*sizeof(m_c_to_leaf[0]));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/include/sdsl/wt_helper.hpp:287:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) m_path, fixed_sigma*sizeof(m_path[0]));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:20:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (n + read <= 64) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:21:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (((*d >> read)&bits::lo_set[n]) == bits::lo_set[n])
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:24:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:24:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:25:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            value = 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:27:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            n -= (64-read);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:47:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:48:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:50:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:91:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:92:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:94:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:101:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:102:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:104:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:117:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:118:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:120:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:127:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:128:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:130:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:143:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:144:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:146:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:153:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:154:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_delta.cpp:156:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:20:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (n + read <= 64) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:21:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (((*d >> read)&bits::lo_set[n]) == bits::lo_set[n])
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:24:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:24:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:25:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            value = 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:27:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            n -= (64-read);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:47:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:48:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:50:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:76:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:77:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:79:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:86:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:87:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:89:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:102:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:103:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:105:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:112:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:113:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_elias_gamma.cpp:115:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp:23:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    i = bits::cnt11(*d & ~bits::lo_set[read], carry);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp:31:89:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bits_to_decode += ((w-1)<<6) + bits::sel11(*(d+w), n-(i-temp), oldcarry) + 65 - read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp:34:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bits_to_decode = bits::sel11(*d >> read, n)+1;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp:44:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp:45:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp:47:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/coder_fibonacci.cpp:48:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                bits_to_decode -= (64-read);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/construct_lcp_helper.cpp:90:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            m_stream.read((char*) m_read_buf, m_buffer_size);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/io.cpp:19:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    uint64_t n = strlen((const char*)v);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/io.cpp:74:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(buf, size);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/memory_management.cpp:630:28:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            auto ps = std::mismatch(ps_str.begin(),ps_str.end(), line.begin());
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/lib/memory_management.cpp:634:28:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            auto pf = std::mismatch(pf_str.begin(),pf_str.end(), line.begin());
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:59:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:81:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:105:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:141:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:165:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),stdvec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:190:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),stdvec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:208:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),ivmu.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:209:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:213:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmu.begin(),ivmu.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:215:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmu.begin(),ivmu.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:222:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),ivmu.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:240:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:248:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:254:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/deps/sdsl-lite/test/int_vector_mapper_test.cpp:277:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(tmp_buf.begin(),tmp_buf.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/dynamic_gbwt.cpp:148:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      current.outgoing.resize(ByteCode::read(array.data, offset));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/dynamic_gbwt.cpp:152:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        outedge.first = ByteCode::read(array.data, offset) + prev;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/dynamic_gbwt.cpp:154:36:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        outedge.second = ByteCode::read(array.data, offset);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/dynamic_gbwt.cpp:163:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          run_type run = decoder.read(array.data, offset);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/bwtmerge.h:259:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->read();
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/bwtmerge.h:276:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void operator++() { this->pos++; this->read(); }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/bwtmerge.h:293:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read()
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/bwtmerge.h:301:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    size_type node_diff = ByteCode::read(this->array->data, this->data_pointer);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/bwtmerge.h:304:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->value.second += ByteCode::read(this->array->data, this->data_pointer);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/bwtmerge.h:316:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
template<> void GapIterator<BlockArray>::read();
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/bwtmerge.h:359:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->read();
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/bwtmerge.h:395:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if(this->bufferEnd()) { this->read(); }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/bwtmerge.h:431:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read()
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/internal.h:52:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static bool read(std::istream& in, Element* data, size_type n = 1)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/internal.h:57:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      in.read(reinterpret_cast<char*>(data + offset), bytes);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/internal.h:120:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    DiskIO::read(in, data.data(), data_size);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/internal.h:149:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static value_type read(ByteArray& array, size_type& i)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/internal.h:205:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  run_type read(ByteArray& array, size_type& i)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/internal.h:210:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      run.first = ByteCode::read(array, i);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/internal.h:211:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      run.second = ByteCode::read(array, i) + 1;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/internal.h:216:71:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if(run.second >= this->run_continues) { run.second += ByteCode::read(array, i); }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/internal.h:352:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->read();
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/internal.h:356:68:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void operator++() { this->curr_offset = this->next_offset; this->read(); }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/internal.h:402:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read()
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/internal.h:412:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->run = this->decoder.read(this->record.body, this->next_offset);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/variants.h:318:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void begin() { this->site = 0; this->data_offset = 0; this->read(); }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/variants.h:319:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void operator++() { this->site++; this->read(); }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/include/gbwt/variants.h:331:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read();
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/support.cpp:313:42:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  if(subtract_equal) { reverse_offset -= equal; }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/support.cpp:431:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  this->outgoing.resize(ByteCode::read(source, start));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/support.cpp:435:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    outedge.first = ByteCode::read(source, start) + prev;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/support.cpp:437:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    outedge.second = ByteCode::read(source, start);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/support.cpp:447:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  return (ByteCode::read(source, start) == 0);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/support.cpp:894:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if(this->data.size() > 0) { DiskIO::read(in, this->data.data(), this->data.size()); }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/variants.cpp:754:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void PhasingInformation::read()
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/variants.cpp:763:36:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  size_type max_allele = ByteCode::read(this->data, this->data_offset);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/variants.cpp:765:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  run_type run = decoder.read(this->data, this->data_offset);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/gbwt/variants.cpp:768:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if(run.second == 0) { run = decoder.read(this->data, this->data_offset); }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp:82:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(magic_bytes, 4);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:47:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    len = strlen(forbid);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp:237:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:233:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:236:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googlemock/test/gmock-generated-matchers_test.cc:465:58:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    nested.push_back(list<char>(strings[i], strings[i] + strlen(strings[i])));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googlemock/test/gmock-matchers_test.cc:3933:59:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  int operator()(const char* s) { return static_cast<int>(strlen(s)); }
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2388:10:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  return strncpy(dest, src, n);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2410:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  return static_cast<int>(read(fd, buf, count));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/samples/sample2.cc:42:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t len = strlen(a_c_string);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/samples/sample2.h:77:36:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    return c_string_ == NULL ? 0 : strlen(c_string_);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:599:33:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t full_regex_len = strlen(regex) + 10;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:853:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t len = strlen(regex);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:325:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    PrintCharsAsStringTo(s, strlen(s), os);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:342:34:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    PrintCharsAsStringTo(s, std::wcslen(s), os);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:857:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const int length = strlen(ansi);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1822:34:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    num_chars = static_cast<int>(wcslen(str));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:3596:32:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      segment = next_segment + strlen("]]>");
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:3762:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  result.reserve(strlen(str) + 1);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:5001:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t prefix_len = strlen(prefix);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:5397:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  else if (temp_dir[strlen(temp_dir) - 1] == '\\')
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:876:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(a, a + kSize, numbers.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget.cc:60:3:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  strncpy(buffer, name_.c_str(), max_size-1);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/external/libdivsufsort/examples/sasearch.c:83:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  Psize = strlen(P);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:340:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*data)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:341:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:343:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:380:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:381:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:388:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector.hpp:1590:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) p, conf::SDSL_BLOCK_SIZE*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector.hpp:1594:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*) p, ((capacity()>>6)-idx)*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:65:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                m_ifile.read((char*) m_buffer.data(), (m_buffersize*width())/8);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:96:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        uint64_t read(const uint64_t idx)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:414:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    return m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:433:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t x = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:449:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t x = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:465:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t w = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:473:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t w = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp:94:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    in.read((char*)&w, sizeof(uint8_t));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:313:25:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            return std::equal(begin(), end(), v.begin());
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:359:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            return std::string(tmp_file_name,strlen(tmp_file_name));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/io.hpp:103:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&t, sizeof(t));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/io.hpp:214:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                in.read((char*)v.data(), file_size);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/io.hpp:224:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    in.read((char*)buf.data(), block_size);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/io.hpp:227:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint8_t* end   = begin+read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/k2_treap.hpp:201:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                auto v = read<uint32_t,uint32_t,uint32_t>(bufs);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/k2_treap.hpp:204:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                auto v = read<uint64_t,uint64_t,uint64_t>(bufs);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/k2_treap.hpp:211:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                            read(std::vector<int_vector_buffer<>*>& bufs)
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/lcp_support_tree2.hpp:295:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        big_lcp_in.read((char*)&y, sizeof(y));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/select_support_mcl.hpp:469:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*) &m_arg_cnt, sizeof(size_type)/sizeof(char));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/wt_helper.hpp:125:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) child, 2*sizeof(child[0]));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/wt_helper.hpp:286:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) m_c_to_leaf, fixed_sigma*sizeof(m_c_to_leaf[0]));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/include/sdsl/wt_helper.hpp:287:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) m_path, fixed_sigma*sizeof(m_path[0]));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:20:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (n + read <= 64) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:21:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (((*d >> read)&bits::lo_set[n]) == bits::lo_set[n])
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:24:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:24:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:25:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            value = 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:27:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            n -= (64-read);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:47:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:48:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:50:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:91:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:92:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:94:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:101:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:102:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:104:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:117:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:118:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:120:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:127:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:128:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:130:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:143:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:144:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:146:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:153:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:154:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_delta.cpp:156:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:20:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (n + read <= 64) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:21:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (((*d >> read)&bits::lo_set[n]) == bits::lo_set[n])
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:24:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:24:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:25:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            value = 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:27:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            n -= (64-read);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:47:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:48:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:50:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:76:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:77:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:79:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:86:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:87:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:89:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:102:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:103:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:105:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:112:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:113:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_elias_gamma.cpp:115:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_fibonacci.cpp:23:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    i = bits::cnt11(*d & ~bits::lo_set[read], carry);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_fibonacci.cpp:31:89:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bits_to_decode += ((w-1)<<6) + bits::sel11(*(d+w), n-(i-temp), oldcarry) + 65 - read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_fibonacci.cpp:34:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bits_to_decode = bits::sel11(*d >> read, n)+1;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_fibonacci.cpp:44:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_fibonacci.cpp:45:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_fibonacci.cpp:47:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/coder_fibonacci.cpp:48:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                bits_to_decode -= (64-read);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/construct_lcp_helper.cpp:90:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            m_stream.read((char*) m_read_buf, m_buffer_size);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/io.cpp:19:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    uint64_t n = strlen((const char*)v);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/io.cpp:74:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(buf, size);
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/memory_management.cpp:630:28:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            auto ps = std::mismatch(ps_str.begin(),ps_str.end(), line.begin());
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/lib/memory_management.cpp:634:28:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            auto pf = std::mismatch(pf_str.begin(),pf_str.end(), line.begin());
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp:59:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp:81:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp:105:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp:141:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp:165:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),stdvec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp:190:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),stdvec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp:208:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),ivmu.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp:209:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp:213:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmu.begin(),ivmu.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp:215:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmu.begin(),ivmu.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp:222:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),ivmu.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp:240:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp:248:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp:254:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/deps/sdsl-lite/test/int_vector_mapper_test.cpp:277:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(tmp_buf.begin(),tmp_buf.end(),vec.begin()));
data/vg-1.27.1+ds/deps/gbwtgraph/gbwtgraph.cpp:354:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  in.read(reinterpret_cast<char*>(&(this->header)), sizeof(Header));
data/vg-1.27.1+ds/deps/gbwtgraph/gbwtgraph.cpp:369:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(this->sequences.data() + offset, bytes);
data/vg-1.27.1+ds/deps/gbwtgraph/include/gbwtgraph/io.h:39:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  in.read(reinterpret_cast<char*>(&element), sizeof(element));
data/vg-1.27.1+ds/deps/gbwtgraph/include/gbwtgraph/io.h:97:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(reinterpret_cast<char*>(v.data() + i), byte_size);
data/vg-1.27.1+ds/deps/gcsa2/algorithms.cpp:97:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  std::vector<KMer> kmers; graph.read(kmers);
data/vg-1.27.1+ds/deps/gcsa2/convert_graph.cpp:52:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      graph.read(kmers, i, false);
data/vg-1.27.1+ds/deps/gcsa2/files.cpp:161:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if(!DiskIO::read(in, kmers.data() + old_size, header.kmer_count))
data/vg-1.27.1+ds/deps/gcsa2/files.cpp:224:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  DiskIO::read(in, this);
data/vg-1.27.1+ds/deps/gcsa2/files.cpp:402:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
InputGraph::read(std::vector<KMer>& kmers) const
data/vg-1.27.1+ds/deps/gcsa2/files.cpp:409:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->read(kmers, file, true);
data/vg-1.27.1+ds/deps/gcsa2/files.cpp:421:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
InputGraph::read(std::vector<KMer>& kmers, size_type file, bool append) const
data/vg-1.27.1+ds/deps/gcsa2/files.cpp:450:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->read(kmers, file, false);
data/vg-1.27.1+ds/deps/gcsa2/files.cpp:483:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->read(kmers, file, false);
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/files.h:103:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read(std::vector<KMer>& kmers) const;
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/files.h:104:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read(std::vector<KMer>& kmers, size_type file, bool append = false) const;
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/internal.h:60:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static bool read(std::istream& in, Element* data, size_type n = 1, bool update = true)
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/internal.h:65:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      in.read(reinterpret_cast<char*>(data + offset), bytes);
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/internal.h:397:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if(!(this->buffer.buffered(i))) { this->read(i); }
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/internal.h:405:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read(size_type i); // Read i into buffer, possibly seeking backwards.
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/internal.h:511:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if(!DiskIO::read(this->file, this->read_buffer.data(), this->read_buffer.size()))
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/internal.h:523:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
ReadBuffer<Element>::read(size_type i)
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/internal.h:541:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if(!DiskIO::read(this->file, this->read_buffer.data(), this->read_buffer.size()))
data/vg-1.27.1+ds/deps/gcsa2/include/gcsa/path_graph.h:341:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read(std::vector<PathNode>& paths, std::vector<PathNode::rank_type>& labels, size_type file) const;
data/vg-1.27.1+ds/deps/gcsa2/lcp.cpp:242:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if(!DiskIO::read(in, reinterpret_cast<uint8_t*>(this->data.data()), this->size()))
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:405:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  this->graph.read(paths, labels, file);
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:504:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read(PriorityNode& path);
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:517:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->inputs[file].file = file; this->read(this->inputs[file]);
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:649:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  this->read(this->inputs[0]);  // Read the next.
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:654:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
PathGraphMerger::read(PriorityNode& path)
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:705:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    source.read(kmers, file);
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:954:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->read(paths, labels, file);
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:1033:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    this->read(paths, labels, file);
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:1076:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
PathGraph::read(std::vector<PathNode>& paths, std::vector<PathNode::rank_type>& labels, size_type file) const
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:1083:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if(!DiskIO::read(path_file, paths.data(), this->path_counts[file]))
data/vg-1.27.1+ds/deps/gcsa2/path_graph.cpp:1088:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if(!DiskIO::read(rank_file, labels.data(), this->rank_counts[file]))
data/vg-1.27.1+ds/deps/gcsa2/support.cpp:325:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if(this->size() > 0) { DiskIO::read(in, this->mapping.data(), this->size(), false); }
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/pliib.hpp:134:44:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                *(split_sizes + (i - 1)) = strlen(ret[i - 1]); 
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/pliib.hpp:139:36:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        split_sizes[retsize - 1] = strlen(ret[retsize - 1]);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/pliib.hpp:146:9:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
        strncpy(s_to_split, s.c_str(), slen);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/pliib.hpp:170:9:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
        strncpy(s_to_split, s.c_str(), slen);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:183:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                pliib::trim_after_char(name, strlen(name), ' ');
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:185:40:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                entry->name_len = std::strlen(name);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:236:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    int len = strlen(fastaName);
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:305:25:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                cerr << strlen(seq) << endl;
data/vg-1.27.1+ds/deps/gfakluge/src/tinyFA/tinyfa.hpp:322:26:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    end = min(end, (int) strlen(seq));
data/vg-1.27.1+ds/deps/gssw/src/example.c:47:51:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    int8_t* mat = gssw_create_score_matrix(match, mismatch);
data/vg-1.27.1+ds/deps/gssw/src/example.c:70:54:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    gssw_graph_print_score_matrices(graph, read_seq, strlen(read_seq), stdout);
data/vg-1.27.1+ds/deps/gssw/src/example.c:73:53:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                                    strlen(read_seq),
data/vg-1.27.1+ds/deps/gssw/src/example.c:90:61:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                                            strlen(read_seq),
data/vg-1.27.1+ds/deps/gssw/src/example.c:109:69:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                                                    strlen(read_seq),
data/vg-1.27.1+ds/deps/gssw/src/example.c:129:54:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    gssw_graph_print_score_matrices(graph, read_seq, strlen(read_seq), stdout);
data/vg-1.27.1+ds/deps/gssw/src/example.c:132:33:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                strlen(read_seq),
data/vg-1.27.1+ds/deps/gssw/src/example_adj.c:16:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    int len = strlen(qual_str);
data/vg-1.27.1+ds/deps/gssw/src/example_adj.c:65:83:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                                                           &gap_extension, match, mismatch,
data/vg-1.27.1+ds/deps/gssw/src/example_adj.c:89:54:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    gssw_graph_print_score_matrices(graph, read_seq, strlen(read_seq), stdout);
data/vg-1.27.1+ds/deps/gssw/src/example_adj.c:93:62:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                                             strlen(read_seq),
data/vg-1.27.1+ds/deps/gssw/src/example_adj.c:109:70:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                                                     strlen(read_seq),
data/vg-1.27.1+ds/deps/gssw/src/example_adj.c:128:78:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                                                                             strlen(read_seq),
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1724:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
gssw_profile* gssw_init (const int8_t* read, const int32_t readLen, const int8_t* mat, const int32_t n,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1738:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        p->profile_byte = gssw_qP_byte (read, mat, readLen, n, bias, start_full_length_bonus, end_full_length_bonus);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1740:77:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (score_size == 1 || score_size == 2) p->profile_word = gssw_qP_word (read, mat, readLen, n,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1743:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    p->read = read;
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1751:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
gssw_profile* gssw_qual_adj_init (const int8_t* read, const int8_t* qual, const int32_t readLen, const int8_t* adj_mat,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1767:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        p->profile_byte = gssw_adj_qP_byte (read, qual, adj_mat, readLen, n, bias, start_full_length_bonus,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1771:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        p->profile_word = gssw_adj_qP_word(read, qual, adj_mat, readLen, n, start_full_length_bonus, end_full_length_bonus);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1773:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    p->read = read;
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1852:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    alignment->read_end1 = bests[0].read;
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1898:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                              const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1916:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            fprintf(out, "%c\t", read[j]);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1928:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            fprintf(out, "%c\t", read[j]);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1973:69:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void gssw_graph_print_score_matrices(gssw_graph* graph, const char* read, int32_t readLen, FILE* out) {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:1979:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        gssw_print_score_matrix(n->seq, n->len, read, readLen, n->alignment, out);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2004:52:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                       const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2027:47:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                              read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2050:47:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                              read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2075:57:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                            const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2113:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        fprintf(stderr, "%c\t", read[k]);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2126:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        fprintf(stderr, "%c\t", read[k]);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2139:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        fprintf(stderr, "%c\t", read[k]);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2244:50:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            if (ref[i] == 'N' || read[j] == 'N') {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2247:47:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            else if(ref[i] == read[j]) {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2250:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            else if (ref[i] != read[j]) {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2286:105:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        fprintf(stderr, "score=%i at %i,%i with %c vs %c, gRef=%i gRead=%i\n", scoreHere, i, j, ref[i], read[j], gRef, gRead);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2543:115:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                align_score = score_matrix[qual_num[j] * 25 + nt_table[(uint8_t) ref[i]] * 5 + nt_table[(uint8_t) read[j]]];
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2546:96:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                align_score = score_matrix[nt_table[(uint8_t) ref[i]] * 5 + nt_table[(uint8_t) read[j]]];
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2568:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (ref[i] == 'N' || read[j] == 'N') {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2576:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    else if(ref[i] == read[j]) {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2583:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    else if (ref[i] != read[j]) {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2629:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (ref[i] == 'N' || read[j] == 'N') {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2633:99:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        fprintf(stderr, "Alignment start N-match, ref = %c, read = %c\n", ref[i], read[j]);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2636:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    else if (ref[i] == read[j]) {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2641:97:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        fprintf(stderr, "Alignment start match, ref = %c, read = %c\n", ref[i], read[j]);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2649:100:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        fprintf(stderr, "Alignment start mismatch, ref = %c, read = %c\n", ref[i], read[j]);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2841:57:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                            const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2879:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        fprintf(stderr, "%c\t", read[k]);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2892:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        fprintf(stderr, "%c\t", read[k]);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:2905:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        fprintf(stderr, "%c\t", read[k]);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3010:50:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            if (ref[i] == 'N' || read[j] == 'N') {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3013:47:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            else if(ref[i] == read[j]) {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3016:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            else if (ref[i] != read[j]) {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3052:105:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        fprintf(stderr, "score=%i at %i,%i with %c vs %c, gRef=%i gRead=%i\n", scoreHere, i, j, ref[i], read[j], gRef, gRead);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3309:115:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                align_score = score_matrix[qual_num[j] * 25 + nt_table[(uint8_t) ref[i]] * 5 + nt_table[(uint8_t) read[j]]];
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3312:96:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                align_score = score_matrix[nt_table[(uint8_t) ref[i]] * 5 + nt_table[(uint8_t) read[j]]];
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3334:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (ref[i] == 'N' || read[j] == 'N') {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3342:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    else if(ref[i] == read[j]) {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3349:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    else if (ref[i] != read[j]) {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3395:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (ref[i] == 'N' || read[j] == 'N') {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3399:99:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        fprintf(stderr, "Alignment start N-match, ref = %c, read = %c\n", ref[i], read[j]);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3402:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    else if (ref[i] == read[j]) {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3407:97:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        fprintf(stderr, "Alignment start match, ref = %c, read = %c\n", ref[i], read[j]);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3415:100:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        fprintf(stderr, "Alignment start mismatch, ref = %c, read = %c\n", ref[i], read[j]);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3683:66:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                     const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3696:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    gssw_graph_print_score_matrices(graph, read, readLen, stderr);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:3916:52:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                   read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4034:46:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            char read_char = read[readEnd];
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4083:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    char readChar = read[readEnd];
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4346:46:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            char read_char = read[readEnd];
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4391:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    char readChar = read[readEnd];
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4663:56:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                           const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4676:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                              read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4693:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                    const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4707:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                              read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4724:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                  const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4739:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                              read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4756:72:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                           const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4772:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                              read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4791:70:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                         const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4806:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                          read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4822:79:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                                  const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4837:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                          read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4954:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    int32_t len = strlen(seq);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:4958:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(n->seq, seq, len); n->seq[len] = 0;
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:5156:27:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    int32_t read_length = strlen(read_seq);
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:5397:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    alignment->read_end1 = bests[0].read;
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:5471:57:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
int8_t* gssw_create_score_matrix(int32_t match, int32_t mismatch) {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:5482:63:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        for (m = 0; m < 4; ++m) mat[k++] = l == m ? match : - mismatch;    /* weight_match : -weight_mismatch */
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:5655:55:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
double gssw_dna_recover_log_base(int8_t match, int8_t mismatch, double gc_content, double tol) {
data/vg-1.27.1+ds/deps/gssw/src/gssw.c:5664:59:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            score_matrix[i * 4 + j] = (i == j) ? match : -mismatch;
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:118:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	int32_t read;    //alignment ending position on read, 0-based
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:142:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	const int8_t* read;
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:260:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
gssw_profile* gssw_init (const int8_t* read, const int32_t readLen, const int8_t* mat, const int32_t n,
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:286:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
gssw_profile* gssw_qual_adj_init (const int8_t* read, const int8_t* qual, const int32_t readLen, const int8_t* adj_mat,
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:402:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                              const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:429:52:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                       const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:452:57:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                            const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:475:57:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                            const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:487:56:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                           const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:497:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                    const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:510:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                  const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:522:72:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                           const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:540:70:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                         const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:554:79:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                                  const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:676:50:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                     const char* read,
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:690:57:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
int8_t* gssw_create_score_matrix(int32_t match, int32_t mismatch);
data/vg-1.27.1+ds/deps/gssw/src/gssw.h:704:55:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
double gssw_dna_recover_log_base(int8_t match, int8_t mismatch, double gc_content, double tol);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:153:56:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
gssw_graph* align_strings(char* const ref, char* const read, uint8_t scoreSize) {
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:169:51:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    int8_t* mat = gssw_create_score_matrix(match, mismatch);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:177:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    gssw_graph_fill(graph, read, nt_table, mat, gap_open, gap_extension, 0, 0, 15, scoreSize, true);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:190:111:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
gssw_graph* align_diamond(char* const start, char* const alt1, char* const alt2, char* const end, char* const read,
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:207:51:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    int8_t* mat = gssw_create_score_matrix(match, mismatch);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:227:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    gssw_graph_fill(graph, read, nt_table, mat, gap_open, gap_extension, 0, 0, 15, scoreSize, true);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:366:71:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void check_string_alignments_match(char* const reference, char* const read) {
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:373:61:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        gssw_graph* sse2_aligned = align_strings(reference, read, scoreSize);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:376:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        gssw_graph* software_aligned = align_strings(reference, read, scoreSize);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:379:91:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        int match = check_gssw_graph_score_matrices_equal(sse2_aligned, software_aligned, strlen(read));
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:379:98:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        int match = check_gssw_graph_score_matrices_equal(sse2_aligned, software_aligned, strlen(read));
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:387:59:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            gssw_graph_print_score_matrices(sse2_aligned, read, strlen(read), stdout);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:387:65:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            gssw_graph_print_score_matrices(sse2_aligned, read, strlen(read), stdout);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:387:72:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            gssw_graph_print_score_matrices(sse2_aligned, read, strlen(read), stdout);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:389:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            gssw_graph_print_score_matrices(software_aligned, read, strlen(read), stdout);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:389:69:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            gssw_graph_print_score_matrices(software_aligned, read, strlen(read), stdout);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:389:76:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            gssw_graph_print_score_matrices(software_aligned, read, strlen(read), stdout);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:402:121:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void check_diamond_alignments_match(char* const start, char* const alt1, char* const alt2, char* const end, char* const read) {
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:409:74:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        gssw_graph* sse2_aligned = align_diamond(start, alt1, alt2, end, read, scoreSize);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:412:78:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        gssw_graph* software_aligned = align_diamond(start, alt1, alt2, end, read, scoreSize);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:415:91:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        int match = check_gssw_graph_score_matrices_equal(sse2_aligned, software_aligned, strlen(read));
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:415:98:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        int match = check_gssw_graph_score_matrices_equal(sse2_aligned, software_aligned, strlen(read));
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:423:59:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            gssw_graph_print_score_matrices(sse2_aligned, read, strlen(read), stdout);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:423:65:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            gssw_graph_print_score_matrices(sse2_aligned, read, strlen(read), stdout);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:423:72:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            gssw_graph_print_score_matrices(sse2_aligned, read, strlen(read), stdout);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:425:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            gssw_graph_print_score_matrices(software_aligned, read, strlen(read), stdout);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:425:69:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            gssw_graph_print_score_matrices(software_aligned, read, strlen(read), stdout);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:425:76:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            gssw_graph_print_score_matrices(software_aligned, read, strlen(read), stdout);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:483:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            for (i = strlen(reference); i >= 0; i--) {
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:484:83:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                {start_test("should produce identical results on a %d bp string", strlen(reference) - i);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:497:54:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            check_string_alignments_match(reference, read);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:504:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            check_string_alignments_match(ref, read);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:510:54:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            check_string_alignments_match(reference, read);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:516:54:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            check_string_alignments_match(reference, read);
data/vg-1.27.1+ds/deps/gssw/src/gssw_test.c:526:68:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            check_diamond_alignments_match(start, alt1, alt2, end, read);
data/vg-1.27.1+ds/deps/gssw/src/main.c:38:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	int32_t end = strlen(seq), start = 0;
data/vg-1.27.1+ds/deps/gssw/src/main.c:62:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			kseq_t* read,
data/vg-1.27.1+ds/deps/gssw/src/main.c:317:65:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
		for (m = 0; LIKELY(m < 4); ++m) mata[k++] = l == m ? match : -mismatch;	/* weight_match : -weight_mismatch */
data/vg-1.27.1+ds/deps/gssw/src/simde/x86/sse4.2.h:167:35:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    int64x2_t eq_hi = vshrq_n_s64(equal, 63);
data/vg-1.27.1+ds/deps/gssw/src/ssw_cpp.cpp:250:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  int query_len = strlen(query);
data/vg-1.27.1+ds/deps/gssw/src/ssw_cpp.cpp:286:19:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  int query_len = strlen(query);
data/vg-1.27.1+ds/deps/ips4o/ips4o/block_permutation.hpp:68:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    diff_t write, read;
data/vg-1.27.1+ds/deps/ips4o/ips4o/block_permutation.hpp:69:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    std::tie(write, read) = bp.template decRead<kIsParallel>();
data/vg-1.27.1+ds/deps/ips4o/ips4o/block_permutation.hpp:71:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (read < write) {
data/vg-1.27.1+ds/deps/ips4o/ips4o/block_permutation.hpp:78:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    local_.swap[0].readFrom(begin_ + read);
data/vg-1.27.1+ds/deps/ips4o/ips4o/block_permutation.hpp:91:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    diff_t write, read;
data/vg-1.27.1+ds/deps/ips4o/ips4o/block_permutation.hpp:95:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        std::tie(write, read) = bp.template incWrite<kIsParallel>();
data/vg-1.27.1+ds/deps/ips4o/ips4o/block_permutation.hpp:96:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (write > read) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:784:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_size), sizeof(_size));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:785:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_nchar), sizeof(_nchar));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:787:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char *>(_bitArray), (std::streamsize)(sizeof(uint64_t) * _nchar));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:790:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char *>(&sizer),  sizeof(size_t));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:792:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:1201:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_gamma), sizeof(_gamma));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:1202:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_nb_levels), sizeof(_nb_levels));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:1203:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_lastbitsetrank), sizeof(_lastbitsetrank));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:1204:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_nelem), sizeof(_nelem));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:1236:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char *>(&final_hash_size), sizeof(size_t));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:1243:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				is.read(reinterpret_cast<char *>(&key), sizeof(elem_t));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/BBHash/BooPHF.h:1244:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				is.read(reinterpret_cast<char *>(&value), sizeof(uint64_t));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/algorithms/cw_bwt.hpp:343:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			s = ca.ASCIItoCode( bwIt->read() );//this symbol has as context the current state of the automaton
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/algorithms/cw_bwt.hpp:495:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			head = ca.ASCIItoCode( bwIt->read() );//this symbol has context corresponding to ca.currentState(). symbol entering from left in context
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/alphabet_encoder.hpp:276:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&encode_size,sizeof(encode_size));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/alphabet_encoder.hpp:277:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&decode_size,sizeof(decode_size));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/alphabet_encoder.hpp:282:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			in.read((char*)&c,sizeof(c));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/alphabet_encoder.hpp:297:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			in.read((char*)&c,sizeof(c));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/alphabet_encoder.hpp:303:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&sigma,sizeof(sigma));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/alphabet_encoder.hpp:305:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&log_sigma,sizeof(log_sigma));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/alphabet_encoder.hpp:307:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&enc_type,sizeof(enc_type));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/alphabet_encoder.hpp:345:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&size,sizeof(size));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/alphabet_encoder.hpp:352:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)w.data(),n_words*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/bwt.hpp:412:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&a_size,sizeof(a_size));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/bwt.hpp:413:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&terminator_position,sizeof(terminator_position));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/bwt.hpp:418:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			in.read((char*)&a,sizeof(a));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/BackwardFileIterator.h:84:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	symbol read(){
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/BackwardIterator.h:27:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	virtual symbol read(){return 0;};
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/BackwardStringIterator.h:45:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	symbol read(){
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/ContextAutomata.h:156:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
							sampled_text.push_back( bfr->read() );
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/ContextAutomata.h:171:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			bfr->read();//skip character on text
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/ContextAutomata.h:310:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			symbol s = bwIt->read();
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/cw_bwt/ContextAutomata.h:403:46:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			context = shift(context, ASCIItoCode(bfr->read()) );
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/fm_index.hpp:190:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&sample_rate,sizeof(sample_rate));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/gap_bitvector.hpp:345:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&size_,sizeof(size_));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/gap_bitvector.hpp:346:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&bits_set_,sizeof(bits_set_));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/hacked_vector.hpp:395:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&w_size,sizeof(w_size));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/hacked_vector.hpp:400:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)words.data(),sizeof(uint64_t)*w_size);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/hacked_vector.hpp:404:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&MASK,sizeof(MASK));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/hacked_vector.hpp:406:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&size_,sizeof(size_));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/hacked_vector.hpp:408:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&width_,sizeof(width_));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/hacked_vector.hpp:410:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&int_per_word_,sizeof(int_per_word_));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/lciv.hpp:1167:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&subtree_sizes_len,sizeof(subtree_sizes_len));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/lciv.hpp:1169:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&children_len,sizeof(children_len));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/lciv.hpp:1171:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&leaves_len,sizeof(leaves_len));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/lciv.hpp:1176:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)subtree_sizes.data(),sizeof(uint64_t)*subtree_sizes_len);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/lciv.hpp:1178:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&has_leaves_,sizeof(has_leaves_));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/lciv.hpp:1200:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&rank_,sizeof(rank_));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/lciv.hpp:1202:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&nr_children,sizeof(nr_children));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/packed_vector.hpp:738:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&w_size,sizeof(w_size));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/packed_vector.hpp:743:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	    in.read((char*)words.data(),sizeof(uint64_t)*w_size);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/packed_vector.hpp:747:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&psum_,sizeof(psum_));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/packed_vector.hpp:749:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&MASK,sizeof(MASK));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/packed_vector.hpp:751:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&size_,sizeof(size_));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/packed_vector.hpp:753:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&width_,sizeof(width_));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/packed_vector.hpp:755:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&int_per_word_,sizeof(int_per_word_));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/rle_string.hpp:607:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&rpl_size, sizeof(rpl_size));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/rle_string.hpp:612:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			in.read((char*)&key,sizeof(key));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/sparse_vector.hpp:339:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&NIL,sizeof(NIL));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/spsi.hpp:1338:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&subtree_sizes_len, sizeof(subtree_sizes_len));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/spsi.hpp:1340:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&subtree_psums_len, sizeof(subtree_psums_len));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/spsi.hpp:1342:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&children_len, sizeof(children_len));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/spsi.hpp:1344:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&leaves_len, sizeof(leaves_len));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/spsi.hpp:1353:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)subtree_sizes.data(), sizeof(uint64_t) * subtree_sizes.size());
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/spsi.hpp:1354:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)subtree_psums.data(), sizeof(uint64_t) * subtree_psums.size());
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/spsi.hpp:1356:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&has_leaves_, sizeof(has_leaves_));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/spsi.hpp:1374:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&rank_, sizeof(rank_));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/spsi.hpp:1376:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&nr_children, sizeof(nr_children));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/wm_string.hpp:146:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&n, sizeof(n));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/wm_string.hpp:147:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&sigma, sizeof(sigma));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/wm_string.hpp:148:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&bit_width, sizeof(bit_width));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/wm_string.hpp:150:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)begin_one.data(), sizeof(ulint) * bit_width);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/wt_string.hpp:223:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&n, sizeof(n));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/wt_string.hpp:655:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&l_, sizeof(l_));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/wt_string.hpp:657:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&is_leaf_, sizeof(is_leaf_));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/wt_string.hpp:664:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&has_child0, sizeof(has_child0));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/DYNAMIC/include/dynamic/internal/wt_string.hpp:665:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&has_child1, sizeof(has_child1));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/bhopscotch_map.h:135:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                        m_ht(bucket_count, hash, equal, alloc, ht::DEFAULT_MAX_LOAD_FACTOR, comp)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/bhopscotch_map.h:158:92:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                const Allocator& alloc = Allocator()) : bhopscotch_map(bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/bhopscotch_map.h:183:82:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    bhopscotch_map(init.begin(), init.end(), bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/bhopscotch_set.h:118:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                        m_ht(bucket_count, hash, equal, alloc, ht::DEFAULT_MAX_LOAD_FACTOR, comp)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/bhopscotch_set.h:141:92:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                const Allocator& alloc = Allocator()) : bhopscotch_set(bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/bhopscotch_set.h:166:82:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    bhopscotch_set(init.begin(), init.end(), bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/hopscotch_hash.h:599:35:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                  const KeyEqual& equal,
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/hopscotch_hash.h:602:54:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                                            KeyEqual(equal),
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/hopscotch_hash.h:636:35:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                  const KeyEqual& equal,
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/hopscotch_hash.h:640:68:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                                                          KeyEqual(equal),
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/hopscotch_map.h:146:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                        m_ht(bucket_count, hash, equal, alloc, ht::DEFAULT_MAX_LOAD_FACTOR)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/hopscotch_map.h:169:91:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                const Allocator& alloc = Allocator()) : hopscotch_map(bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/hopscotch_map.h:194:81:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    hopscotch_map(init.begin(), init.end(), bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/hopscotch_set.h:130:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                        m_ht(bucket_count, hash, equal, alloc, ht::DEFAULT_MAX_LOAD_FACTOR)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/hopscotch_set.h:153:91:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                const Allocator& alloc = Allocator()) : hopscotch_set(bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/hopscotch-map/include/tsl/hopscotch_set.h:178:81:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    hopscotch_set(init.begin(), init.end(), bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp:82:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(magic_bytes, 4);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/attr.h:370:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    if (!a.name || strlen(a.name) == 0)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/detail/class.h:561:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        size_t size = strlen(rec.doc) + 1;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/detail/common.h:229:27:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        size_t len = std::strlen(compiled_ver);                                \
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/numpy.h:1428:19:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        if (!std::equal(buffers[i].shape.cbegin(), buffers[i].shape.cend(), shape.cbegin()))
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/pybind11.h:381:28:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            if (it->doc && strlen(it->doc) > 0 && options::show_user_defined_docstrings()) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/pybind11.h:1426:31:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    if (other.equal(arg))
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/pybind11.h:1437:52:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    if (handle(kv.second[int_(0)]).equal(arg))
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/pybind11.h:1497:68:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            PYBIND11_ENUM_OP_CONV_LHS("__eq__", !b.is_none() &&  a.equal(b));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/pybind11.h:1498:68:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            PYBIND11_ENUM_OP_CONV_LHS("__ne__",  b.is_none() || !a.equal(b));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/pybind11.h:1515:56:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            PYBIND11_ENUM_OP_STRICT("__eq__",  int_(a).equal(int_(b)), return false);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/pybind11.h:1516:56:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            PYBIND11_ENUM_OP_STRICT("__ne__", !int_(a).equal(int_(b)), return true);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/pytypes.h:118:10:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    bool equal(object_api const &other) const      { return rich_compare(other, Py_EQ); }
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/pytypes.h:633:65:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    friend bool operator==(const It &a, const It &b) { return a.equal(b); }
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/pytypes.h:665:10:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    bool equal(const sequence_fast_readonly &b) const { return ptr == b.ptr; }
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/pytypes.h:686:10:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    bool equal(const sequence_slow_readwrite &b) const { return index == b.index; }
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/include/pybind11/pytypes.h:707:10:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    bool equal(const dict_readonly &b) const { return pos == b.pos; }
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_builtin_casters.cpp:60:42:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    m.def("strlen", [](char *s) { return strlen(s); });
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/pybind11/tests/test_pytypes.cpp:289:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        l.append(a.equal(b));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:47:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    len = strlen(forbid);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp:237:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:233:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:236:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-generated-matchers_test.cc:465:58:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    nested.push_back(list<char>(strings[i], strings[i] + strlen(strings[i])));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-matchers_test.cc:3933:59:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  int operator()(const char* s) { return static_cast<int>(strlen(s)); }
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2388:10:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  return strncpy(dest, src, n);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2410:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  return static_cast<int>(read(fd, buf, count));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample2.cc:42:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t len = strlen(a_c_string);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample2.h:77:36:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    return c_string_ == NULL ? 0 : strlen(c_string_);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:599:33:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t full_regex_len = strlen(regex) + 10;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:853:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t len = strlen(regex);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:325:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    PrintCharsAsStringTo(s, strlen(s), os);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:342:34:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    PrintCharsAsStringTo(s, std::wcslen(s), os);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:857:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const int length = strlen(ansi);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1822:34:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    num_chars = static_cast<int>(wcslen(str));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:3596:32:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      segment = next_segment + strlen("]]>");
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:3762:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  result.reserve(strlen(str) + 1);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:5001:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t prefix_len = strlen(prefix);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:5397:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  else if (temp_dir[strlen(temp_dir) - 1] == '\\')
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:876:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(a, a + kSize, numbers.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget.cc:60:3:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  strncpy(buffer, name_.c_str(), max_size-1);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/external/libdivsufsort/examples/sasearch.c:83:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  Psize = strlen(P);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:340:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*data)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:341:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:343:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:380:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:381:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:388:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector.hpp:1590:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) p, conf::SDSL_BLOCK_SIZE*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector.hpp:1594:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*) p, ((capacity()>>6)-idx)*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:65:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                m_ifile.read((char*) m_buffer.data(), (m_buffersize*width())/8);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:96:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        uint64_t read(const uint64_t idx)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:414:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    return m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:433:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t x = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:449:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t x = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:465:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t w = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:473:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t w = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp:94:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    in.read((char*)&w, sizeof(uint8_t));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:313:25:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            return std::equal(begin(), end(), v.begin());
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:359:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            return std::string(tmp_file_name,strlen(tmp_file_name));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/io.hpp:103:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&t, sizeof(t));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/io.hpp:214:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                in.read((char*)v.data(), file_size);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/io.hpp:224:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    in.read((char*)buf.data(), block_size);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/io.hpp:227:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint8_t* end   = begin+read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/k2_treap.hpp:201:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                auto v = read<uint32_t,uint32_t,uint32_t>(bufs);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/k2_treap.hpp:204:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                auto v = read<uint64_t,uint64_t,uint64_t>(bufs);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/k2_treap.hpp:211:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                            read(std::vector<int_vector_buffer<>*>& bufs)
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/lcp_support_tree2.hpp:295:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        big_lcp_in.read((char*)&y, sizeof(y));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/select_support_mcl.hpp:469:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*) &m_arg_cnt, sizeof(size_type)/sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/wt_helper.hpp:125:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) child, 2*sizeof(child[0]));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/wt_helper.hpp:286:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) m_c_to_leaf, fixed_sigma*sizeof(m_c_to_leaf[0]));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/include/sdsl/wt_helper.hpp:287:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) m_path, fixed_sigma*sizeof(m_path[0]));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:20:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (n + read <= 64) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:21:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (((*d >> read)&bits::lo_set[n]) == bits::lo_set[n])
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:24:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:24:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:25:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            value = 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:27:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            n -= (64-read);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:47:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:48:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:50:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:91:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:92:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:94:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:101:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:102:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:104:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:117:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:118:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:120:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:127:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:128:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:130:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:143:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:144:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:146:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:153:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:154:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:156:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:20:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (n + read <= 64) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:21:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (((*d >> read)&bits::lo_set[n]) == bits::lo_set[n])
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:24:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:24:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:25:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            value = 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:27:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            n -= (64-read);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:47:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:48:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:50:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:76:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:77:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:79:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:86:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:87:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:89:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:102:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:103:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:105:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:112:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:113:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:115:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_fibonacci.cpp:23:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    i = bits::cnt11(*d & ~bits::lo_set[read], carry);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_fibonacci.cpp:31:89:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bits_to_decode += ((w-1)<<6) + bits::sel11(*(d+w), n-(i-temp), oldcarry) + 65 - read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_fibonacci.cpp:34:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bits_to_decode = bits::sel11(*d >> read, n)+1;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_fibonacci.cpp:44:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_fibonacci.cpp:45:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_fibonacci.cpp:47:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/coder_fibonacci.cpp:48:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                bits_to_decode -= (64-read);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/construct_lcp_helper.cpp:90:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            m_stream.read((char*) m_read_buf, m_buffer_size);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/io.cpp:19:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    uint64_t n = strlen((const char*)v);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/io.cpp:74:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(buf, size);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/memory_management.cpp:630:28:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            auto ps = std::mismatch(ps_str.begin(),ps_str.end(), line.begin());
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/lib/memory_management.cpp:634:28:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            auto pf = std::mismatch(pf_str.begin(),pf_str.end(), line.begin());
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:59:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:81:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:105:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:141:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:165:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),stdvec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:190:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),stdvec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:208:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),ivmu.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:209:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:213:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmu.begin(),ivmu.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:215:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmu.begin(),ivmu.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:222:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),ivmu.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:240:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:248:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:254:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:277:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(tmp_buf.begin(),tmp_buf.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/serialize_stream.cc:26:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        istream->read((char*)&size, sizeof(size));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/serialize_stream.cc:28:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        istream->read(first, size);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/examples/serialize_stream.cc:32:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        istream->read((char *)&value->second, sizeof(value->second));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp.h:201:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        return fp->read(reinterpret_cast<char*>(data),
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp.h:1658:22:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                std::equal(_group, _group + _num_items(), x._group));
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_dlalloc.h:1646:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    read(fd, buf, sizeof(buf)) == sizeof(buf))
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/sparsepp/spp_memory.h:122:26:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                auto i = strlen(line);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:106:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    size_t len = strlen(str);
data/vg-1.27.1+ds/deps/libbdsg/bdsg/deps/sparsepp/tests/spp_test.cc:2683:28:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            EXPECT_EQ(EOF, fgetc(fp));       // check we're *exactly* the right size
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:784:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_size), sizeof(_size));
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:785:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_nchar), sizeof(_nchar));
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:787:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char *>(_bitArray), (std::streamsize)(sizeof(uint64_t) * _nchar));
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:790:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char *>(&sizer),  sizeof(size_t));
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:792:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size()));
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:1201:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_gamma), sizeof(_gamma));
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:1202:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_nb_levels), sizeof(_nb_levels));
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:1203:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_lastbitsetrank), sizeof(_lastbitsetrank));
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:1204:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_nelem), sizeof(_nelem));
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:1236:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char *>(&final_hash_size), sizeof(size_t));
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:1243:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				is.read(reinterpret_cast<char *>(&key), sizeof(elem_t));
data/vg-1.27.1+ds/deps/libbdsg/deps/BBHash/BooPHF.h:1244:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				is.read(reinterpret_cast<char *>(&value), sizeof(uint64_t));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/cw_bwt.hpp:343:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			s = ca.ASCIItoCode( bwIt->read() );//this symbol has as context the current state of the automaton
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/cw_bwt.hpp:495:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			head = ca.ASCIItoCode( bwIt->read() );//this symbol has context corresponding to ca.currentState(). symbol entering from left in context
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/structures/BackwardFileIterator.h:84:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	symbol read(){
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/structures/BackwardIterator.h:27:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	virtual symbol read(){return 0;};
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/structures/BackwardStringIterator.h:45:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	symbol read(){
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/structures/ContextAutomata.h:156:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
							sampled_text.push_back( bfr->read() );
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/structures/ContextAutomata.h:171:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			bfr->read();//skip character on text
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/structures/ContextAutomata.h:310:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			symbol s = bwIt->read();
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/algorithms/cw-bwt/structures/ContextAutomata.h:403:46:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			context = shift(context, ASCIItoCode(bfr->read()) );
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:276:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&encode_size,sizeof(encode_size));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:277:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&decode_size,sizeof(decode_size));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:282:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			in.read((char*)&c,sizeof(c));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:297:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			in.read((char*)&c,sizeof(c));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:303:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&sigma,sizeof(sigma));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:305:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&log_sigma,sizeof(log_sigma));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:307:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&enc_type,sizeof(enc_type));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:345:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&size,sizeof(size));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/alphabet_encoder.hpp:352:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)w.data(),n_words*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/bwt.hpp:397:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&a_size,sizeof(a_size));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/bwt.hpp:398:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&terminator_position,sizeof(terminator_position));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/bwt.hpp:403:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			in.read((char*)&a,sizeof(a));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/fm_index.hpp:190:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&sample_rate,sizeof(sample_rate));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/gap_bitvector.hpp:346:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&size_,sizeof(size_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/gap_bitvector.hpp:347:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&bits_set_,sizeof(bits_set_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/hacked_vector.hpp:395:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&w_size,sizeof(w_size));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/hacked_vector.hpp:400:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)words.data(),sizeof(uint64_t)*w_size);
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/hacked_vector.hpp:404:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&MASK,sizeof(MASK));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/hacked_vector.hpp:406:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&size_,sizeof(size_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/hacked_vector.hpp:408:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&width_,sizeof(width_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/hacked_vector.hpp:410:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&int_per_word_,sizeof(int_per_word_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/lciv.hpp:1167:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&subtree_sizes_len,sizeof(subtree_sizes_len));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/lciv.hpp:1169:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&children_len,sizeof(children_len));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/lciv.hpp:1171:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&leaves_len,sizeof(leaves_len));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/lciv.hpp:1176:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)subtree_sizes.data(),sizeof(uint64_t)*subtree_sizes_len);
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/lciv.hpp:1178:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&has_leaves_,sizeof(has_leaves_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/lciv.hpp:1200:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&rank_,sizeof(rank_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/lciv.hpp:1202:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&nr_children,sizeof(nr_children));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/packed_vector.hpp:715:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&w_size,sizeof(w_size));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/packed_vector.hpp:720:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	    in.read((char*)words.data(),sizeof(uint64_t)*w_size);
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/packed_vector.hpp:724:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&psum_,sizeof(psum_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/packed_vector.hpp:726:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&MASK,sizeof(MASK));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/packed_vector.hpp:728:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&size_,sizeof(size_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/packed_vector.hpp:730:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&width_,sizeof(width_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/packed_vector.hpp:732:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	 in.read((char*)&int_per_word_,sizeof(int_per_word_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/rle_string.hpp:607:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&rpl_size, sizeof(rpl_size));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/rle_string.hpp:612:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			in.read((char*)&key,sizeof(key));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/sparse_vector.hpp:339:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		in.read((char*)&NIL,sizeof(NIL));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/spsi.hpp:1338:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&subtree_sizes_len, sizeof(subtree_sizes_len));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/spsi.hpp:1340:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&subtree_psums_len, sizeof(subtree_psums_len));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/spsi.hpp:1342:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&children_len, sizeof(children_len));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/spsi.hpp:1344:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&leaves_len, sizeof(leaves_len));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/spsi.hpp:1353:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)subtree_sizes.data(), sizeof(uint64_t) * subtree_sizes.size());
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/spsi.hpp:1354:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)subtree_psums.data(), sizeof(uint64_t) * subtree_psums.size());
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/spsi.hpp:1356:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&has_leaves_, sizeof(has_leaves_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/spsi.hpp:1374:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&rank_, sizeof(rank_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/spsi.hpp:1376:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&nr_children, sizeof(nr_children));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/wm_string.hpp:234:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&n,sizeof(n));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/wm_string.hpp:580:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&l_,sizeof(l_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/wm_string.hpp:582:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&is_leaf_,sizeof(is_leaf_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/wm_string.hpp:589:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&has_child0,sizeof(has_child0));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/wm_string.hpp:590:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*)&has_child1,sizeof(has_child1));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/wt_string.hpp:223:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&n, sizeof(n));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/wt_string.hpp:655:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&l_, sizeof(l_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/wt_string.hpp:657:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&is_leaf_, sizeof(is_leaf_));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/wt_string.hpp:664:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&has_child0, sizeof(has_child0));
data/vg-1.27.1+ds/deps/libbdsg/deps/DYNAMIC/include/internal/wt_string.hpp:665:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&has_child1, sizeof(has_child1));
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/bhopscotch_map.h:135:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                        m_ht(bucket_count, hash, equal, alloc, ht::DEFAULT_MAX_LOAD_FACTOR, comp)
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/bhopscotch_map.h:158:92:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                const Allocator& alloc = Allocator()) : bhopscotch_map(bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/bhopscotch_map.h:183:82:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    bhopscotch_map(init.begin(), init.end(), bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/bhopscotch_set.h:118:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                        m_ht(bucket_count, hash, equal, alloc, ht::DEFAULT_MAX_LOAD_FACTOR, comp)
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/bhopscotch_set.h:141:92:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                const Allocator& alloc = Allocator()) : bhopscotch_set(bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/bhopscotch_set.h:166:82:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    bhopscotch_set(init.begin(), init.end(), bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/hopscotch_hash.h:599:35:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                  const KeyEqual& equal,
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/hopscotch_hash.h:602:54:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                                            KeyEqual(equal),
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/hopscotch_hash.h:636:35:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                  const KeyEqual& equal,
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/hopscotch_hash.h:640:68:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                                                          KeyEqual(equal),
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/hopscotch_map.h:146:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                        m_ht(bucket_count, hash, equal, alloc, ht::DEFAULT_MAX_LOAD_FACTOR)
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/hopscotch_map.h:169:91:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                const Allocator& alloc = Allocator()) : hopscotch_map(bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/hopscotch_map.h:194:81:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    hopscotch_map(init.begin(), init.end(), bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/hopscotch_set.h:130:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                        m_ht(bucket_count, hash, equal, alloc, ht::DEFAULT_MAX_LOAD_FACTOR)
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/hopscotch_set.h:153:91:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                const Allocator& alloc = Allocator()) : hopscotch_set(bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/deps/hopscotch-map/include/tsl/hopscotch_set.h:178:81:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    hopscotch_set(init.begin(), init.end(), bucket_count, hash, equal, alloc)
data/vg-1.27.1+ds/deps/libbdsg/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp:82:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(magic_bytes, 4);
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/attr.h:370:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    if (!a.name || strlen(a.name) == 0)
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/detail/class.h:561:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        size_t size = strlen(rec.doc) + 1;
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/detail/common.h:229:27:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        size_t len = std::strlen(compiled_ver);                                \
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/numpy.h:1428:19:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        if (!std::equal(buffers[i].shape.cbegin(), buffers[i].shape.cend(), shape.cbegin()))
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/pybind11.h:381:28:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            if (it->doc && strlen(it->doc) > 0 && options::show_user_defined_docstrings()) {
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/pybind11.h:1426:31:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    if (other.equal(arg))
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/pybind11.h:1437:52:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    if (handle(kv.second[int_(0)]).equal(arg))
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/pybind11.h:1497:68:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            PYBIND11_ENUM_OP_CONV_LHS("__eq__", !b.is_none() &&  a.equal(b));
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/pybind11.h:1498:68:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            PYBIND11_ENUM_OP_CONV_LHS("__ne__",  b.is_none() || !a.equal(b));
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/pybind11.h:1515:56:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            PYBIND11_ENUM_OP_STRICT("__eq__",  int_(a).equal(int_(b)), return false);
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/pybind11.h:1516:56:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            PYBIND11_ENUM_OP_STRICT("__ne__", !int_(a).equal(int_(b)), return true);
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/pytypes.h:118:10:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    bool equal(object_api const &other) const      { return rich_compare(other, Py_EQ); }
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/pytypes.h:633:65:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    friend bool operator==(const It &a, const It &b) { return a.equal(b); }
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/pytypes.h:665:10:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    bool equal(const sequence_fast_readonly &b) const { return ptr == b.ptr; }
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/pytypes.h:686:10:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    bool equal(const sequence_slow_readwrite &b) const { return index == b.index; }
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/include/pybind11/pytypes.h:707:10:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    bool equal(const dict_readonly &b) const { return pos == b.pos; }
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_builtin_casters.cpp:60:42:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    m.def("strlen", [](char *s) { return strlen(s); });
data/vg-1.27.1+ds/deps/libbdsg/deps/pybind11/tests/test_pytypes.cpp:289:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        l.append(a.equal(b));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:47:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    len = strlen(forbid);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp:237:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:233:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:236:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-generated-matchers_test.cc:465:58:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    nested.push_back(list<char>(strings[i], strings[i] + strlen(strings[i])));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-matchers_test.cc:3933:59:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  int operator()(const char* s) { return static_cast<int>(strlen(s)); }
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2388:10:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  return strncpy(dest, src, n);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2410:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  return static_cast<int>(read(fd, buf, count));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample2.cc:42:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t len = strlen(a_c_string);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/samples/sample2.h:77:36:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    return c_string_ == NULL ? 0 : strlen(c_string_);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:599:33:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t full_regex_len = strlen(regex) + 10;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:853:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t len = strlen(regex);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:325:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    PrintCharsAsStringTo(s, strlen(s), os);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:342:34:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    PrintCharsAsStringTo(s, std::wcslen(s), os);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:857:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const int length = strlen(ansi);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1822:34:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    num_chars = static_cast<int>(wcslen(str));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:3596:32:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      segment = next_segment + strlen("]]>");
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:3762:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  result.reserve(strlen(str) + 1);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:5001:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t prefix_len = strlen(prefix);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:5397:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  else if (temp_dir[strlen(temp_dir) - 1] == '\\')
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:876:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(a, a + kSize, numbers.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget.cc:60:3:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  strncpy(buffer, name_.c_str(), max_size-1);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/external/libdivsufsort/examples/sasearch.c:83:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  Psize = strlen(P);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:340:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*data)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:341:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:343:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:380:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:381:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:388:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector.hpp:1590:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) p, conf::SDSL_BLOCK_SIZE*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector.hpp:1594:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*) p, ((capacity()>>6)-idx)*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:65:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                m_ifile.read((char*) m_buffer.data(), (m_buffersize*width())/8);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:96:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        uint64_t read(const uint64_t idx)
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:414:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    return m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:433:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t x = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:449:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t x = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:465:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t w = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:473:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t w = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp:94:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    in.read((char*)&w, sizeof(uint8_t));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:313:25:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            return std::equal(begin(), end(), v.begin());
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:359:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            return std::string(tmp_file_name,strlen(tmp_file_name));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/io.hpp:103:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&t, sizeof(t));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/io.hpp:214:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                in.read((char*)v.data(), file_size);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/io.hpp:224:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    in.read((char*)buf.data(), block_size);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/io.hpp:227:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint8_t* end   = begin+read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/k2_treap.hpp:201:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                auto v = read<uint32_t,uint32_t,uint32_t>(bufs);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/k2_treap.hpp:204:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                auto v = read<uint64_t,uint64_t,uint64_t>(bufs);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/k2_treap.hpp:211:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                            read(std::vector<int_vector_buffer<>*>& bufs)
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/lcp_support_tree2.hpp:295:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        big_lcp_in.read((char*)&y, sizeof(y));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/select_support_mcl.hpp:469:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*) &m_arg_cnt, sizeof(size_type)/sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/wt_helper.hpp:125:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) child, 2*sizeof(child[0]));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/wt_helper.hpp:286:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) m_c_to_leaf, fixed_sigma*sizeof(m_c_to_leaf[0]));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/include/sdsl/wt_helper.hpp:287:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) m_path, fixed_sigma*sizeof(m_path[0]));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:20:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (n + read <= 64) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:21:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (((*d >> read)&bits::lo_set[n]) == bits::lo_set[n])
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:24:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:24:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:25:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            value = 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:27:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            n -= (64-read);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:47:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:48:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:50:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:91:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:92:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:94:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:101:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:102:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:104:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:117:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:118:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:120:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:127:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:128:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:130:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:143:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:144:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:146:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:153:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:154:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_delta.cpp:156:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:20:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (n + read <= 64) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:21:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (((*d >> read)&bits::lo_set[n]) == bits::lo_set[n])
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:24:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:24:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:25:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            value = 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:27:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            n -= (64-read);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:47:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:48:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:50:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:76:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:77:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:79:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:86:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:87:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:89:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:102:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:103:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:105:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:112:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:113:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:115:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_fibonacci.cpp:23:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    i = bits::cnt11(*d & ~bits::lo_set[read], carry);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_fibonacci.cpp:31:89:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bits_to_decode += ((w-1)<<6) + bits::sel11(*(d+w), n-(i-temp), oldcarry) + 65 - read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_fibonacci.cpp:34:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bits_to_decode = bits::sel11(*d >> read, n)+1;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_fibonacci.cpp:44:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_fibonacci.cpp:45:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_fibonacci.cpp:47:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/coder_fibonacci.cpp:48:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                bits_to_decode -= (64-read);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/construct_lcp_helper.cpp:90:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            m_stream.read((char*) m_read_buf, m_buffer_size);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/io.cpp:19:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    uint64_t n = strlen((const char*)v);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/io.cpp:74:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(buf, size);
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/memory_management.cpp:630:28:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            auto ps = std::mismatch(ps_str.begin(),ps_str.end(), line.begin());
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/lib/memory_management.cpp:634:28:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            auto pf = std::mismatch(pf_str.begin(),pf_str.end(), line.begin());
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:59:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:81:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:105:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:141:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:165:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),stdvec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:190:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),stdvec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:208:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),ivmu.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:209:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:213:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmu.begin(),ivmu.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:215:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmu.begin(),ivmu.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:222:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),ivmu.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:240:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:248:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:254:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:277:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(tmp_buf.begin(),tmp_buf.end(),vec.begin()));
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/serialize_stream.cc:26:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        istream->read((char*)&size, sizeof(size));
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/serialize_stream.cc:28:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        istream->read(first, size);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/examples/serialize_stream.cc:32:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        istream->read((char *)&value->second, sizeof(value->second));
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp.h:201:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        return fp->read(reinterpret_cast<char*>(data),
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp.h:1658:22:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                std::equal(_group, _group + _num_items(), x._group));
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_dlalloc.h:1646:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    read(fd, buf, sizeof(buf)) == sizeof(buf))
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/sparsepp/spp_memory.h:122:26:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                auto i = strlen(line);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:106:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    size_t len = strlen(str);
data/vg-1.27.1+ds/deps/libbdsg/deps/sparsepp/tests/spp_test.cc:2683:28:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            EXPECT_EQ(EOF, fgetc(fp));       // check we're *exactly* the right size
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:895:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) &is_circular, sizeof(is_circular) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:898:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) &path_id_in, sizeof(path_id_in) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:902:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) &name_size_in, sizeof(name_size_in) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:907:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*) &name[i], sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:911:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) &num_mappings_in, sizeof(num_mappings_in) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:918:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*) &step_in, sizeof(step_in) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:951:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) &seq_size_in, sizeof(seq_size_in) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:955:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*) &sequence[i], sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:959:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) &num_left_edges_in, sizeof(num_left_edges_in) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:964:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*) &next_in, sizeof(next_in) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:970:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) &num_right_edges_in, sizeof(num_right_edges_in) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:975:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*) &next_in, sizeof(next_in) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:1011:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) &max_id_in, sizeof(max_id_in) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:1015:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) &min_id_in, sizeof(min_id_in) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:1019:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) &next_path_id_in, sizeof(next_path_id_in) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:1023:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) &num_nodes_in, sizeof(num_nodes_in) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:1029:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*) &node_id_in, sizeof(node_id_in) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/hash_graph.cpp:1035:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) &num_paths_in, sizeof(num_paths_in) / sizeof(char));
data/vg-1.27.1+ds/deps/libbdsg/src/node.cpp:170:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&_seq_bytes, sizeof(uint32_t));
data/vg-1.27.1+ds/deps/libbdsg/src/node.cpp:171:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&_edge_bytes, sizeof(uint32_t));
data/vg-1.27.1+ds/deps/libbdsg/src/node.cpp:172:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&_edge_count, sizeof(uint32_t));
data/vg-1.27.1+ds/deps/libbdsg/src/node.cpp:174:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&node_size, sizeof(node_size));
data/vg-1.27.1+ds/deps/libbdsg/src/node.cpp:176:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)bytes.data(), node_size*sizeof(uint8_t));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1765:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&_max_node_rank,sizeof(_max_node_rank));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1766:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&_min_node_rank,sizeof(_min_node_rank));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1767:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&_node_count,sizeof(_node_count));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1768:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&_edge_count,sizeof(_edge_count));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1769:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&_path_count,sizeof(_path_count));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1770:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&_path_rank_next,sizeof(_path_rank_next));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1771:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&_deleted_node_count,sizeof(_deleted_node_count));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1772:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&_id_increment,sizeof(_id_increment));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1774:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&hidden_count,sizeof(hidden_count));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1777:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&hidden,sizeof(hidden));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1787:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&i,sizeof(size_t));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1792:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&m.length,sizeof(m.length));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1793:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&m.first,sizeof(m.first));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1794:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&m.last,sizeof(m.last));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1796:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&s,sizeof(size_t));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1798:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read(n,s);
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1801:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&i,sizeof(size_t));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1805:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&s,sizeof(size_t));
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1807:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read(k,s);
data/vg-1.27.1+ds/deps/libbdsg/src/odgi.cpp:1809:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)&v,sizeof(v));
data/vg-1.27.1+ds/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp:82:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(magic_bytes, 4);
data/vg-1.27.1+ds/deps/libvgio/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp:82:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(magic_bytes, 4);
data/vg-1.27.1+ds/deps/libvgio/include/vg/io/fdstream.hpp:158:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        num = read (fd, buffer+pbSize, bufSize);
data/vg-1.27.1+ds/deps/libvgio/include/vg/io/hfile_internal.hpp:16:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ssize_t (*read)(hFILE*, void*, size_t);
data/vg-1.27.1+ds/deps/libvgio/src/hfile_cppstream.cpp:43:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    fp->input->read((char*) buffer, nbytes);
data/vg-1.27.1+ds/deps/libvgio/src/registry.cpp:241:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                read_pipe.read(&chunk[0], chunk.size());
data/vg-1.27.1+ds/deps/mmmultimap/src/mmmultimap.hpp:162:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)magic.c_str(), 9);
data/vg-1.27.1+ds/deps/mmmultimap/src/mmmultimap.hpp:164:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) &version, sizeof(version));
data/vg-1.27.1+ds/deps/progress_bar/progress_bar.cpp:16:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	desc_width = std::strlen(description);	// character width of description field
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:47:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    len = strlen(forbid);
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp:237:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:233:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:236:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:340:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*data)>>read)<<buffered);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:341:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:343:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:380:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:381:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:388:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector.hpp:1590:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) p, conf::SDSL_BLOCK_SIZE*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector.hpp:1594:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*) p, ((capacity()>>6)-idx)*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:65:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                m_ifile.read((char*) m_buffer.data(), (m_buffersize*width())/8);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:96:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        uint64_t read(const uint64_t idx)
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:414:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    return m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:433:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t x = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:449:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t x = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:465:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t w = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:473:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t w = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp:94:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    in.read((char*)&w, sizeof(uint8_t));
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:313:25:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            return std::equal(begin(), end(), v.begin());
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:359:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            return std::string(tmp_file_name,strlen(tmp_file_name));
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/io.hpp:103:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&t, sizeof(t));
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/io.hpp:214:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                in.read((char*)v.data(), file_size);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/io.hpp:224:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    in.read((char*)buf.data(), block_size);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/io.hpp:227:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint8_t* end   = begin+read;
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/k2_treap.hpp:201:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                auto v = read<uint32_t,uint32_t,uint32_t>(bufs);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/k2_treap.hpp:204:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                auto v = read<uint64_t,uint64_t,uint64_t>(bufs);
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/k2_treap.hpp:211:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                            read(std::vector<int_vector_buffer<>*>& bufs)
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/lcp_support_tree2.hpp:295:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        big_lcp_in.read((char*)&y, sizeof(y));
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/select_support_mcl.hpp:469:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*) &m_arg_cnt, sizeof(size_type)/sizeof(char));
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/wt_helper.hpp:125:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) child, 2*sizeof(child[0]));
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/wt_helper.hpp:286:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) m_c_to_leaf, fixed_sigma*sizeof(m_c_to_leaf[0]));
data/vg-1.27.1+ds/deps/sdsl-lite/include/sdsl/wt_helper.hpp:287:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) m_path, fixed_sigma*sizeof(m_path[0]));
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:20:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (n + read <= 64) {
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:21:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (((*d >> read)&bits::lo_set[n]) == bits::lo_set[n])
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:24:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:24:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:25:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            value = 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:27:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            n -= (64-read);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:47:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:48:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:50:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:91:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:92:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:94:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:101:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:102:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:104:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:117:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:118:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:120:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:127:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:128:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:130:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:143:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:144:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:146:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:153:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:154:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_delta.cpp:156:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:20:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (n + read <= 64) {
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:21:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (((*d >> read)&bits::lo_set[n]) == bits::lo_set[n])
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:24:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:24:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:25:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            value = 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:27:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            n -= (64-read);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:47:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:48:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:50:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:76:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:77:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:79:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:86:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:87:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:89:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:102:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:103:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:105:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:112:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:113:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_elias_gamma.cpp:115:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:23:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    i = bits::cnt11(*d & ~bits::lo_set[read], carry);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:31:89:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bits_to_decode += ((w-1)<<6) + bits::sel11(*(d+w), n-(i-temp), oldcarry) + 65 - read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:34:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bits_to_decode = bits::sel11(*d >> read, n)+1;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:44:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:45:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:47:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/sdsl-lite/lib/coder_fibonacci.cpp:48:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                bits_to_decode -= (64-read);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/construct_lcp_helper.cpp:90:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            m_stream.read((char*) m_read_buf, m_buffer_size);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/io.cpp:19:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    uint64_t n = strlen((const char*)v);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/io.cpp:74:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(buf, size);
data/vg-1.27.1+ds/deps/sdsl-lite/lib/memory_management.cpp:630:28:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            auto ps = std::mismatch(ps_str.begin(),ps_str.end(), line.begin());
data/vg-1.27.1+ds/deps/sdsl-lite/lib/memory_management.cpp:634:28:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            auto pf = std::mismatch(pf_str.begin(),pf_str.end(), line.begin());
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp:59:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp:81:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp:105:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp:141:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp:165:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),stdvec.begin()));
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp:190:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),stdvec.begin()));
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp:208:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),ivmu.begin()));
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp:209:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),vec.begin()));
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp:213:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmu.begin(),ivmu.end(),vec.begin()));
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp:215:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmu.begin(),ivmu.end(),vec.begin()));
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp:222:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),ivmu.begin()));
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp:240:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp:248:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp:254:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/sdsl-lite/test/int_vector_mapper_test.cpp:277:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(tmp_buf.begin(),tmp_buf.end(),vec.begin()));
data/vg-1.27.1+ds/deps/sha1/sha1.cpp:238:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        is.read(sbuf, BLOCK_BYTES - buffer.size());
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:130:17:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    int64_t k = strlen(sequence);
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:164:16:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while((j = getc(fastaFile)) != EOF) { //initial terminating characters
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:170:21:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                j = getc(fastaFile);
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:183:21:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                j = getc(fastaFile);
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:553:37:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        register int64_t ch = (char)getc(f);
data/vg-1.27.1+ds/deps/sonLib/C/impl/bioioC.c:556:17:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            ch= getc(f);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:804:36:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    cA = st_malloc(sizeof(char) * (strlen(tempFilePath) + 50));
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:807:14:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    for (i = strlen(tempFilePath) + 1; i < (int64_t) strlen(tempFilePath) + 11; i++) {
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:807:54:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    for (i = strlen(tempFilePath) + 1; i < (int64_t) strlen(tempFilePath) + 11; i++) {
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:831:36:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    cA = st_malloc(sizeof(char) * (strlen(tempDir) + 50));
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:869:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        char *pattern = stString_print(tmpdir[strlen(tmpdir)-1] == '/' ? "%sstTmp%" PRIi64 "_%" PRIi64 "" : "%s/stTmp%" PRIi64 "_%" PRIi64 "", tmpdir, getpid(), counter++);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:910:25:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    i = sizeof(char) * (strlen(rootDir) + 30 * levelNumber + 1);
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:916:55:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    tempFileTree->rootDir = st_malloc(sizeof(char) * (strlen(cA) + 1));
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:971:25:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    i = sizeof(char) * (strlen(tempFileTree->rootDir) + 30
data/vg-1.27.1+ds/deps/sonLib/C/impl/commonC.c:1006:45:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            cA4 = st_malloc(sizeof(char) * (strlen(cA) + 1));
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:81:60:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    pA->contig1 = strcpy((char *)st_malloc(sizeof(char)*(1+strlen(contig1))), contig1);
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:86:60:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    pA->contig2 = strcpy((char *)st_malloc(sizeof(char)*(1+strlen(contig2))), contig2);
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:151:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        assert(strlen(cA2) <= STRING_ARRAY_SIZE);
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:152:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        assert(strlen(cA3) <= STRING_ARRAY_SIZE);
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:153:64:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        pA->contig2 = strcpy((char *)st_malloc(sizeof(char)*(1+strlen(cA2))), cA2);
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:154:64:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        pA->contig1 = strcpy((char *)st_malloc(sizeof(char)*(1+strlen(cA3))), cA3);
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:162:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            assert(strlen(cA) < BIG_STRING_ARRAY_SIZE);
data/vg-1.27.1+ds/deps/sonLib/C/impl/pairwiseAlignment.c:165:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                assert(strlen(cA2) == 1);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCommon.c:55:33:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        for (int64_t i = 0; i < strlen(string); i++) {
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibCommon.c:125:12:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    assert(strlen(cA) < 100000);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibFile.c:25:38:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        register int64_t ch = (char) getc(f);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibFile.c:28:18:  [1] (buffer) getc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            ch = getc(f);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibFile.c:55:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    if (i == -1 && strlen(cA) == 0) {
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibFile.c:65:12:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    return strlen(pathPrefix) == 0 || pathPrefix[strlen(pathPrefix) - 1] == '/' ? stString_print(
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibFile.c:65:50:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    return strlen(pathPrefix) == 0 || pathPrefix[strlen(pathPrefix) - 1] == '/' ? stString_print(
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_BigRecordFile.c:53:17:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	int64_t size = strlen(basePath) + strlen(name) +
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_BigRecordFile.c:53:36:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	int64_t size = strlen(basePath) + strlen(name) +
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_BigRecordFile.c:54:4:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
			strlen(RECORD_FILE_TAG) + 65;
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_BigRecordFile.c:101:37:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	const char* keyString = fileName + strlen(RECORD_FILE_TAG);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibKVDatabase_MySql.c:78:45:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    if (mysql_real_query(dbImpl->conn, sql, strlen(sql)) != 0) {
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:20:49:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        return strcpy(st_malloc(sizeof(char)*(1+strlen(string))), string);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:83:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    for(i=0; i<strlen(pattern); i++) {
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:96:12:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    assert(strlen(toReplace) > 0); //Must be non zero length replacement string.
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:102:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            i += strlen(toReplace);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:108:41:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    newString = st_malloc(sizeof(char)*(strlen(originalString) + j*strlen(replacement) - j*strlen(toReplace) + 1));
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:108:68:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    newString = st_malloc(sizeof(char)*(strlen(originalString) + j*strlen(replacement) - j*strlen(toReplace) + 1));
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:108:92:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    newString = st_malloc(sizeof(char)*(strlen(originalString) + j*strlen(replacement) - j*strlen(toReplace) + 1));
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:113:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            for(j=0; j<strlen(replacement); j++) {
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:116:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            i += strlen(toReplace);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:127:25:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    int64_t padLength = strlen(pad);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:131:14:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        j += strlen(strings[i]);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:137:30:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        int64_t k = (int64_t)strlen(cA2);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:168:26:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    size_t tokenLength = strlen(delim);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibString.c:249:9:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    j = strlen(string);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibTree.c:276:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        assert(strlen(*token) == 1);
data/vg-1.27.1+ds/deps/sonLib/C/impl/sonLibTree.c:280:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            assert(strlen(*token) == 1);
data/vg-1.27.1+ds/deps/sonLib/C/impl/stJson.c:65:2:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
	strncpy(*js, buf, r);
data/vg-1.27.1+ds/deps/sonLib/C/impl/stSafeC.c:28:32:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    int nbytes = write(2, buf, strlen(buf));
data/vg-1.27.1+ds/deps/sonLib/C/impl/stSafeC.c:85:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    int bufSize = 2*strlen(format);
data/vg-1.27.1+ds/deps/sonLib/C/tests/fastaCTest.c:35:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        assert(strlen(seqs->list[i]) == *((int64_t *)seqLengths->list[i]));
data/vg-1.27.1+ds/deps/sonLib/C/tests/sonLibEdgeContainerTests.c:9:2:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
	strcpy(a, "a");
data/vg-1.27.1+ds/deps/sonLib/C/tests/sonLibEdgeContainerTests.c:11:2:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
	strcpy(b, "b");
data/vg-1.27.1+ds/deps/sonLib/C/tests/sonLibEdgeContainerTests.c:13:2:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
	strcpy(c, "c");
data/vg-1.27.1+ds/deps/sonLib/C/tests/sonLibEdgeContainerTests.c:38:2:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
	strcpy(a, "a");
data/vg-1.27.1+ds/deps/sonLib/C/tests/sonLibEdgeContainerTests.c:40:2:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
	strcpy(b, "b");
data/vg-1.27.1+ds/deps/sonLib/C/tests/sonLibEdgeContainerTests.c:42:2:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
	strcpy(c, "c");
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:22:12:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	int len = strlen(old);
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:71:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	length = strlen(text);
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTest.c:98:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	int length = strlen(text);
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:17:6:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
	int mismatch;
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:22:27:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		const size_t frontLen = strlen(front);
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:23:30:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
		const size_t expectedLen = strlen(expected);
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:28:8:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
		if (!mismatch) {
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:30:4:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
			mismatch |= (matchStr == NULL || strncmp(matchStr, ": ", 2));
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:31:9:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
			if (!mismatch) {
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:33:5:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
				mismatch |= (strncmp(matchStr, expected, expectedLen) != 0);
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:38:42:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
	CuAssert_Line(tc, file, line, message, !mismatch);
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:385:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	CuAssertStrEquals(tc, back, details.buffer + strlen(details.buffer) - strlen(back));
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:385:72:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	CuAssertStrEquals(tc, back, details.buffer + strlen(details.buffer) - strlen(back));
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:386:17:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	details.buffer[strlen(front)] = 0;
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:475:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	CuAssertStrEquals(tc, back, details.buffer + strlen(details.buffer) - strlen(back));
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:475:72:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	CuAssertStrEquals(tc, back, details.buffer + strlen(details.buffer) - strlen(back));
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:477:17:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	details.buffer[strlen(front)] = 0;
data/vg-1.27.1+ds/deps/sonLib/externalTools/cutest/CuTestTest.c:506:54:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	CuAssert(tc, "length of str->buffer is 300", 300 == strlen(str->buffer));
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/align.c:73:16:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while (( c = fgetc(stream)) != EOF) {
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/align.c:89:11:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      c = fgetc(stream);
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/align.c:92:25:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ( isspace(c = fgetc(stream)) );
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/align.c:113:11:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      c = fgetc(stream);
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/align.c:265:57:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      aln->seqs[thisseq]->name = (char *) malloc_util( (strlen( name_ptr ) + 1) * sizeof(char));
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/align.c:269:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      for ( last_idx = strlen(seq_ptr) - 1; strchr(whitespace, seq_ptr[last_idx]) != NULL; last_idx--);	  
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/align.c:278:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      for ( last_idx = strlen(seq_ptr) - 1; strchr(whitespace, seq_ptr[last_idx]) != NULL; last_idx--);
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/options.c:56:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      arglen = strlen(argv[optindex]);
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/options.c:64:36:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      if (matches > 1 && arglen != strlen(opt[opti].name)) 
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/sequence.c:30:41:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    dest->name = (char *) malloc_util( (strlen(source->name)+1) * sizeof(char));
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/tree.c:393:3:  [1] (buffer) fscanf:
  It's unclear if the %s limit in the format string is small enough
  (CWE-120). Check that the limit is sufficiently small, or use a different
  input function.
  fscanf( handle, "%1s", &c);
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/tree.c:406:5:  [1] (buffer) fscanf:
  It's unclear if the %s limit in the format string is small enough
  (CWE-120). Check that the limit is sufficiently small, or use a different
  input function.
    fscanf( handle, "%1s", &c); /* should be , */
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/tree.c:417:5:  [1] (buffer) fscanf:
  It's unclear if the %s limit in the format string is small enough
  (CWE-120). Check that the limit is sufficiently small, or use a different
  input function.
    fscanf( handle, "%1s", &c);  /* should be ) */
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/tree.c:420:5:  [1] (buffer) fscanf:
  It's unclear if the %s limit in the format string is small enough
  (CWE-120). Check that the limit is sufficiently small, or use a different
  input function.
    fscanf( handle, "%1s", &c);  /* should be : */
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/tree.c:433:42:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    for( index=0; (newseq->name[index] = fgetc( handle )) != ':'; index++);
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/tree.c:475:3:  [1] (buffer) fscanf:
  It's unclear if the %s limit in the format string is small enough
  (CWE-120). Check that the limit is sufficiently small, or use a different
  input function.
  fscanf( handle, "%1s", &c ); /* should be , */
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/tree.c:484:3:  [1] (buffer) fscanf:
  It's unclear if the %s limit in the format string is small enough
  (CWE-120). Check that the limit is sufficiently small, or use a different
  input function.
  fscanf( handle, "%1s", &c ); /* should be , */
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/tree.c:493:3:  [1] (buffer) fscanf:
  It's unclear if the %s limit in the format string is small enough
  (CWE-120). Check that the limit is sufficiently small, or use a different
  input function.
  fscanf( handle, "%1s", &c);
data/vg-1.27.1+ds/deps/sonLib/externalTools/quicktree_1.1/src/tree.c:496:3:  [1] (buffer) fscanf:
  It's unclear if the %s limit in the format string is small enough
  (CWE-120). Check that the limit is sufficiently small, or use a different
  input function.
  fscanf( handle, "%1s", &c);
data/vg-1.27.1+ds/deps/sparsepp/examples/serialize_stream.cc:26:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        istream->read((char*)&size, sizeof(size));
data/vg-1.27.1+ds/deps/sparsepp/examples/serialize_stream.cc:28:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        istream->read(first, size);
data/vg-1.27.1+ds/deps/sparsepp/examples/serialize_stream.cc:32:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        istream->read((char *)&value->second, sizeof(value->second));
data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp.h:201:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        return fp->read(reinterpret_cast<char*>(data),
data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp.h:1658:22:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                std::equal(_group, _group + _num_items(), x._group));
data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_dlalloc.h:1646:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    read(fd, buf, sizeof(buf)) == sizeof(buf))
data/vg-1.27.1+ds/deps/sparsepp/sparsepp/spp_memory.h:122:26:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                auto i = strlen(line);
data/vg-1.27.1+ds/deps/sparsepp/tests/spp_test.cc:2675:28:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            EXPECT_EQ(EOF, fgetc(fp));       // check we're *exactly* the right size
data/vg-1.27.1+ds/deps/structures/src/tests.cpp:540:21:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        assert(std::equal(group.begin(), group.end(), correct_group.begin()));
data/vg-1.27.1+ds/deps/structures/src/tests.cpp:634:21:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        assert(std::equal(group_of_0_1.begin(), group_of_0_1.end(), group_of_0_1_from_all.begin()));
data/vg-1.27.1+ds/deps/structures/src/tests.cpp:635:21:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        assert(std::equal(group_of_0_1.begin(), group_of_0_1.end(), group_of_0_2_from_all.begin()));
data/vg-1.27.1+ds/deps/structures/src/tests.cpp:636:21:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        assert(std::equal(group_of_0_1.begin(), group_of_0_1.end(), group_of_0_2.begin()));
data/vg-1.27.1+ds/deps/structures/src/tests.cpp:638:21:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        assert(std::equal(group_of_4_1.begin(), group_of_4_1.end(), group_of_4_1_from_all.begin()));
data/vg-1.27.1+ds/deps/structures/src/tests.cpp:639:21:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        assert(std::equal(group_of_4_1.begin(), group_of_4_1.end(), group_of_4_2_from_all.begin()));
data/vg-1.27.1+ds/deps/structures/src/tests.cpp:640:21:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        assert(std::equal(group_of_4_1.begin(), group_of_4_1.end(), group_of_4_2.begin()));
data/vg-1.27.1+ds/deps/structures/src/tests.cpp:642:21:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        assert(std::equal(group_of_9_1.begin(), group_of_9_1.end(), group_of_9_1_from_all.begin()));
data/vg-1.27.1+ds/deps/structures/src/tests.cpp:643:21:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        assert(std::equal(group_of_9_1.begin(), group_of_9_1.end(), group_of_9_2_from_all.begin()));
data/vg-1.27.1+ds/deps/structures/src/tests.cpp:644:21:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        assert(std::equal(group_of_9_1.begin(), group_of_9_1.end(), group_of_9_2.begin()));
data/vg-1.27.1+ds/deps/structures/src/tests.cpp:764:23:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            if (!std::equal(groups_from_all[i].begin(), groups_from_all[i].end(),
data/vg-1.27.1+ds/deps/structures/src/tests.cpp:784:25:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            assert(std::equal(groups_from_all[i].begin(), groups_from_all[i].end(),
data/vg-1.27.1+ds/deps/structures/src/tests.cpp:786:25:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            assert(std::equal(groups_from_all[i].begin(), groups_from_all[i].end(),
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:8544:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        return s.size() >= prefix.size() && std::equal(prefix.begin(), prefix.end(), s.begin());
data/vg-1.27.1+ds/deps/sublinear-Li-Stephens/src/test/catch.hpp:8550:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        return s.size() >= suffix.size() && std::equal(suffix.rbegin(), suffix.rend(), s.rbegin());
data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractfeatures.cpp:16:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  cin.read (reinterpret_cast<char*> (&magic), sizeof (uint32_t));
data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractfeatures.cpp:21:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  cin.read (reinterpret_cast<char*> (&n_images), sizeof (uint32_t));
data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractfeatures.cpp:25:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  cin.read (reinterpret_cast<char*> (&n_rows), sizeof (uint32_t));
data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractfeatures.cpp:29:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  cin.read (reinterpret_cast<char*> (&n_columns), sizeof (uint32_t));
data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractfeatures.cpp:35:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  for (cin.read (reinterpret_cast<char*> (buf), rc);
data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractfeatures.cpp:37:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
       cin.read (reinterpret_cast<char*> (buf), rc))
data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractpixels.cpp:16:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  cin.read (reinterpret_cast<char*> (&magic), sizeof (uint32_t));
data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractpixels.cpp:21:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  cin.read (reinterpret_cast<char*> (&n_images), sizeof (uint32_t));
data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractpixels.cpp:25:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  cin.read (reinterpret_cast<char*> (&n_rows), sizeof (uint32_t));
data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractpixels.cpp:29:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  cin.read (reinterpret_cast<char*> (&n_columns), sizeof (uint32_t));
data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractpixels.cpp:35:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  for (cin.read (reinterpret_cast<char*> (buf), rc);
data/vg-1.27.1+ds/deps/vowpal_wabbit/big_tests/testCode/mnist.extractpixels.cpp:37:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
       cin.read (reinterpret_cast<char*> (buf), rc))
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h:347:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    char feature_str[strlen] = { 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h:351:40:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      { chars = sprintf_s(feature_str, strlen, "%d:", m_features[i].Id);
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h:354:40:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      { chars = sprintf_s(feature_str, strlen, " %d:", m_features[i].Id);
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h:1104:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    char feature_str[strlen] = { 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h:1108:40:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      { chars = sprintf_s(feature_str, strlen, "%d:", m_features[i].Id);
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/MWTExplorer.h:1111:40:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      { chars = sprintf_s(feature_str, strlen, " %d:", m_features[i].Id);
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h:357:26:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        char feature_str[strlen] = { 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h:363:48:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                chars = sprintf_s(feature_str, strlen, "%d:", m_features[i].Id);
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h:367:48:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                chars = sprintf_s(feature_str, strlen, " %d:", m_features[i].Id);
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h:1191:26:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        char feature_str[strlen] = { 0 };
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h:1197:48:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                chars = sprintf_s(feature_str, strlen, "%d:", m_features[i].Id);
data/vg-1.27.1+ds/deps/vowpal_wabbit/explore/cpp/static/MWTExplorer.h:1201:48:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                chars = sprintf_s(feature_str, strlen, " %d:", m_features[i].Id);
data/vg-1.27.1+ds/deps/vowpal_wabbit/library/gd_mf_weights.cc:67:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  ssize_t read;
data/vg-1.27.1+ds/deps/vowpal_wabbit/library/gd_mf_weights.cc:78:10:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  { line[strlen(line)-1] = 0; // chop
data/vg-1.27.1+ds/deps/vowpal_wabbit/library/recommend.cc:58:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  get_hashv(line,strlen(line),hashv);
data/vg-1.27.1+ds/deps/vowpal_wabbit/library/recommend.cc:70:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  get_hashv(line,strlen(line),hashv);
data/vg-1.27.1+ds/deps/vowpal_wabbit/library/recommend.cc:145:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  ssize_t read;
data/vg-1.27.1+ds/deps/vowpal_wabbit/library/recommend.cc:177:7:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    u[strlen(u)-1] = 0; // chop
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/OjaNewton.cc:508:56:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load(OjaNewton& ON, io_buf& model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/OjaNewton.cc:511:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/OjaNewton.cc:522:81:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bin_text_read_write_fixed(model_file, (char *)&resume, sizeof (resume), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/OjaNewton.cc:526:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      GD::save_load_online_state(all, model_file, read, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/OjaNewton.cc:528:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      GD::save_load_regressor(all, model_file, read, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc:962:71:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load_regularizer(vw& all, bfgs& b, io_buf& model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc:969:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if(b.output_regularizer && !read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc:976:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc:1004:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc:1007:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while ((!read && i < length) || (read && brw >0));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc:1007:36:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while ((!read && i < length) || (read && brw >0));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc:1009:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc:1014:50:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load(bfgs& b, io_buf& model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc:1020:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc:1059:47:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool reg_vector = (b.output_regularizer && !read) || (all->per_feature_regularizer_input.length() > 0 && read);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc:1059:108:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool reg_vector = (b.output_regularizer && !read) || (all->per_feature_regularizer_input.length() > 0 && read);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc:1066:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                              "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc:1069:50:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      save_load_regularizer(*all, b, model_file, read, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/bfgs.cc:1071:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      GD::save_load_regressor(*all, model_file, read, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/boosting.cc:272:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load_sampling(boosting &o, io_buf &model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/boosting.cc:278:76:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bin_text_read_write_fixed(model_file, (char *) &(o.N),  sizeof(o.N), "", read, os, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/boosting.cc:280:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/boosting.cc:287:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/boosting.cc:301:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/boosting.cc:314:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/boosting.cc:341:54:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load(boosting &o, io_buf &model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/boosting.cc:347:76:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bin_text_read_write_fixed(model_file, (char *) &(o.N),  sizeof(o.N), "", read, os, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/boosting.cc:349:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/boosting.cc:354:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/boosting.cc:369:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb.cc:109:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  size_t len_str = strlen(str);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb_adf.cc:368:52:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load(cb_adf& c, io_buf& model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb_adf.cc:375:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cb_adf.cc:379:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/cost_sensitive.cc:126:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  size_t len_str = strlen(str);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/ftrl.cc:205:50:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load(ftrl& b, io_buf& model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/ftrl.cc:208:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/ftrl.cc:216:80:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bin_text_read_write_fixed(model_file,(char *)&resume, sizeof (resume), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/ftrl.cc:219:52:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      GD::save_load_online_state(*all, model_file, read, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/ftrl.cc:221:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      GD::save_load_regressor(*all, model_file, read, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:668:60:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load_regressor(vw& all, io_buf& model_file, bool read, bool text, T& weights)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:696:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:738:60:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load_regressor(vw& all, io_buf& model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:741:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    save_load_regressor(all, model_file, read, text, all.weights.sparse_weights);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:743:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    save_load_regressor(all, model_file, read, text, all.weights.dense_weights);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:747:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load_online_state(vw& all, io_buf& model_file, bool read, bool text, gd* g, stringstream& msg, T& weights)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:755:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:821:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load_online_state(vw& all, io_buf& model_file, bool read, bool text, gd* g)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:828:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:832:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:836:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:840:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:844:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:848:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:852:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:856:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:860:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:864:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:868:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:872:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:876:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:878:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (!read || all.model_file_ver >= VERSION_SAVE_RESUME_FIX)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:884:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (!read && g != nullptr) total_weight = g->total_weight;
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:887:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                              "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:888:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (read && g != nullptr) g->total_weight = total_weight;
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:893:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                              "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:899:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:904:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:910:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read && (!all.training || !all.preserve_performance_counters)) // reset various things so that we report test set performance properly
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:924:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    save_load_online_state(all, model_file, read, text, g, msg, all.weights.sparse_weights);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:926:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    save_load_online_state(all, model_file, read, text, g, msg, all.weights.dense_weights);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:939:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load(gd& g, io_buf& model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:942:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if(read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:969:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                              "", read,
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:973:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if (read && all.model_file_ver < VERSION_SAVE_RESUME_FIX)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:976:47:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      save_load_online_state(all, model_file, read, text, &g);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.cc:979:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      save_load_regressor(all, model_file, read, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.h:25:60:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load_regressor(vw& all, io_buf& model_file, bool read, bool text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd.h:26:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load_online_state(vw& all, io_buf& model_file, bool read, bool text, GD::gd *g = nullptr);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd_mf.cc:249:50:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load(gdmf& d, io_buf& model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd_mf.cc:253:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if(read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd_mf.cc:277:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                       "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd_mf.cc:286:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                           "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd_mf.cc:293:46:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                         "", read, msg,text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd_mf.cc:296:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd_mf.cc:299:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((!read && i < length) || (read && brw >0));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/gd_mf.cc:299:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((!read && i < length) || (read && brw >0));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/global_data.cc:37:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
           read(sock,buf,(unsigned int)(count-done))
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/global_data.h:150:38:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    memcpy(temp, label_list.c_str(), strlen(label_list.c_str()));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/io_buf.cc:137:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  return read(f, buf, (unsigned int)nbytes);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/io_buf.h:279:66:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                  const char* read_message, bool read,
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/io_buf.h:281:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
{ if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/io_buf.h:301:72:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                        const char* read_message, bool read,
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/io_buf.h:303:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
{ if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/io_buf.h:310:36:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    const char* read_message, bool read,
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/io_buf.h:312:74:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
{ size_t nbytes = bin_text_read_write_fixed(io, data, len, read_message, read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/io_buf.h:313:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read && len > 0) // only validate bytes read/write if expected length > 0
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc:217:53:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
int save_load_flat_example(io_buf& model_file, bool read, flat_example*& fec)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc:220:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if(read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc:278:71:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load_svm_model(svm_params& params, io_buf& model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc:287:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc:291:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if(read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc:296:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if(read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc:298:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      save_load_flat_example(model_file, read, fec);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc:306:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      save_load_flat_example(model_file, read, fec);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc:310:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if(read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc:313:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc:314:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if(read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc:317:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc:320:61:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load(svm_params& params, io_buf& model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/kernel_svm.cc:328:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  save_load_svm_model(params, model_file, read, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:735:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load(lda &l, io_buf &model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:739:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:758:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if (!read && text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:761:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if (!read || all.model_file_ver >= VERSION_FILE_WITH_HEADER_ID)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:762:81:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        brw += bin_text_read_write_fixed(model_file, (char *)&i, sizeof(i), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:767:81:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        brw += bin_text_read_write_fixed(model_file, (char *)&j, sizeof(j), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:777:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          if (!read && text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:779:83:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          brw += bin_text_read_write_fixed(model_file, (char *)v, sizeof(*v), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:784:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:786:70:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        brw += bin_text_read_write_fixed(model_file, nullptr, 0, "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:788:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:791:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((!read && i < length) || (read && brw > 0));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/lda_core.cc:791:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((!read && i < length) || (read && brw > 0));
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/learner.h:68:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void (*save_load_f)(void*, io_buf&, bool read, bool text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/learner.h:88:47:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
typedef void (*tsl)(void* d, io_buf& io, bool read, bool text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/learner.h:168:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inline void save_load(io_buf& io, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/learner.h:169:53:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  { save_load_fd.save_load_f(save_load_fd.data, io, read, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/learner.h:170:61:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (save_load_fd.base) save_load_fd.base->save_load(io, read, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:398:60:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load_tree(log_multi& b, io_buf& model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:404:85:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bin_text_read_write_fixed(model_file,(char*)&b.max_predictors, sizeof(b.k), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:408:74:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bin_text_read_write_fixed(model_file,(char*)&temp, sizeof(temp), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:409:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:414:98:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bin_text_read_write_fixed(model_file,(char*)&b.max_predictors, sizeof(b.max_predictors), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:417:100:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bin_text_read_write_fixed(model_file,(char*)&b.predictors_used, sizeof(b.predictors_used), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:420:86:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bin_text_read_write_fixed(model_file,(char*)&b.progress, sizeof(b.progress), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:423:92:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bin_text_read_write_fixed(model_file,(char*)&b.swap_resist, sizeof(b.swap_resist), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:431:84:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bin_text_read_write_fixed(model_file,(char*)&n.parent, sizeof(n.parent), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:436:76:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bin_text_read_write_fixed(model_file,(char*)&temp, sizeof(temp), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:437:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:442:90:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bin_text_read_write_fixed(model_file,(char*)&n.min_count, sizeof(n.min_count), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:445:88:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bin_text_read_write_fixed(model_file,(char*)&n.internal, sizeof(n.internal), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:450:102:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bin_text_read_write_fixed(model_file,(char*)&n.base_predictor, sizeof(n.base_predictor), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:453:82:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bin_text_read_write_fixed(model_file,(char*)&n.left, sizeof(n.left), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:456:84:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bin_text_read_write_fixed(model_file,(char*)&n.right, sizeof(n.right), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:459:88:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bin_text_read_write_fixed(model_file,(char*)&n.norm_Eh, sizeof(n.norm_Eh), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:462:78:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bin_text_read_write_fixed(model_file,(char*)&n.Eh, sizeof(n.Eh), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:465:76:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bin_text_read_write_fixed(model_file,(char*)&n.n, sizeof(n.n), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:470:92:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bin_text_read_write_fixed(model_file,(char*)&n.max_count, sizeof(n.max_count), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:472:104:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bin_text_read_write_fixed(model_file,(char*)&n.max_count_label, sizeof(n.max_count_label), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:480:80:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bin_text_read_write_fixed(model_file,(char*)&p.Ehk, sizeof(p.Ehk), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:483:90:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bin_text_read_write_fixed(model_file,(char*)&p.norm_Ehk, sizeof(p.norm_Ehk), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:486:78:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bin_text_read_write_fixed(model_file,(char*)&p.nk, sizeof(p.nk), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:489:84:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bin_text_read_write_fixed(model_file,(char*)&p.label, sizeof(p.label), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/log_multi.cc:492:96:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bin_text_read_write_fixed(model_file,(char*)&p.label_count, sizeof(p.label_count), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:251:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load(data& sm, io_buf& io, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:259:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:264:87:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bin_text_read_write_fixed_validated(io, (char*)&total_size, sizeof(total_size), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:270:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:275:69:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bin_text_read_write_fixed(io, (char*)&index, sizeof(index), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:277:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:282:77:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bin_text_read_write_fixed(io, (char*)&numerator, sizeof(numerator), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:284:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:289:81:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bin_text_read_write_fixed(io, (char*)&denominator, sizeof(denominator), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:290:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:298:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:303:89:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bin_text_read_write_fixed_validated(io, (char*)&total_size, sizeof(total_size), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:309:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:314:71:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bin_text_read_write_fixed(io, (char*)&index, sizeof(index), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:316:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:326:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bin_text_read_write_fixed(io, (char*)&r1, sizeof(r1), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:327:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if(!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:329:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bin_text_read_write_fixed(io, (char*)&c1, sizeof(c1), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:330:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if(!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:332:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bin_text_read_write_fixed(io, (char*)&w1, sizeof(w1), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:333:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if(!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:335:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bin_text_read_write_fixed(io, (char*)&r2, sizeof(r2), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:336:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if(!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:338:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bin_text_read_write_fixed(io, (char*)&c2, sizeof(c2), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:339:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if(!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:341:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bin_text_read_write_fixed(io, (char*)&w2, sizeof(w2), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/marginal.cc:343:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/mwt.cc:198:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load(mwt& c, io_buf& model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/mwt.cc:207:89:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bin_text_read_write_fixed_validated(model_file, (char*)&c.total, sizeof(c.total), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/mwt.cc:211:101:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bin_text_read_write_fixed_validated(model_file, (char*)&policies_size, sizeof(policies_size), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/mwt.cc:213:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/mwt.cc:226:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                      "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/mwt.cc:232:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/mwt.cc:235:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                        "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:266:50:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  dictionary_info info = { calloc_or_throw<char>(strlen(s)+1), fd_hash, map };
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:443:8:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  if (!equal(vw1.spelling_features, vw1.spelling_features + (sizeof(vw1.spelling_features) / sizeof(bool)), vw2.spelling_features))
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:446:8:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  if (!equal(vw1.affix_features, vw1.affix_features + (sizeof(vw1.affix_features) / sizeof(uint32_t)), vw2.affix_features))
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:449:8:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  if (!equal(vw1.ngram, vw1.ngram + (sizeof(vw1.ngram) / sizeof(uint32_t)), vw2.ngram))
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:452:8:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  if (!equal(vw1.skips, vw1.skips + (sizeof(vw1.skips) / sizeof(uint32_t)), vw2.skips))
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:455:8:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  if (!equal(vw1.limit, vw1.limit + (sizeof(vw1.limit) / sizeof(uint32_t)), vw2.limit))
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:470:27:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  if (vw1.ignore_some && !equal(vw1.ignore, vw1.ignore + (sizeof(vw1.ignore) / sizeof(bool)), vw2.ignore))
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:476:34:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  if (vw1.ignore_some_linear && !equal(vw1.ignore_linear, vw1.ignore_linear + (sizeof(vw1.ignore_linear) / sizeof(bool)), vw2.ignore_linear))
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:482:29:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  if (vw1.redefine_some && !equal(vw1.redefine, vw1.redefine + (sizeof(vw1.redefine) / sizeof(unsigned char)), vw2.redefine))
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_args.cc:491:8:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  if (!equal(vw1.dictionary_path.begin(), vw1.dictionary_path.end(), vw2.dictionary_path.begin()))
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_example.cc:444:30:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  substring ss = {line, line+strlen(line)};
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:177:57:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load_header(vw& all, io_buf& model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:192:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:199:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                              "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:212:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:215:53:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:218:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (read && find(all.opts_n_args.args.begin(), all.opts_n_args.args.end(), "--id") == all.opts_n_args.args.end() && !all.id.empty())
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:228:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                          "file is not a model file", read,
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:233:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                          "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:238:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                          "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:243:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                          "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:245:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if (read && find(all.opts_n_args.args.begin(), all.opts_n_args.args.end(), "--bit_precision") == all.opts_n_args.args.end())
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:265:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:272:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:279:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                              "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:280:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:291:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:297:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:304:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:310:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                              "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:311:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:321:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:330:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                              "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:335:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:341:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:342:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:356:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:362:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                              "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:380:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:398:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                          "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:404:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                          "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:409:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:415:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:416:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:428:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                          "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:434:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                          "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:439:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (!read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:446:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:447:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:458:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                          "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:460:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:479:53:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                                "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.cc:494:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/parse_regressor.h:19:57:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load_header(vw& all, io_buf& model_file, bool read, bool text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/recall_tree.cc:477:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                 read,                  \
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/recall_tree.cc:492:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                 read,                  \
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/recall_tree.cc:498:62:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load_tree(recall_tree& b, io_buf& model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/recall_tree.cc:508:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/recall_tree.cc:537:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/recall_tree.cc:555:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:1450:50:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  size_t condition_on_cnt = condition_on_names ? strlen(condition_on_names) : 0;
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:1546:54:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
          ensure_size(priv.learn_condition_on_names, strlen(condition_on_names)+1);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/search.cc:2439:27:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    substring me = { p, p+strlen(p) };
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/stagewise_poly.cc:661:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load(stagewise_poly &poly, io_buf &model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/stagewise_poly.cc:666:108:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bin_text_read_write_fixed(model_file, (char *) poly.depthsbits, (uint32_t)depthsbits_sizeof(poly), "", read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/svrg.cc:144:50:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void save_load(svrg& s, io_buf& model_file, bool read, bool text)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/svrg.cc:146:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read)
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/svrg.cc:157:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                              read, msg, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/svrg.cc:160:54:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      GD::save_load_online_state(*s.all, model_file, read, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/svrg.cc:162:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      GD::save_load_regressor(*s.all, model_file, read, text);
data/vg-1.27.1+ds/deps/vowpal_wabbit/vowpalwabbit/vw.h:147:23:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  ss.end = ss.begin + strlen(fstr);
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:784:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_size), sizeof(_size));
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:785:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_nchar), sizeof(_nchar));
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:787:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char *>(_bitArray), (std::streamsize)(sizeof(uint64_t) * _nchar));
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:790:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char *>(&sizer),  sizeof(size_t));
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:792:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size()));
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:1201:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_gamma), sizeof(_gamma));
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:1202:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_nb_levels), sizeof(_nb_levels));
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:1203:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_lastbitsetrank), sizeof(_lastbitsetrank));
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:1204:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char*>(&_nelem), sizeof(_nelem));
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:1236:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			is.read(reinterpret_cast<char *>(&final_hash_size), sizeof(size_t));
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:1243:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				is.read(reinterpret_cast<char *>(&key), sizeof(elem_t));
data/vg-1.27.1+ds/deps/xg/deps/BBHash/BooPHF.h:1244:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				is.read(reinterpret_cast<char *>(&value), sizeof(uint64_t));
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:8304:36:  [1] (buffer) getchar:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            static_cast<void>(std::getchar());
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:8309:36:  [1] (buffer) getchar:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            static_cast<void>(std::getchar());
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:8490:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        return s.size() >= prefix.size() && std::equal(prefix.begin(), prefix.end(), s.begin());
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:8496:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        return s.size() >= suffix.size() && std::equal(suffix.rbegin(), suffix.rend(), s.rbegin());
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:8588:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        m_size( static_cast<size_type>( std::strlen( rawChars ) ) )
data/vg-1.27.1+ds/deps/xg/deps/args/catch.hpp:8597:84:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        size_type rawSize = rawChars == nullptr ? 0 : static_cast<size_type>( std::strlen( rawChars ) );
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/pliib.hpp:134:44:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                *(split_sizes + (i - 1)) = strlen(ret[i - 1]); 
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/pliib.hpp:139:36:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        split_sizes[retsize - 1] = strlen(ret[retsize - 1]);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/pliib.hpp:146:9:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
        strncpy(s_to_split, s.c_str(), slen);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/pliib.hpp:170:9:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
        strncpy(s_to_split, s.c_str(), slen);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:183:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                pliib::trim_after_char(name, strlen(name), ' ');
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:185:40:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                entry->name_len = std::strlen(name);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:236:15:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    int len = strlen(fastaName);
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:305:25:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                cerr << strlen(seq) << endl;
data/vg-1.27.1+ds/deps/xg/deps/gfakluge/src/tinyFA/tinyfa.hpp:322:26:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    end = min(end, (int) strlen(seq));
data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/block_permutation.hpp:68:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    diff_t write, read;
data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/block_permutation.hpp:69:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    std::tie(write, read) = bp.template decRead<kIsParallel>();
data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/block_permutation.hpp:71:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (read < write) {
data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/block_permutation.hpp:78:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    local_.swap[0].readFrom(begin_ + read);
data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/block_permutation.hpp:91:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    diff_t write, read;
data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/block_permutation.hpp:95:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        std::tie(write, read) = bp.template incWrite<kIsParallel>();
data/vg-1.27.1+ds/deps/xg/deps/ips4o/ips4o/block_permutation.hpp:96:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (write > read) {
data/vg-1.27.1+ds/deps/xg/deps/libhandlegraph/src/include/handlegraph/serializable_handle_graph.hpp:82:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(magic_bytes, 4);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmmultimap.hpp:162:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*)magic.c_str(), 9);
data/vg-1.27.1+ds/deps/xg/deps/mmmultimap/src/mmmultimap.hpp:164:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) &version, sizeof(version));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_count/src/genpatterns.c:47:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    len = strlen(forbid);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_count/src/run_queries_sdsl.cpp:237:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_extract/src/run_queries_sdsl.cpp:233:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/benchmark/indexing_locate/src/run_queries_sdsl.cpp:236:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(stdin)) != 0) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-generated-matchers_test.cc:465:58:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    nested.push_back(list<char>(strings[i], strings[i] + strlen(strings[i])));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googlemock/test/gmock-matchers_test.cc:3933:59:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  int operator()(const char* s) { return static_cast<int>(strlen(s)); }
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2388:10:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  return strncpy(dest, src, n);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/include/gtest/internal/gtest-port.h:2410:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  return static_cast<int>(read(fd, buf, count));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample2.cc:42:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t len = strlen(a_c_string);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/samples/sample2.h:77:36:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    return c_string_ == NULL ? 0 : strlen(c_string_);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:599:33:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t full_regex_len = strlen(regex) + 10;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-port.cc:853:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t len = strlen(regex);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:325:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    PrintCharsAsStringTo(s, strlen(s), os);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest-printers.cc:342:34:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    PrintCharsAsStringTo(s, std::wcslen(s), os);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:857:22:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const int length = strlen(ansi);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:1822:34:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    num_chars = static_cast<int>(wcslen(str));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:3596:32:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      segment = next_segment + strlen("]]>");
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:3762:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  result.reserve(strlen(str) + 1);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:5001:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  const size_t prefix_len = strlen(prefix);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/src/gtest.cc:5397:21:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  else if (temp_dir[strlen(temp_dir) - 1] == '\\')
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/test/gtest-printers_test.cc:876:20:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  EXPECT_TRUE(std::equal(a, a + kSize, numbers.begin()));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/googletest/googletest/xcode/Samples/FrameworkSample/widget.cc:60:3:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  strncpy(buffer, name_.c_str(), max_size-1);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/external/libdivsufsort/examples/sasearch.c:83:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  Psize = strlen(P);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:340:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*data)>>read)<<buffered);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:341:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:343:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:380:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:381:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/coder_fibonacci.hpp:388:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector.hpp:1590:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) p, conf::SDSL_BLOCK_SIZE*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector.hpp:1594:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*) p, ((capacity()>>6)-idx)*sizeof(uint64_t));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:65:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                m_ifile.read((char*) m_buffer.data(), (m_buffersize*width())/8);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:96:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        uint64_t read(const uint64_t idx)
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:414:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    return m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:433:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t x = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:449:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t x = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:465:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t w = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_buffer.hpp:473:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint64_t w = m_int_vector_buffer->read(m_idx);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_io_wrappers.hpp:94:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    in.read((char*)&w, sizeof(uint8_t));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:313:25:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            return std::equal(begin(), end(), v.begin());
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/int_vector_mapper.hpp:359:46:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            return std::string(tmp_file_name,strlen(tmp_file_name));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/io.hpp:103:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*)&t, sizeof(t));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/io.hpp:214:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                in.read((char*)v.data(), file_size);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/io.hpp:224:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    in.read((char*)buf.data(), block_size);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/io.hpp:227:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    uint8_t* end   = begin+read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/k2_treap.hpp:201:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                auto v = read<uint32_t,uint32_t,uint32_t>(bufs);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/k2_treap.hpp:204:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                auto v = read<uint64_t,uint64_t,uint64_t>(bufs);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/k2_treap.hpp:211:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                                            read(std::vector<int_vector_buffer<>*>& bufs)
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/lcp_support_tree2.hpp:295:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        big_lcp_in.read((char*)&y, sizeof(y));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/select_support_mcl.hpp:469:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read((char*) &m_arg_cnt, sizeof(size_type)/sizeof(char));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/wt_helper.hpp:125:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) child, 2*sizeof(child[0]));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/wt_helper.hpp:286:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) m_c_to_leaf, fixed_sigma*sizeof(m_c_to_leaf[0]));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/include/sdsl/wt_helper.hpp:287:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) m_path, fixed_sigma*sizeof(m_path[0]));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:20:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (n + read <= 64) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:21:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (((*d >> read)&bits::lo_set[n]) == bits::lo_set[n])
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:24:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:24:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:25:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            value = 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:27:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            n -= (64-read);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:47:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:48:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:50:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:91:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:92:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:94:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:101:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:102:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:104:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:117:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:118:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:120:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:127:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:128:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:130:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:143:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:144:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:146:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:153:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:154:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_delta.cpp:156:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:20:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (n + read <= 64) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:21:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (((*d >> read)&bits::lo_set[n]) == bits::lo_set[n])
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:24:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:24:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if ((*d >> read) == bits::lo_set[64-read]) {// all bits are set to 1
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:25:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            value = 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:27:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            n -= (64-read);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:47:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:48:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:50:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:76:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:77:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:79:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:86:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:87:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:89:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:102:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:103:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    if (read >= buffered) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:105:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        buffered += 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:112:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:113:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        if (read >= buffered) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_elias_gamma.cpp:115:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            buffered += 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_fibonacci.cpp:23:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    i = bits::cnt11(*d & ~bits::lo_set[read], carry);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_fibonacci.cpp:31:89:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bits_to_decode += ((w-1)<<6) + bits::sel11(*(d+w), n-(i-temp), oldcarry) + 65 - read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_fibonacci.cpp:34:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bits_to_decode = bits::sel11(*d >> read, n)+1;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_fibonacci.cpp:44:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            w |= (((*d)>>read)<<buffered);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_fibonacci.cpp:45:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (read >= buffered) {
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_fibonacci.cpp:47:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                buffered += 64-read;
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/coder_fibonacci.cpp:48:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                bits_to_decode -= (64-read);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/construct_lcp_helper.cpp:90:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            m_stream.read((char*) m_read_buf, m_buffer_size);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/io.cpp:19:18:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    uint64_t n = strlen((const char*)v);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/io.cpp:74:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    in.read(buf, size);
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/memory_management.cpp:630:28:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            auto ps = std::mismatch(ps_str.begin(),ps_str.end(), line.begin());
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/lib/memory_management.cpp:634:28:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            auto pf = std::mismatch(pf_str.begin(),pf_str.end(), line.begin());
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:59:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:81:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:105:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:141:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),vec.begin()));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:165:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),stdvec.begin()));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:190:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivm.begin(),ivm.end(),stdvec.begin()));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:208:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),ivmu.begin()));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:209:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),vec.begin()));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:213:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmu.begin(),ivmu.end(),vec.begin()));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:215:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmu.begin(),ivmu.end(),vec.begin()));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:222:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(ivmc.begin(),ivmc.end(),ivmu.begin()));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:240:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:248:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:254:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(bvm.begin(),bvm.end(),bv.begin()));
data/vg-1.27.1+ds/deps/xg/deps/sdsl-lite/test/int_vector_mapper_test.cpp:277:30:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ASSERT_TRUE(std::equal(tmp_buf.begin(),tmp_buf.end(),vec.begin()));
data/vg-1.27.1+ds/deps/xg/src/xg.cpp:86:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            in.read((char*) &file_version, sizeof(file_version));
data/vg-1.27.1+ds/deps/xg/src/xg.cpp:107:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        in.read((char*) &file_version, sizeof(file_version));
data/vg-1.27.1+ds/src/algorithms/simplify_siblings.cpp:261:40:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            auto mismatch_iters = std::mismatch(reference_string.begin(), reference_string.end(), other_string.begin());
data/vg-1.27.1+ds/src/aligner.cpp:570:77:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    double identity = 1. - (double)(l * match - max_aln.score()) / (match + mismatch) / l;
data/vg-1.27.1+ds/src/aligner.cpp:688:82:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    double identity1 = 1. - (double)(len1 * match - max_aln1.score()) / (match + mismatch) / len1;
data/vg-1.27.1+ds/src/aligner.cpp:691:82:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    double identity2 = 1. - (double)(len2 * match - max_aln2.score()) / (match + mismatch) / len2;
data/vg-1.27.1+ds/src/aligner.cpp:740:56:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    return ((length - min_diffs) * match - min_diffs * mismatch);
data/vg-1.27.1+ds/src/aligner.cpp:751:79:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    double max_score = log_base * ((length - min_diffs) * match - min_diffs * mismatch);
data/vg-1.27.1+ds/src/aligner.cpp:752:94:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    double next_max_score = log_base * ((length - next_min_diffs) * match - next_min_diffs * mismatch);
data/vg-1.27.1+ds/src/aligner.cpp:1291:82:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    int64_t worst_score = (alignment.sequence().size() + total_bases) * -max(max(mismatch, gap_open), gap_extension);
data/vg-1.27.1+ds/src/aligner.cpp:1344:82:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    int64_t worst_score = (alignment.sequence().size() + total_bases) * -max(max(mismatch, gap_open), gap_extension);
data/vg-1.27.1+ds/src/aligner.cpp:1442:13:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    return -mismatch * (seq_end - seq_begin);
data/vg-1.27.1+ds/src/aligner.cpp:1469:34:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                        score -= mismatch * edit.from_length();
data/vg-1.27.1+ds/src/aligner.cpp:1882:82:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    int64_t worst_score = (alignment.sequence().size() + total_bases) * -max(max(mismatch, gap_open), gap_extension);
data/vg-1.27.1+ds/src/aligner.cpp:1935:82:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    int64_t worst_score = (alignment.sequence().size() + total_bases) * -max(max(mismatch, gap_open), gap_extension);
data/vg-1.27.1+ds/src/aligner.cpp:2162:63:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
void AlignerClient::set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, 
data/vg-1.27.1+ds/src/aligner.cpp:2171:26:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            matrix[i] = -mismatch;
data/vg-1.27.1+ds/src/aligner.hpp:269:16:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        int8_t mismatch;
data/vg-1.27.1+ds/src/aligner.hpp:454:56:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        void set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus);
data/vg-1.27.1+ds/src/alignment.cpp:122:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        buffer[strlen(buffer)-1] = '\0';
data/vg-1.27.1+ds/src/alignment.cpp:137:16:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        buffer[strlen(buffer)-1] = '\0';
data/vg-1.27.1+ds/src/alignment.cpp:150:20:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            buffer[strlen(buffer)-1] = '\0';
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:289:50:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    int64_t iter_stop = bottom_diag >= (int64_t) read.length() ? band_height + (int64_t) read.length() - bottom_diag - 1 : band_height;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:289:90:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    int64_t iter_stop = bottom_diag >= (int64_t) read.length() ? band_height + (int64_t) read.length() - bottom_diag - 1 : band_height;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:347:75:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bool beyond_bottom_of_matrix = seed_next_bottom_diag >= (int64_t) read.length();
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:349:82:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        int64_t seed_next_bottom_diag_iter = beyond_bottom_of_matrix ? (int64_t) read.length() - 1 : seed_next_bottom_diag;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:362:119:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            match_score = score_mat[25 * base_quality[seed_next_top_diag_iter] + 5 * nt_table[node_seq[0]] + nt_table[read[seed_next_top_diag_iter]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:365:74:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            match_score = score_mat[5 * nt_table[node_seq[0]] + nt_table[read[seed_next_top_diag_iter]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:417:104:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                match_score = score_mat[25 * base_quality[diag] + 5 * nt_table[node_seq[0]] + nt_table[read[diag]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:420:78:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                match_score = score_mat[5 * nt_table[node_seq[0]] + nt_table[read[diag]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:457:126:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                match_score = score_mat[25 * base_quality[seed_next_bottom_diag_iter] + 5 * nt_table[node_seq[0]] + nt_table[read[seed_next_bottom_diag_iter]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:460:78:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                match_score = score_mat[5 * nt_table[node_seq[0]] + nt_table[read[seed_next_bottom_diag_iter]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:501:53:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        int64_t iter_stop = bottom_diag > (int64_t) read.length() ? band_height + (int64_t) read.length() - bottom_diag - 1 : band_height;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:501:93:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        int64_t iter_stop = bottom_diag > (int64_t) read.length() ? band_height + (int64_t) read.length() - bottom_diag - 1 : band_height;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:505:109:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            match[idx] = max<IntType>(score_mat[25 * base_quality[0] + 5 * nt_table[node_seq[0]] + nt_table[read[0]]], match[idx]);
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:508:170:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            cerr << "[BAMatrix::fill_matrix]: set quality adjusted initial match cell to " << (int) match[idx] << " from node char " << node_seq[0] << ", read char " << read[0] << ", base qual " << (int) base_quality[0] << " for adjusted matrix index " << 25 * base_quality[0] + 5 * nt_table[node_seq[0]] + nt_table[read[0]] << " and score " << (int) score_mat[25 * base_quality[0] + 5 * nt_table[node_seq[0]] + nt_table[read[0]]] << endl;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:508:317:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            cerr << "[BAMatrix::fill_matrix]: set quality adjusted initial match cell to " << (int) match[idx] << " from node char " << node_seq[0] << ", read char " << read[0] << ", base qual " << (int) base_quality[0] << " for adjusted matrix index " << 25 * base_quality[0] + 5 * nt_table[node_seq[0]] + nt_table[read[0]] << " and score " << (int) score_mat[25 * base_quality[0] + 5 * nt_table[node_seq[0]] + nt_table[read[0]]] << endl;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:508:422:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            cerr << "[BAMatrix::fill_matrix]: set quality adjusted initial match cell to " << (int) match[idx] << " from node char " << node_seq[0] << ", read char " << read[0] << ", base qual " << (int) base_quality[0] << " for adjusted matrix index " << 25 * base_quality[0] + 5 * nt_table[node_seq[0]] + nt_table[read[0]] << " and score " << (int) score_mat[25 * base_quality[0] + 5 * nt_table[node_seq[0]] + nt_table[read[0]]] << endl;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:512:100:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
             match[idx] = max<IntType>(match[idx] = score_mat[5 * nt_table[node_seq[0]] + nt_table[read[0]]], match[idx]);
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:525:112:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                match_score = score_mat[25 * base_quality[top_diag + i] + 5 * nt_table[node_seq[0]] + nt_table[read[top_diag + i]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:528:78:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                match_score = score_mat[5 * nt_table[node_seq[0]] + nt_table[read[top_diag + i]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:539:222:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            cerr << "[BAMatrix::fill_matrix]: on left edge of matrix at rectangle coords (" << i << ", " << 0 << "), match score of node char " << 0 << " (" << node_seq[0] << ") and read char " << i + top_diag << " (" << read[i + top_diag] << ") is " << (int) match_score << ", leading gap length is " << top_diag + i << " for total match matrix score of " << (int) match[idx] << endl;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:566:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        bool bottom_diag_outside = bottom_diag + j >= int64_t(read.size());
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:571:73:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        int64_t iter_stop = bottom_diag_outside ? band_height + int64_t(read.size()) - bottom_diag - j - 1 : band_height;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:577:121:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            match_score = score_mat[25 * base_quality[iter_start + top_diag + j] + 5 * nt_table[node_seq[j]] + nt_table[read[iter_start + top_diag + j]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:580:74:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            match_score = score_mat[5 * nt_table[node_seq[j]] + nt_table[read[iter_start + top_diag + j]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:587:245:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            cerr << "[BAMatrix::fill_matrix]: on upper edge of matrix at rectangle coords (" << iter_start << ", " << j << "), match score of node char " << j << " (" << node_seq[j] << ") and read char " << iter_start + top_diag + j << " (" << read[iter_start + top_diag + j] << ") is " << (int) match_score << ", leading gap length is " << cumulative_seq_len + j << " for total match matrix score of " << (int) match[idx] << endl;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:624:116:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                match_score = score_mat[25 * base_quality[i + top_diag + j] + 5 * nt_table[node_seq[j]] + nt_table[read[i + top_diag + j]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:627:78:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                match_score = score_mat[5 * nt_table[node_seq[j]] + nt_table[read[i + top_diag + j]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:639:225:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            cerr << "[BAMatrix::fill_matrix]: in interior of matrix at rectangle coords (" << i << ", " << j << "), match score of node char " << j << " (" << node_seq[j] << ") and read char " << i + top_diag + j << " (" << read[i + top_diag + j] << ") is " << (int) match_score << ", leading gap length is " << cumulative_seq_len + j << " for total match matrix score of " << (int) match[idx] << endl;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:652:128:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                match_score = score_mat[25 * base_quality[iter_stop + top_diag + j - 1] + 5 * nt_table[node_seq[j]] + nt_table[read[iter_stop + top_diag + j - 1]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:655:78:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                match_score = score_mat[5 * nt_table[node_seq[j]] + nt_table[read[iter_stop + top_diag + j - 1]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:690:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    i = bottom_diag + ncols > (int64_t) read.length() ? (int64_t) read.length() - top_diag - ncols : bottom_diag - top_diag;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:690:67:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    i = bottom_diag + ncols > (int64_t) read.length() ? (int64_t) read.length() - top_diag - ncols : bottom_diag - top_diag;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:789:120:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    match_score = score_mat[25 * base_quality[i + top_diag + j] + 5 * nt_table[node_seq[j]] + nt_table[read[i + top_diag + j]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:792:82:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    match_score = score_mat[5 * nt_table[node_seq[j]] + nt_table[read[i + top_diag + j]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:796:262:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                cerr << "[BAMatrix::traceback] transitioning from match, current score " << (int) match[idx] << " match/mismatch score " << (int) match_score << " from node char " << j << " (" << node_seq[j] << ") and read char " << i + top_diag + j << " (" << read[i + top_diag + j] << ")" << endl;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:1214:116:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    match_score = score_mat[25 * base_quality[i + top_diag] + 5 * nt_table[node_seq[j]] + nt_table[read[i + top_diag]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:1217:82:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    match_score = score_mat[5 * nt_table[node_seq[j]] + nt_table[read[i + top_diag]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:1520:124:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        match_score = score_mat[25 * base_quality[i + top_diag + j] + 5 * nt_table[node_seq[j]] + nt_table[read[i + top_diag + j]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:1523:86:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        match_score = score_mat[5 * nt_table[node_seq[j]] + nt_table[read[i + top_diag + j]]];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:1530:141:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        cerr << "[BAMatrix::traceback_over_edge] alignment starts with match, adding read char " << top_diag + i << ": " << read[top_diag + i] << endl;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:1587:134:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            cerr << "[BAMatrix::traceback_over_edge] initial row gaps are present, adding read char " << top_diag + i - 1 << ": " << read[top_diag + i - 1] << endl;
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:1686:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    for (int64_t i = 0; i < (int64_t) read.length(); i++) {
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:1687:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        cerr << read[i];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:1741:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            cerr << read[top_diag + i - 1];
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:1745:68:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (i + j < -top_diag || top_diag + i + j >= (int64_t) read.length()) {
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:1756:74:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    for (int64_t i = bottom_diag; i < min(bottom_diag + ncols, (int64_t) read.length()); i++) {
data/vg-1.27.1+ds/src/banded_global_aligner.cpp:1757:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        cerr << read[i] << "\t";
data/vg-1.27.1+ds/src/gapless_extender.cpp:117:16:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        while (mismatch != this->mismatch_positions.end() && *mismatch < limit) {
data/vg-1.27.1+ds/src/gapless_extender.cpp:117:63:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        while (mismatch != this->mismatch_positions.end() && *mismatch < limit) {
data/vg-1.27.1+ds/src/gapless_extender.cpp:118:32:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            if (read_offset < *mismatch) {
data/vg-1.27.1+ds/src/gapless_extender.cpp:126:56:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            edit.set_sequence(std::string(1, sequence[*mismatch]));
data/vg-1.27.1+ds/src/gapless_extender.cpp:128:15:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            ++mismatch;
data/vg-1.27.1+ds/src/gapless_extender.cpp:176:99:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    extension.score -= static_cast<int32_t>(extension.internal_score * (aligner->match + aligner->mismatch));
data/vg-1.27.1+ds/src/gapless_extender.cpp:400:80:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    std::pair<size_t, size_t> current_interval(extension.read_interval.first, *mismatch);
data/vg-1.27.1+ds/src/gapless_extender.cpp:409:12:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    while (mismatch != extension.mismatch_positions.end()) {
data/vg-1.27.1+ds/src/gapless_extender.cpp:411:38:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        if (current_score >= aligner.mismatch) {
data/vg-1.27.1+ds/src/gapless_extender.cpp:413:38:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            current_score -= aligner.mismatch;
data/vg-1.27.1+ds/src/gapless_extender.cpp:418:11:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        ++mismatch;
data/vg-1.27.1+ds/src/gapless_extender.cpp:430:40:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            current_interval.second = *mismatch;
data/vg-1.27.1+ds/src/genotypekit.cpp:399:68:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        const vector<SnarlTraversal>& traversals, const Alignment& read) const {
data/vg-1.27.1+ds/src/genotypekit.cpp:447:56:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                set<int64_t> common_ids = shared_sites(read, trav);
data/vg-1.27.1+ds/src/genotypekit.cpp:469:46:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    read_path = reverse_path(read.path());
data/vg-1.27.1+ds/src/genotypekit.cpp:472:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    read_path = read.path();
data/vg-1.27.1+ds/src/genotypekit.hpp:59:68:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        const vector<SnarlTraversal>& traversals, const Alignment& read) const = 0;
data/vg-1.27.1+ds/src/genotypekit.hpp:319:68:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        const vector<SnarlTraversal>& traversals, const Alignment& read) const;
data/vg-1.27.1+ds/src/genotyper.cpp:870:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aligned_fwd = allele_graph.align_qual_adjusted(*read, &qa_aligner, mems);
data/vg-1.27.1+ds/src/genotyper.cpp:871:94:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aligned_rev = allele_graph.align_qual_adjusted(reverse_complement_alignment(*read, get_node_size), &qa_aligner, mems);
data/vg-1.27.1+ds/src/genotyper.cpp:874:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aligned_fwd = allele_graph.align(*read, &aligner, mems);
data/vg-1.27.1+ds/src/genotyper.cpp:875:80:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aligned_rev = allele_graph.align(reverse_complement_alignment(*read, get_node_size), &aligner, mems);
data/vg-1.27.1+ds/src/genotyper.cpp:941:40:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                auto difference = std::mismatch(seq.begin(), seq.end(), path_seq.begin());
data/vg-1.27.1+ds/src/genotyper.cpp:947:40:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                auto difference = std::mismatch(seq.rbegin(), seq.rend(), path_seq.rbegin());
data/vg-1.27.1+ds/src/genotyper.cpp:965:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            to_return[read].push_back(affinity);
data/vg-1.27.1+ds/src/genotyper.cpp:984:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        for(auto& affinity : to_return[read]) {
data/vg-1.27.1+ds/src/genotyper.cpp:997:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        for(auto& affinity : to_return[read]) {
data/vg-1.27.1+ds/src/genotyper.cpp:1118:40:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                auto difference = std::mismatch(seq.begin(), seq.end(), path_seq.begin());
data/vg-1.27.1+ds/src/genotyper.cpp:1124:40:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                auto difference = std::mismatch(seq.rbegin(), seq.rend(), path_seq.rbegin());
data/vg-1.27.1+ds/src/genotyper.cpp:1247:61:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        auto read_qual = alignment_qual_score(graph, snarl, read);
data/vg-1.27.1+ds/src/genotyper.cpp:1263:80:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                logprob_wrong = logprob_invert(logprob_invert(phred_to_logprob(read.mapping_quality())) +
data/vg-1.27.1+ds/src/hts_alignment_emitter.cpp:72:5:  [1] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant character.
    strcpy(out_mode, "w");
data/vg-1.27.1+ds/src/index.cpp:205:13:  [1] (obsolete) usleep:
  This C routine is considered obsolete (as opposed to the shell command by
  the same name). The interaction of this function with SIGALRM and other
  timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
  unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
            usleep(10000);
data/vg-1.27.1+ds/src/io/json_stream_helper.hpp:71:22:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            peeked = fgetc(this->_fp);
data/vg-1.27.1+ds/src/mapper.cpp:2318:60:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
void BaseMapper::set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend,
data/vg-1.27.1+ds/src/mapper.cpp:2321:48:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    AlignerClient::set_alignment_scores(match, mismatch, gap_open, gap_extend, full_length_bonus);
data/vg-1.27.1+ds/src/mapper.cpp:4121:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
vector<Alignment> Mapper::make_bands(const Alignment& read, int band_width, int band_overlap, vector<pair<int, int>>& to_strip) {
data/vg-1.27.1+ds/src/mapper.cpp:4122:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    int segment_size = min((int)read.sequence().size(), band_width);
data/vg-1.27.1+ds/src/mapper.cpp:4125:62:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        cerr << "Segment size be " << segment_size << "/" << read.sequence().size() << endl;
data/vg-1.27.1+ds/src/mapper.cpp:4132:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while (offset+segment_size < read.sequence().size()) {
data/vg-1.27.1+ds/src/mapper.cpp:4142:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    if (offset < read.sequence().size()) {
data/vg-1.27.1+ds/src/mapper.cpp:4143:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        start_positions.push_back(read.sequence().size()-segment_size);
data/vg-1.27.1+ds/src/mapper.cpp:4164:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        aln.set_name(read.name());
data/vg-1.27.1+ds/src/mapper.cpp:4165:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        aln.set_sequence(read.sequence().substr(p, segment_size));
data/vg-1.27.1+ds/src/mapper.cpp:4166:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (!read.quality().empty()) aln.set_quality(read.quality().substr(p, segment_size));
data/vg-1.27.1+ds/src/mapper.cpp:4166:54:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        if (!read.quality().empty()) aln.set_quality(read.quality().substr(p, segment_size));
data/vg-1.27.1+ds/src/mapper.cpp:4172:57:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
vector<Alignment> Mapper::align_banded(const Alignment& read, int kmer_size, int stride, int max_mem_length, int band_width, int band_overlap, bool xdrop_alignment) {
data/vg-1.27.1+ds/src/mapper.cpp:4174:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    auto aligner = get_aligner(!read.quality().empty());
data/vg-1.27.1+ds/src/mapper.cpp:4211:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    vector<Alignment> bands = make_bands(read, band_width, band_overlap, to_strip);
data/vg-1.27.1+ds/src/mapper.cpp:4283:54:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    vector<Alignment> alignments = chainer.traceback(read, total_multimaps, false, debug);
data/vg-1.27.1+ds/src/mapper.cpp:4293:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        alignments.push_back(read);
data/vg-1.27.1+ds/src/mapper.cpp:5032:67:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
vector<Alignment> AlignmentChainModel::traceback(const Alignment& read, int alt_alns, bool paired, bool debug) {
data/vg-1.27.1+ds/src/mapper.cpp:5106:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        merged.set_quality(read.quality());
data/vg-1.27.1+ds/src/mapper.cpp:5107:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        merged.set_name(read.name());
data/vg-1.27.1+ds/src/mapper.hpp:88:50:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    vector<Alignment> traceback(const Alignment& read, int alt_alns, bool paired, bool debug);
data/vg-1.27.1+ds/src/mapper.hpp:210:52:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    void set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus,
data/vg-1.27.1+ds/src/mapper.hpp:461:53:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    vector<Alignment> align_banded(const Alignment& read,
data/vg-1.27.1+ds/src/mapper.hpp:502:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    vector<Alignment> make_bands(const Alignment& read, int band_width, int band_overlap, vector<pair<int, int>>& to_strip);
data/vg-1.27.1+ds/src/mapper.hpp:567:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    Alignment align(const Alignment& read,
data/vg-1.27.1+ds/src/minimizer_mapper.cpp:2977:43:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    return n * (aligner->match + aligner->mismatch);
data/vg-1.27.1+ds/src/multipath_alignment_graph.cpp:3396:51:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    - (graph_dist > 0) * aligner->mismatch;
data/vg-1.27.1+ds/src/multipath_alignment_graph.cpp:3403:50:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    - (read_dist > 0) * aligner->mismatch;
data/vg-1.27.1+ds/src/multipath_alignment_graph.cpp:3407:112:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    edge_weights[make_pair(i, edge.first)] = -((graph_dist > 0) + (graph_dist > 1)) * aligner->mismatch;
data/vg-1.27.1+ds/src/multipath_mapper.cpp:889:69:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    void MultipathMapper::set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend,
data/vg-1.27.1+ds/src/multipath_mapper.cpp:891:52:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        AlignerClient::set_alignment_scores(match, mismatch, gap_open, gap_extend, full_length_bonus);
data/vg-1.27.1+ds/src/multipath_mapper.hpp:107:56:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        void set_alignment_scores(int8_t match, int8_t mismatch, int8_t gap_open, int8_t gap_extend, int8_t full_length_bonus);
data/vg-1.27.1+ds/src/path.cpp:15:55:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    if (path_name.length() < prefix.length() || !std::equal(prefix.begin(), prefix.end(), path_name.begin())) {
data/vg-1.27.1+ds/src/readfilter.cpp:491:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ++counts.counts[Counts::FilterName::read];
data/vg-1.27.1+ds/src/readfilter.cpp:772:57:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
       << counts.counts[ReadFilter::Counts::FilterName::read] << endl
data/vg-1.27.1+ds/src/readfilter.hpp:189:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool sample_read(const Alignment& read);
data/vg-1.27.1+ds/src/snarl_caller.cpp:671:14:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    if (std::equal(genotype.begin() + 1, genotype.end(), genotype.begin())) {
data/vg-1.27.1+ds/src/srpe.cpp:73:54:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    void SRPE::aln_to_bseq(Alignment& a, fml_seq1_t* read){
data/vg-1.27.1+ds/src/srpe.hpp:158:56:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            void aln_to_bseq(Alignment& a, fml_seq1_t* read);
data/vg-1.27.1+ds/src/ssw_aligner.cpp:21:43:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                                          mismatch,
data/vg-1.27.1+ds/src/ssw_aligner.hpp:23:11:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        , mismatch(_mismatch)
data/vg-1.27.1+ds/src/ssw_aligner.hpp:30:13:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    uint8_t mismatch;
data/vg-1.27.1+ds/src/stream_index.cpp:591:14:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    if (std::equal(MAGIC_BYTES.begin(), MAGIC_BYTES.end(), buffer)) {
data/vg-1.27.1+ds/src/subcommand/align_main.cpp:205:44:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        SSWAligner ssw = SSWAligner(match, mismatch, gap_open, gap_extend);
data/vg-1.27.1+ds/src/subcommand/align_main.cpp:221:40:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                    score_matrix[i] = -mismatch;
data/vg-1.27.1+ds/src/subcommand/crash_main.cpp:102:17:  [1] (obsolete) usleep:
  This C routine is considered obsolete (as opposed to the shell command by
  the same name). The interaction of this function with SIGALRM and other
  timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
  unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
                usleep(1);
data/vg-1.27.1+ds/src/subcommand/crash_main.cpp:111:17:  [1] (obsolete) usleep:
  This C routine is considered obsolete (as opposed to the shell command by
  the same name). The interaction of this function with SIGALRM and other
  timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
  unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
                usleep(1);
data/vg-1.27.1+ds/src/subcommand/map_main.cpp:833:44:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            m->set_alignment_scores(match, mismatch, gap_open, gap_extend, full_length_bonus, haplotype_consistency_exponent);
data/vg-1.27.1+ds/src/subcommand/msga_main.cpp:675:49:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
            mapper->set_alignment_scores(match, mismatch, gap_open, gap_extend, full_length_bonus);
data/vg-1.27.1+ds/src/subcommand/paths_main.cpp:353:67:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                if (name.length() >= path_prefix.length() && std::equal(path_prefix.begin(), path_prefix.end(), name.begin())) {
data/vg-1.27.1+ds/src/subcommand/sim_main.cpp:786:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                read.set_score(aligner.score_contiguous_alignment(read, strip_bonuses));
data/vg-1.27.1+ds/src/subcommand/sim_main.cpp:786:67:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                read.set_score(aligner.score_contiguous_alignment(read, strip_bonuses));
data/vg-1.27.1+ds/src/subcommand/sim_main.cpp:789:62:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    alignment_emitter->emit_single(std::move(read));
data/vg-1.27.1+ds/src/subcommand/sim_main.cpp:793:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    cout << read.sequence() << endl;
data/vg-1.27.1+ds/src/unittest/aligner.cpp:45:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln1.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/aligner.cpp:46:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln2.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/aligner.cpp:82:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln1.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/aligner.cpp:83:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln2.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/aligner.cpp:118:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln1.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/aligner.cpp:119:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln2.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/aligner.cpp:146:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln1.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/aligner.cpp:147:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln2.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/aligner.cpp:187:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln1.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/aligner.cpp:188:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln2.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/aligner.cpp:237:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln1.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/aligner.cpp:238:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln2.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/aligner.cpp:281:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln1.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/aligner.cpp:282:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln2.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/aligner.cpp:325:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln1.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/aligner.cpp:326:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln2.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:43:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:93:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:143:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:197:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:255:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:313:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:371:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:429:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:488:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:544:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:598:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:652:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:706:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:756:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:798:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:848:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:890:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:932:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:982:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1029:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1071:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1117:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1165:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1215:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1267:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1323:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1363:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1415:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1477:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1529:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1575:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln_full.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1580:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln_reduced.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1657:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1704:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1749:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1846:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:1899:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2007:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2111:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2230:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2314:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2355:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2390:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2425:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2469:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2501:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2559:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2611:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2667:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2721:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2737:69:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                REQUIRE(aln.path().mapping(0).edit(0).sequence() == read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2764:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2797:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2851:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2900:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2916:69:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                REQUIRE(aln.path().mapping(0).edit(0).sequence() == read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2938:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2959:70:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                REQUIRE((aln.path().mapping(0).edit(0).sequence() == read) != (aln.path().mapping(1).edit(0).sequence() == read));
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2959:124:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                REQUIRE((aln.path().mapping(0).edit(0).sequence() == read) != (aln.path().mapping(1).edit(0).sequence() == read));
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:2982:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:3003:70:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                REQUIRE((aln.path().mapping(0).edit(0).sequence() == read) != (aln.path().mapping(1).edit(0).sequence() == read));
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:3003:124:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                REQUIRE((aln.path().mapping(0).edit(0).sequence() == read) != (aln.path().mapping(1).edit(0).sequence() == read));
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:3011:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:3053:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:3130:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:3168:93:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    is_second_opt = is_second_opt && (path.mapping(0).edit(0).sequence() == read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:3215:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:3269:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:3328:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:3385:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:3431:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/banded_global_aligner.cpp:3490:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/catch.hpp:8404:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        return s.size() >= prefix.size() && std::equal(prefix.begin(), prefix.end(), s.begin());
data/vg-1.27.1+ds/src/unittest/catch.hpp:8410:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        return s.size() >= suffix.size() && std::equal(suffix.rbegin(), suffix.rend(), s.rbegin());
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:116:56:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    expected_score -= extension.mismatches() * aligner.mismatch;
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:188:95:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void full_length_match(const std::vector<std::pair<pos_t, size_t>>& seeds, const std::string& read, const std::vector<std::pair<pos_t, std::string>>& correct_alignment, const GaplessExtender& extender, size_t error_bound, bool check_seeds) {
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:193:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    auto result = extender.extend(cluster, read, nullptr, error_bound);
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:208:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        paths_match(result.front().to_path(*(extender.graph), read), get_path(correct_alignment));
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:219:97:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void full_length_matches(const std::vector<std::pair<pos_t, size_t>>& seeds, const std::string& read, const std::vector<std::vector<std::pair<pos_t, std::string>>>& correct_alignments, const GaplessExtender& extender, size_t error_bound, double overlap_threshold) {
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:224:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    auto result = extender.extend(cluster, read, nullptr, error_bound, overlap_threshold);
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:232:58:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        paths_match(result[i].to_path(*(extender.graph), read), get_path(correct_alignments[i]));
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:236:93:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void partial_matches(const std::vector<std::pair<pos_t, size_t>>& seeds, const std::string& read, const std::vector<std::vector<std::pair<pos_t, std::string>>>& correct_extensions, const std::vector<size_t>& correct_offsets, const GaplessExtender& extender, size_t error_bound) {
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:241:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    auto result = extender.extend(cluster, read, nullptr, error_bound);
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:251:58:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        paths_match(result[i].to_path(*(extender.graph), read), get_path(correct_extensions[i]));
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:616:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        full_length_match(seeds, read, correct_alignment, extender, error_bound, true);
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:633:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        full_length_match(seeds, read, correct_alignment, extender, error_bound, true);
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:651:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        full_length_match(seeds, read, correct_alignment, extender, error_bound, false);
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:667:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        full_length_match(seeds, read, correct_alignment, extender, error_bound, true);
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:677:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        full_length_match(seeds, read, { }, extender, error_bound, false);
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:702:36:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        full_length_matches(seeds, read, correct_alignments, extender, error_bound, overlap_threshold);
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:721:36:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        full_length_matches(seeds, read, correct_alignments, extender, error_bound, overlap_threshold);
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:782:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        partial_matches(seeds, read, correct_extensions, correct_offsets, extender, error_bound);
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:801:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        partial_matches(seeds, read, correct_extensions, correct_offsets, extender, error_bound);
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:820:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        partial_matches(seeds, read, correct_extensions, correct_offsets, extender, error_bound);
data/vg-1.27.1+ds/src/unittest/gapless_extender.cpp:840:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        partial_matches(seeds, read, correct_extensions, correct_offsets, extender, error_bound);
data/vg-1.27.1+ds/src/unittest/mapper.cpp:61:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/mcmc_genotyper.cpp:54:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/mcmc_genotyper.cpp:131:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/mcmc_genotyper.cpp:365:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment.cpp:45:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment.cpp:88:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment.cpp:163:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment.cpp:201:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment.cpp:263:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment.cpp:339:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment.cpp:425:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment.cpp:503:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment.cpp:606:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment.cpp:781:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment.cpp:910:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment.cpp:1079:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment.cpp:1280:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment.cpp:1326:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                multipath_aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment_graph.cpp:54:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    string read("GATTACAA");
data/vg-1.27.1+ds/src/unittest/multipath_alignment_graph.cpp:59:24:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    query.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment_graph.cpp:205:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            REQUIRE(out.sequence() == read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment_graph.cpp:242:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            REQUIRE(out.sequence() == read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment_graph.cpp:298:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            REQUIRE(out.sequence() == read);
data/vg-1.27.1+ds/src/unittest/multipath_alignment_graph.cpp:335:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            REQUIRE(out.sequence() == read);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:46:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    string read("GATTACA");
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:55:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.begin(), make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:55:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.begin(), make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:65:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.begin() + 1, make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:65:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.begin() + 1, make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:75:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.end(), make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:75:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.end(), make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:80:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        REQUIRE(covered == read.size());
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:85:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.begin() + 5, make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:85:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.begin() + 5, make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:88:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin() + 2, read.end(), make_pair(6, 6), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:88:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin() + 2, read.end(), make_pair(6, 6), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:95:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        REQUIRE(covered == read.size());
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:100:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.begin() + 3, make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:100:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.begin() + 3, make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:102:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin() + 3, read.end(), make_pair(6, 6), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:102:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin() + 3, read.end(), make_pair(6, 6), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:109:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        REQUIRE(covered == read.size());
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:182:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.begin() + 3, make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:182:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.begin() + 3, make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:219:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.begin() + 3, make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:219:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.begin() + 3, make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:221:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin() + 3, read.end(), make_pair(6, 6), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:221:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin() + 3, read.end(), make_pair(6, 6), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:256:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.begin() + 3, make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:256:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin(), read.begin() + 3, make_pair(5, 5), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:258:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin() + 3, read.end(), make_pair(6, 6), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:258:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        mems.emplace_back(read.begin() + 3, read.end(), make_pair(6, 6), 1);
data/vg-1.27.1+ds/src/unittest/multipath_mapper.cpp:336:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:41:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:98:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:154:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:217:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:276:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:336:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:396:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:451:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:505:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:565:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:629:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:693:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:757:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:809:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:840:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:883:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:943:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1003:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1053:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1114:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1164:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1225:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1294:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1361:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1416:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1486:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1556:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1622:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1694:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1761:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1827:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1893:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:1966:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:2013:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:2056:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:2157:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:2199:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:2236:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:2346:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:2471:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:2488:67:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        REQUIRE(path_to_length(alt_aln.path()) == read.size());
data/vg-1.27.1+ds/src/unittest/pinned_alignment.cpp:2515:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/seed_clusterer.cpp:1805:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                for (size_t read = 0 ; read < 2 ; read ++) {
data/vg-1.27.1+ds/src/unittest/seed_clusterer.cpp:1822:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        all_seeds[read].push_back({ pos, 0, std::get<0>(chain_info), std::get<1>(chain_info), std::get<2>(chain_info),
data/vg-1.27.1+ds/src/unittest/splicing.cpp:1685:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/surject.cpp:48:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    Alignment read;
data/vg-1.27.1+ds/src/unittest/surject.cpp:50:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    Path* rpath = read.mutable_path();
data/vg-1.27.1+ds/src/unittest/surject.cpp:61:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read.set_sequence(seq);
data/vg-1.27.1+ds/src/unittest/surject.cpp:63:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read.set_score(Aligner().score_contiguous_alignment(read));
data/vg-1.27.1+ds/src/unittest/surject.cpp:63:57:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read.set_score(Aligner().score_contiguous_alignment(read));
data/vg-1.27.1+ds/src/unittest/surject.cpp:66:45:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    Alignment surjected = surjector.surject(read, path_names, true, true);
data/vg-1.27.1+ds/src/unittest/surject.cpp:78:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(surjected.score() == read.score() - Aligner().mismatch - Aligner().match);
data/vg-1.27.1+ds/src/unittest/surject.cpp:112:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(rev_surjected.score() == read.score() - Aligner().mismatch - Aligner().match);
data/vg-1.27.1+ds/src/unittest/variant_adder.cpp:365:49:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                REQUIRE(match1.from_length() == strlen("GCGCAAAAAAAAAAA"));
data/vg-1.27.1+ds/src/unittest/variant_adder.cpp:375:49:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
                REQUIRE(match2.from_length() == strlen("AAAAAAAAAAGCGC"));
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:40:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:48:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.score() == read.size());
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:79:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:88:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.score() == read.size());
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:120:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:133:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.score() == read.size());
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:162:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:175:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    size_t expected_score = read.size() + 10 * 1;
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:199:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:206:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    size_t expected_score = read.size() + 10 * 1;
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:230:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:239:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        REQUIRE(aln.score() == read.size());
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:286:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:293:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.score() == read.size() + 10 - 1 - 4);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:358:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:366:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.score() == read.size() + 10 - 6 - 50);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:381:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:395:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.score() == read.size() + 10 - 6 - 15 - 16);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:418:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:426:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.score() == read.size() + 10 - 1 - 4);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:457:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:465:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.score() == read.size() + 10 - 2 * 1 - 6);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:474:60:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.path().mapping(0).edit(1).from_length() == read.size());
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:475:58:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.path().mapping(0).edit(1).to_length() == read.size());
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:491:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:500:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.score() == read.size() - 1 + 10 - 6);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:510:60:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.path().mapping(0).edit(1).from_length() == read.size() - 1);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:511:58:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.path().mapping(0).edit(1).to_length() == read.size() - 1);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:527:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:535:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.score() == read.size() + 10 - 6);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:545:60:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.path().mapping(0).edit(1).from_length() == read.size());
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:546:58:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.path().mapping(0).edit(1).to_length() == read.size());
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:562:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:571:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.score() == read.size() - 1 + 10 - 6);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:578:60:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.path().mapping(0).edit(0).from_length() == read.size() - 1);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:579:58:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.path().mapping(0).edit(0).to_length() == read.size() - 1);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:602:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:613:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.sequence() == read);
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:621:58:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.path().mapping(0).edit(0).to_length() == read.size());
data/vg-1.27.1+ds/src/unittest/xdrop_aligner.cpp:622:57:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    REQUIRE(aln.path().mapping(0).edit(0).sequence() == read);
data/vg-1.27.1+ds/src/variant_adder.cpp:749:68:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                mapper.set_alignment_scores(aligner.match, aligner.mismatch, aligner.gap_open, aligner.gap_extension,
data/vg-1.27.1+ds/src/vg.cpp:4503:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    edit->set_from_length(read.size());
data/vg-1.27.1+ds/src/vg.cpp:4504:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    edit->set_to_length(read.size());
data/vg-1.27.1+ds/src/vg.cpp:4505:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while (read.size() < read_len) {
data/vg-1.27.1+ds/src/vg.cpp:4515:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        read.append(addition);
data/vg-1.27.1+ds/src/vg.cpp:4525:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    aln.set_sequence(read);
data/vg-1.27.1+ds/src/vg.cpp:4527:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read = read.substr(0, read_len);

ANALYSIS SUMMARY:

Hits = 4885
Lines analyzed = 1806567 in approximately 40.14 seconds (45012 lines/second)
Physical Source Lines of Code (SLOC) = 1265166
Hits@level = [0] 4107 [1] 2446 [2] 1603 [3] 538 [4] 298 [5]   0
Hits@level+ = [0+] 8992 [1+] 4885 [2+] 2439 [3+] 836 [4+] 298 [5+]   0
Hits/KSLOC@level+ = [0+] 7.10737 [1+] 3.86115 [2+] 1.92781 [3+] 0.660783 [4+] 0.235542 [5+]   0
Dot directories skipped = 2 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.