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/seqan2-2.4.0+dfsg/apps/alf/alf.cpp Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.h Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/bisar_base.h Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/bisar_score.h Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/bisar_score_data.h Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar_alphabets.h Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar_calling.h Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar_consensus_realign.h Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar_realignment.h Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar_score.h Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar_score_data.h Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar_util.h Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp Examining data/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.h Examining data/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp Examining data/seqan2-2.4.0+dfsg/apps/fiona/compute_gain.cpp Examining data/seqan2-2.4.0+dfsg/apps/fiona/error_rate_from_sam.cpp Examining data/seqan2-2.4.0+dfsg/apps/fiona/fiona.cpp Examining data/seqan2-2.4.0+dfsg/apps/fiona/index_qgram_parallel.h Examining data/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp Examining data/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp Examining data/seqan2-2.4.0+dfsg/apps/gustaf/create_stellarmatches_from_file.h Examining data/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp Examining data/seqan2-2.4.0+dfsg/apps/gustaf/gustaf_matepairs.h Examining data/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp Examining data/seqan2-2.4.0+dfsg/apps/gustaf/msplazer.h Examining data/seqan2-2.4.0+dfsg/apps/gustaf/msplazer_algorithms.h Examining data/seqan2-2.4.0+dfsg/apps/gustaf/msplazer_main.h Examining data/seqan2-2.4.0+dfsg/apps/gustaf/msplazer_out.h Examining data/seqan2-2.4.0+dfsg/apps/gustaf/msplazer_parse_options.h Examining data/seqan2-2.4.0+dfsg/apps/gustaf/stellar_routines.h Examining data/seqan2-2.4.0+dfsg/apps/insegt/base.h Examining data/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h Examining data/seqan2-2.4.0+dfsg/apps/insegt/fusion.h Examining data/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp Examining data/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h Examining data/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.h Examining data/seqan2-2.4.0+dfsg/apps/mason2/fragment_generation.h Examining data/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h Examining data/seqan2-2.4.0+dfsg/apps/mason2/individual_genome.h Examining data/seqan2-2.4.0+dfsg/apps/mason2/mason_frag_sequencing.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/mason_genome.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/mason_materializer.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/mason_methylation.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h Examining data/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/mason_splicing.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/mason_types.h Examining data/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h Examining data/seqan2-2.4.0+dfsg/apps/mason2/omp_wrapper.h Examining data/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h Examining data/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h Examining data/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/variation_size_tsv.h Examining data/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp Examining data/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h Examining data/seqan2-2.4.0+dfsg/apps/micro_razers/micro_razers.cpp Examining data/seqan2-2.4.0+dfsg/apps/micro_razers/outputFormat.h Examining data/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.h Examining data/seqan2-2.4.0+dfsg/apps/ngs_roi/png_canvas.h Examining data/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp Examining data/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h Examining data/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp Examining data/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h Examining data/seqan2-2.4.0+dfsg/apps/ngs_roi/record_ext.h Examining data/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_builder.cpp Examining data/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_builder.h Examining data/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp Examining data/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp Examining data/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp Examining data/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp Examining data/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp Examining data/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp Examining data/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h Examining data/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp Examining data/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp Examining data/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp Examining data/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp Examining data/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h Examining data/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp Examining data/seqan2-2.4.0+dfsg/apps/rabema/find_hamming_simple_ext.h Examining data/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_ext.h Examining data/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h Examining data/seqan2-2.4.0+dfsg/apps/rabema/io_gsi.h Examining data/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp Examining data/seqan2-2.4.0+dfsg/apps/rabema/rabema.cpp Examining data/seqan2-2.4.0+dfsg/apps/rabema/rabema.h Examining data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp Examining data/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp Examining data/seqan2-2.4.0+dfsg/apps/rabema/rabema_stats.h Examining data/seqan2-2.4.0+dfsg/apps/rabema/ref_id_mapping.h Examining data/seqan2-2.4.0+dfsg/apps/rabema/sorting.h Examining data/seqan2-2.4.0+dfsg/apps/razers/outputFormat.h Examining data/seqan2-2.4.0+dfsg/apps/razers/paramChooser.h Examining data/seqan2-2.4.0+dfsg/apps/razers/param_tabs.cpp Examining data/seqan2-2.4.0+dfsg/apps/razers/param_tabs.h Examining data/seqan2-2.4.0+dfsg/apps/razers/razers.cpp Examining data/seqan2-2.4.0+dfsg/apps/razers/razers.h Examining data/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h Examining data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h Examining data/seqan2-2.4.0+dfsg/apps/razers/readSimulator.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/compPHSens.cpp Examining data/seqan2-2.4.0+dfsg/apps/razers3/job_queue.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/parallel_job_queue.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/parallel_misc.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/parallel_store.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/paramChooser.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/param_tabs.cpp Examining data/seqan2-2.4.0+dfsg/apps/razers3/param_tabs.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/profile_timeline.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp Examining data/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp Examining data/seqan2-2.4.0+dfsg/apps/razers3/razers.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/razers_window.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/readSimulator.h Examining data/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp Examining data/seqan2-2.4.0+dfsg/apps/rep_sep/assembly_parser.h Examining data/seqan2-2.4.0+dfsg/apps/rep_sep/column_scanner.h Examining data/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp Examining data/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph.h Examining data/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_base.h Examining data/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_construction.h Examining data/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_heuristics.h Examining data/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_score.h Examining data/seqan2-2.4.0+dfsg/apps/rep_sep/utils.h Examining data/seqan2-2.4.0+dfsg/apps/sak/sak.cpp Examining data/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp Examining data/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp Examining data/seqan2-2.4.0+dfsg/apps/searchjoin/db.h Examining data/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h Examining data/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp Examining data/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp Examining data/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h Examining data/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h Examining data/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp Examining data/seqan2-2.4.0+dfsg/apps/seqcons2/seqcons.cpp Examining data/seqan2-2.4.0+dfsg/apps/seqcons2/seqcons_app.cpp Examining data/seqan2-2.4.0+dfsg/apps/seqcons2/seqcons_app.h Examining data/seqan2-2.4.0+dfsg/apps/seqcons2/seqcons_options.cpp Examining data/seqan2-2.4.0+dfsg/apps/seqcons2/seqcons_options.h Examining data/seqan2-2.4.0+dfsg/apps/sgip/sgip.cpp Examining data/seqan2-2.4.0+dfsg/apps/sgip/sgip.h Examining data/seqan2-2.4.0+dfsg/apps/sgip/sgip_base.h Examining data/seqan2-2.4.0+dfsg/apps/sgip/sgip_output.h Examining data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp Examining data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.h Examining data/seqan2-2.4.0+dfsg/apps/splazers/outputFormat.h Examining data/seqan2-2.4.0+dfsg/apps/splazers/paramChooser.h Examining data/seqan2-2.4.0+dfsg/apps/splazers/razers.h Examining data/seqan2-2.4.0+dfsg/apps/splazers/razers_matepairs.h Examining data/seqan2-2.4.0+dfsg/apps/splazers/razers_parallel.h Examining data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h Examining data/seqan2-2.4.0+dfsg/apps/splazers/readSimulator.h Examining data/seqan2-2.4.0+dfsg/apps/splazers/splazers.cpp Examining data/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp Examining data/seqan2-2.4.0+dfsg/apps/stellar/stellar.h Examining data/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h Examining data/seqan2-2.4.0+dfsg/apps/stellar/stellar_output.h Examining data/seqan2-2.4.0+dfsg/apps/stellar/stellar_types.h Examining data/seqan2-2.4.0+dfsg/apps/tree_recon/tree_recon.cpp Examining data/seqan2-2.4.0+dfsg/apps/yara/basic_alphabet.h Examining data/seqan2-2.4.0+dfsg/apps/yara/bits_bucket.h Examining data/seqan2-2.4.0+dfsg/apps/yara/bits_context.h Examining data/seqan2-2.4.0+dfsg/apps/yara/bits_hits.h Examining data/seqan2-2.4.0+dfsg/apps/yara/bits_matches.h Examining data/seqan2-2.4.0+dfsg/apps/yara/bits_reads.h Examining data/seqan2-2.4.0+dfsg/apps/yara/bits_seeds.h Examining data/seqan2-2.4.0+dfsg/apps/yara/file_pair.h Examining data/seqan2-2.4.0+dfsg/apps/yara/file_prefetched.h Examining data/seqan2-2.4.0+dfsg/apps/yara/find_extender.h Examining data/seqan2-2.4.0+dfsg/apps/yara/find_verifier.h Examining data/seqan2-2.4.0+dfsg/apps/yara/index_fm.h Examining data/seqan2-2.4.0+dfsg/apps/yara/indexer.cpp Examining data/seqan2-2.4.0+dfsg/apps/yara/mapper.cpp Examining data/seqan2-2.4.0+dfsg/apps/yara/mapper.h Examining data/seqan2-2.4.0+dfsg/apps/yara/mapper_aligner.h Examining data/seqan2-2.4.0+dfsg/apps/yara/mapper_classifier.h Examining data/seqan2-2.4.0+dfsg/apps/yara/mapper_collector.h Examining data/seqan2-2.4.0+dfsg/apps/yara/mapper_extender.h Examining data/seqan2-2.4.0+dfsg/apps/yara/mapper_filter.h Examining data/seqan2-2.4.0+dfsg/apps/yara/mapper_ranker.h Examining data/seqan2-2.4.0+dfsg/apps/yara/mapper_verifier.h Examining data/seqan2-2.4.0+dfsg/apps/yara/mapper_writer.h Examining data/seqan2-2.4.0+dfsg/apps/yara/misc_options.h Examining data/seqan2-2.4.0+dfsg/apps/yara/misc_tags.h Examining data/seqan2-2.4.0+dfsg/apps/yara/misc_timer.h Examining data/seqan2-2.4.0+dfsg/apps/yara/misc_types.h Examining data/seqan2-2.4.0+dfsg/apps/yara/store_seqs.h Examining data/seqan2-2.4.0+dfsg/demos/blast/blast_in_lowlevel.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/align/align.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/align/compute_alignment_stats.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/align/gaps_example.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/align/global_alignment_banded.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/align/global_alignment_unbanded.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/align/integrate_align.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/align_extend/extend_alignment.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_frac_score.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/align_split/split_alignment.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/arg_parse/argument_parser.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_tags_dict.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/basic/enable_if.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/basic/metaprogramming_control.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/basic/metaprogramming_logic.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/basic/metaprogramming_math.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/basic/metaprogramming_switch.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/basic/simple_type_construction.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/basic/zip_iterator.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/bed_io/UNUSED_bed_stream_read.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/consensus/consensus_alignment.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/find/finder_aho_corasick.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/find/finder_online.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/gff_io/UNUSED_gff_stream_read.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/all_pairs_shortest_path.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/bellman_ford_algorithm.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/breadth_first_search.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/dag_shortest_path.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/depth_first_search.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/dijkstra.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/floyd_warshall_algorithm.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/ford_fulkerson_algorithm.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/heaviest_increasing_subsequence.cpp Examining data/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/kruskals_algorithm.cpp Examining 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data/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp Examining data/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp Examining data/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.h Examining data/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled_iterator.h Examining data/seqan2-2.4.0+dfsg/tests/simd/test_simd_vector.cpp Examining data/seqan2-2.4.0+dfsg/tests/simd/test_simd_vector.h Examining data/seqan2-2.4.0+dfsg/tests/simple_intervals_io/test_simple_intervals_io.cpp Examining data/seqan2-2.4.0+dfsg/tests/statistics/test_statistics.cpp Examining data/seqan2-2.4.0+dfsg/tests/statistics/test_statistics_base.h Examining data/seqan2-2.4.0+dfsg/tests/statistics/test_statistics_markov_model.h Examining data/seqan2-2.4.0+dfsg/tests/store/test_store.cpp Examining data/seqan2-2.4.0+dfsg/tests/store/test_store_io.h Examining data/seqan2-2.4.0+dfsg/tests/store/test_store_io_bam.h Examining data/seqan2-2.4.0+dfsg/tests/stream/test_stream.cpp Examining data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h Examining data/seqan2-2.4.0+dfsg/tests/stream/test_stream_generic.h Examining data/seqan2-2.4.0+dfsg/tests/stream/test_stream_lexical_cast.h Examining data/seqan2-2.4.0+dfsg/tests/stream/test_stream_tokenization.h Examining data/seqan2-2.4.0+dfsg/tests/stream/test_stream_virtual_stream.h Examining data/seqan2-2.4.0+dfsg/tests/stream/test_stream_write.h Examining data/seqan2-2.4.0+dfsg/tests/swift_local/test_find_swift.cpp Examining data/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp Examining data/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.h Examining data/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp Examining data/seqan2-2.4.0+dfsg/tests/translation/test_translation.h Examining data/seqan2-2.4.0+dfsg/tests/ucsc_io/test_ucsc_io.cpp Examining data/seqan2-2.4.0+dfsg/tests/vcf_io/test_vcf_io.cpp Examining data/seqan2-2.4.0+dfsg/tests/vcf_io/test_vcf_io.h Examining data/seqan2-2.4.0+dfsg/util/cmake/GetCurrentDate.cpp Examining data/seqan2-2.4.0+dfsg/util/makefile_project/src/main.cpp Examining data/seqan2-2.4.0+dfsg/util/raw_cmake_project/src/main.cpp Examining data/seqan2-2.4.0+dfsg/util/skel/app_template/app.cpp Examining data/seqan2-2.4.0+dfsg/util/skel/demo_template/demo.cpp Examining data/seqan2-2.4.0+dfsg/util/skel/header_template/header.h Examining data/seqan2-2.4.0+dfsg/util/skel/header_template/library_header.h Examining data/seqan2-2.4.0+dfsg/util/skel/module_template/header.h Examining data/seqan2-2.4.0+dfsg/util/skel/module_template/module.h Examining data/seqan2-2.4.0+dfsg/util/skel/test_template/test.cpp Examining data/seqan2-2.4.0+dfsg/util/skel/test_template/test.h FINAL RESULTS: data/seqan2-2.4.0+dfsg/apps/razers3/profile_timeline.h:170:5: [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(pathBuffer, path); data/seqan2-2.4.0+dfsg/apps/razers3/profile_timeline.h:181:9: [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(pathBuffer, buffer); data/seqan2-2.4.0+dfsg/include/seqan/arg_parse/arg_parse_version_check.h:154:14: [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. if (!system("wget --version > /dev/null 2>&1")) data/seqan2-2.4.0+dfsg/include/seqan/arg_parse/arg_parse_version_check.h:156:19: [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. else if (!system("curl --version > /dev/null 2>&1")) data/seqan2-2.4.0+dfsg/include/seqan/arg_parse/arg_parse_version_check.h:159:19: [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. else if (!system("which ftp > /dev/null 2>&1")) data/seqan2-2.4.0+dfsg/include/seqan/arg_parse/arg_parse_version_check.h:276:13: [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. if (system(makeDir.c_str())) data/seqan2-2.4.0+dfsg/include/seqan/arg_parse/arg_parse_version_check.h:408:9: [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. if (system(me._command.c_str())) data/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1120:18: [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. size_t len = snprintf(buffer, sizeof(buffer), data/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1176:18: [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. size_t len = snprintf(buffer, sizeof(buffer), source.format, source.value); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:439:18: [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 (3 == sscanf(symbollist[i], "%*[^(](%4095[^+]+%[^)]) %s", temp, offset, addr)) data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:454:23: [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. else if (3 == sscanf(symbollist[i], "%*d %*s %s %s %*s %s", addr, temp, offset)) data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:465:23: [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. else if (2 == sscanf(symbollist[i], "%s %s", temp, addr)) data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:901:9: [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, comment, args); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:917:9: [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, comment, argp); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:953:13: [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, comment, args); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:983:13: [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, comment, argp); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1027:13: [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, comment, args); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1059:13: [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, comment, argp); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1102:13: [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, comment, args); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1132:13: [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, comment, argp); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1174:13: [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, comment, args); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1204:13: [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, comment, argp); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1246:13: [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, comment, args); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1276:13: [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, comment, argp); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1318:13: [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, comment, args); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1348:13: [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, comment, argp); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1390:13: [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, comment, args); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1420:13: [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, comment, argp); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1459:13: [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, comment, args); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1487:13: [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, comment, argp); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1525:13: [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, comment, args); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:1553:13: [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, comment, argp); data/seqan2-2.4.0+dfsg/include/seqan/file/file_mapping.h:670:9: [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. access, // _In_ DWORD dwDesiredAccess, data/seqan2-2.4.0+dfsg/include/seqan/file/file_page.h:679:30: [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. file.handle, access, strerror(errno)); data/seqan2-2.4.0+dfsg/include/seqan/file/file_page.h:686:56: [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. pf.begin = (TValue *) MapViewOfFile(pf.handle, access, 0, 0, 0); data/seqan2-2.4.0+dfsg/include/seqan/file/file_page.h:691:28: [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. pf.handle, access, strerror(errno)); data/seqan2-2.4.0+dfsg/include/seqan/stream/iostream_zutil.h:200:39: [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 Trace(x) {if (z_verbose>=0) fprintf x ;} data/seqan2-2.4.0+dfsg/include/seqan/stream/iostream_zutil.h:201:39: [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 Tracev(x) {if (z_verbose>0) fprintf x ;} data/seqan2-2.4.0+dfsg/include/seqan/stream/iostream_zutil.h:202:40: [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 Tracevv(x) {if (z_verbose>1) fprintf x ;} data/seqan2-2.4.0+dfsg/include/seqan/stream/iostream_zutil.h:203:48: [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 Tracec(c,x) {if (z_verbose>0 && (c)) fprintf x ;} data/seqan2-2.4.0+dfsg/include/seqan/stream/iostream_zutil.h:204:49: [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 Tracecv(c,x) {if (z_verbose>1 && (c)) fprintf x ;} data/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:491:5: [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(filenameBuffer, tempFilename); data/seqan2-2.4.0+dfsg/tests/store/test_store_io_bam.h:120:5: [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(fastaBuffer, getAbsolutePath("")); data/seqan2-2.4.0+dfsg/tests/store/test_store_io_bam.h:125:5: [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(samBuffer, getAbsolutePath("")); data/seqan2-2.4.0+dfsg/tests/store/test_store_io_bam.h:130:5: [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(tmpBuffer, SEQAN_TEMP_FILENAME()); data/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.cpp:60:19: [3] (tmpfile) GetTempFileName: Temporary file race condition in certain cases (e.g., if run as SYSTEM in many versions of Windows) (CWE-377). uRetVal = GetTempFileName(filePathBuffer, // directory for tmp files data/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.cpp:79:23: [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")) == NULL) data/seqan2-2.4.0+dfsg/apps/razers/readSimulator.h:159:2: [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/seqan2-2.4.0+dfsg/apps/razers3/readSimulator.h:155:5: [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(time(NULL)); data/seqan2-2.4.0+dfsg/include/seqan/arg_parse/arg_parse_version_check.h:298:24: [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. path = std::string(getenv("UserProfile")) + "/.config/seqan"; data/seqan2-2.4.0+dfsg/include/seqan/arg_parse/arg_parse_version_check.h:300:24: [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. path = std::string(getenv("HOME")) + "/.config/seqan"; data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:685:15: [3] (tmpfile) GetTempFileName: Temporary file race condition in certain cases (e.g., if run as SYSTEM in many versions of Windows) (CWE-377). uRetVal = GetTempFileName(filePathBuffer, // directory for tmp files data/seqan2-2.4.0+dfsg/include/seqan/random/random_beta.h:345:16: [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. source.setstate(std::ios::failbit); data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:325:24: [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 ((res = getenv("TMPDIR")) != NULL) data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:327:29: [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. else if ((res = getenv("TMP")) != NULL) data/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:374:10: [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(seed); data/seqan2-2.4.0+dfsg/tests/parallel/test_parallel_queue.h:159:29: [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. seqan::String<unsigned> random; data/seqan2-2.4.0+dfsg/tests/parallel/test_parallel_queue.h:164:12: [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. resize(random, 100000); data/seqan2-2.4.0+dfsg/tests/parallel/test_parallel_queue.h:165:37: [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. for (unsigned i = 0; i < length(random); ++i) data/seqan2-2.4.0+dfsg/tests/parallel/test_parallel_queue.h:167:9: [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[i] = rng(); data/seqan2-2.4.0+dfsg/tests/parallel/test_parallel_queue.h:169:19: [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. chkSum ^= random[i]; data/seqan2-2.4.0+dfsg/tests/parallel/test_parallel_queue.h:191:50: [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. seqan::Splitter<unsigned> splitter(0, length(random), writerCount); data/seqan2-2.4.0+dfsg/tests/parallel/test_parallel_queue.h:209:40: [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. appendValue(queue, random[j], TResizeTag(), TParallelPush()); data/seqan2-2.4.0+dfsg/tests/parallel/test_parallel_queue.h:240:54: [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. std::cout << "throughput: " << (uint64_t)(length(random) / timeSpan) << " values/s" << std::endl; data/seqan2-2.4.0+dfsg/tests/simd/test_simd_vector.h:56:20: [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<TValue> random; data/seqan2-2.4.0+dfsg/tests/simd/test_simd_vector.h:57:12: [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. resize(random, ROWS * COLS); data/seqan2-2.4.0+dfsg/tests/simd/test_simd_vector.h:62:37: [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. for (unsigned i = 0; i < length(random); ++i) data/seqan2-2.4.0+dfsg/tests/simd/test_simd_vector.h:63:9: [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[i] = static_cast<TValue>(pdf(rng)); data/seqan2-2.4.0+dfsg/tests/simd/test_simd_vector.h:68:25: [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. tmp[i][j] = random[i * COLS + j]; data/seqan2-2.4.0+dfsg/tests/simd/test_simd_vector.h:84:40: [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. SEQAN_ASSERT_EQ(tmp[i][j], random[j * ROWS + i]); data/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:164:9: [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(seqFile, toCString(inFile)); data/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.h:1009:10: [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). if (!open(bamFileOut, toCString(options.outputFileName))) data/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.h:1015:10: [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). if (!open(bamFileIn, toCString(options.samFileName))) data/seqan2-2.4.0+dfsg/apps/bs_tools/bisar_base.h:21:10: [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). if (!open(seqFileIn, toCString(fileName))) data/seqan2-2.4.0+dfsg/apps/bs_tools/bisar_base.h:43:7: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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(seqFileInL, toCString(fileNameL)) || data/seqan2-2.4.0+dfsg/apps/bs_tools/bisar_base.h:44:7: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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(seqFileInR, toCString(fileNameR))) data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:91:14: [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). if (!open(seqFileIn, toCString(fileNameList[filecount]))) data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:816:14: [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). if (!open(*bamFileIns[i], toCString(options.readFNames[i]))) data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:842:18: [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). if (!open(*bamFileIns[i], toCString(options.readFNames[i]))) data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:935:10: [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). if (!open(bedFileOut, toCString(options.bedOut))) data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:946:14: [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). if (!open(vcfFileIn, toCString(contigTempFileNamesVcf[i]))) data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:968:14: [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). if (!open(bedFileIn, toCString(contigTempFileNamesBed[i]))) data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar_alphabets.h:50:12: [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 const VALUE[6]; data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar_alphabets.h:59:12: [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 const VALUE[256]; data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar_alphabets.h:95:12: [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 const VALUE[6]; data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar_alphabets.h:107:12: [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 const VALUE[256]; data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar_alphabets.h:216:12: [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 const VALUE[11]; data/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:248:8: [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). if (!open(seqFile, toCString(fileNames[s]))) data/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:537:12: [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). of.open(toCString(options.output)); data/seqan2-2.4.0+dfsg/apps/fiona/compute_gain.cpp:884:10: [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). if (!open(inPre, toCString(options.pathSamPreCorrection))) data/seqan2-2.4.0+dfsg/apps/fiona/compute_gain.cpp:905:19: [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). success = open(inPostBam, toCString(options.pathSamPostCorrection)); data/seqan2-2.4.0+dfsg/apps/fiona/compute_gain.cpp:907:19: [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). success = open(inPostFastq, toCString(options.pathFastaFastqPostCorrection)); data/seqan2-2.4.0+dfsg/apps/fiona/compute_gain.cpp:940:10: [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). if (!open(inGenome, toCString(options.pathGenome))) data/seqan2-2.4.0+dfsg/apps/fiona/compute_gain.cpp:977:23: [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). correctionLog.open(toCString(options.pathCorrectionLog)); data/seqan2-2.4.0+dfsg/apps/fiona/fiona.cpp:578:14: [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). if (!open(seqFile, toCString(fileName))) data/seqan2-2.4.0+dfsg/apps/fiona/fiona.cpp:4817:5: [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(mapping, indexSA(qgramIndex).file); data/seqan2-2.4.0+dfsg/apps/fiona/fiona.cpp:4994:10: [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). if (!open(inFile, toCString(options.inputFilename))) data/seqan2-2.4.0+dfsg/apps/fiona/fiona.cpp:5002:19: [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). success = open(outFile, toCString(options.outputFilename)); data/seqan2-2.4.0+dfsg/apps/fiona/fiona.cpp:5004:19: [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). success = open(outFile, std::cout, Fasta()); data/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:195:10: [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). if (!open(faiIndex, toCString(options.inGenomePath))) data/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:254:10: [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). if (!open(bamFile, toCString(options.inBamPath))) data/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:292:17: [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). outFile.open(toCString(options.outPath), std::ios::binary | std::ios::out); data/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:290:10: [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). if (!open(seqFile, toCString(options.inFilename))) data/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:318:19: [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). outStream.open(toCString(options.outFilename), std::ios::binary | std::ios::out); data/seqan2-2.4.0+dfsg/apps/gustaf/gustaf_matepairs.h:62:10: [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). if (!open(l, toCString(fileNameL)) || !open(r, toCString(fileNameR))) data/seqan2-2.4.0+dfsg/apps/gustaf/gustaf_matepairs.h:62:44: [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). if (!open(l, toCString(fileNameL)) || !open(r, toCString(fileNameR))) data/seqan2-2.4.0+dfsg/apps/gustaf/gustaf_matepairs.h:143:10: [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). if (!open(leftMates, toCString(fileNameL))) data/seqan2-2.4.0+dfsg/apps/gustaf/gustaf_matepairs.h:148:10: [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). if (!open(rightMates, toCString(fileNameR))) data/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:261:10: [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). if (!open(f, toCString(fileName))) data/seqan2-2.4.0+dfsg/apps/gustaf/msplazer_out.h:356:10: [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). if (!open(gffOut, fn_gff.c_str())) data/seqan2-2.4.0+dfsg/apps/gustaf/msplazer_out.h:1054:10: [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). if (!open(vcfOut, fn_vcf.c_str())) data/seqan2-2.4.0+dfsg/apps/gustaf/msplazer_out.h:1149:11: [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). file2.open(toCString(outfile), ::std::ios_base::out | ::std::ios_base::app); data/seqan2-2.4.0+dfsg/apps/gustaf/stellar_routines.h:622:10: [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). if (!open(seqFileIn, toCString(fileName))) data/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:886:13: [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). readOutput.open(toCString(options.readOutputFileName), std::ios_base::out | std::ios_base::trunc | std::ios_base::binary); data/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:893:13: [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). annoOutput.open(toCString(options.annoOutputFileName), std::ios_base::out | std::ios_base::trunc | std::ios_base::binary); data/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:900:14: [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). tupleOutput.open(toCString(options.tupleOutputFileName), std::ios_base::out | std::ios_base::trunc | std::ios_base::binary); data/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:910:22: [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). tupleOutput_Fusion.open(toCString(options.tupleFusionOutputFileName), std::ios_base::out | std::ios_base::trunc | std::ios_base::binary); data/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.cpp:41:18: [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 IdSplitter::open() data/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.cpp:47:9: [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 fileNameBuffer[1000]; data/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.cpp:48:9: [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 filePathBuffer[1000]; data/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.cpp:85:18: [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(&pathTpl[0]); data/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.h:141:10: [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(); data/seqan2-2.4.0+dfsg/apps/mason2/mason_frag_sequencing.cpp:142:10: [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). if (!open(inFragments, toCString(options.inputFileName))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_frag_sequencing.cpp:153:10: [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). if (!open(outReads, toCString(options.outFileNameLeft))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_frag_sequencing.cpp:166:14: [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). if (!open(outReadsRight, toCString(options.outFileNameRight))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_materializer.cpp:103:18: [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). if (!open(outStream, toCString(options.outputFileName))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_materializer.cpp:109:32: [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). breakpointsOut.open(toCString(options.outputBreakpointFile), std::ios::binary | std::ios::out); data/seqan2-2.4.0+dfsg/apps/mason2/mason_materializer.cpp:117:22: [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). if (!open(outMethLevelStream, toCString(options.methFastaOutFile))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_methylation.cpp:116:10: [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). if (!open(faiIndex, toCString(options.fastaInFile))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_methylation.cpp:143:10: [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). if (!open(outStream, toCString(options.methFastaOutFile))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:1086:27: [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). alignmentSplitter.open(); data/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:1139:28: [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). fragmentIdSplitter.open(); data/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:1142:26: [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). fragmentSplitter.open(); data/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:1155:14: [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). if (!open(outSeqsLeft, toCString(options.outFileNameLeft))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:1163:18: [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). if (!open(outSeqsRight, toCString(options.outFileNameRight))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:1173:18: [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). if (!open(*outBamStream, toCString(options.outFileNameSam))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_splicing.cpp:149:18: [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). if (!open(seqFileOut, toCString(options.outputFileName))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_splicing.cpp:152:18: [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). if (!open(gffFileIn, toCString(options.inputGffFile))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp:806:18: [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). if (!open(methFaiIndex, toCString(options.methFastaInFile))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp:823:28: [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). breakpointsOut.open(toCString(options.outputBreakpointFile), std::ios::binary | std::ios::out); data/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp:833:14: [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). if (!open(vcfFileOut, toCString(options.vcfOutFile))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp:884:18: [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). if (!open(outSeqStream, toCString(options.fastaOutFile))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp:894:18: [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). if (!open(outMethLevelStream, toCString(options.methFastaOutFile))) data/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp:1114:9: [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[20]; data/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp:1281:17: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-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[20]; data/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp:1374:13: [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[20]; data/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp:1975:10: [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). if (!open(faiIndex, toCString(options.fastaInFile))) data/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:106:10: [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). if (!open(stream, filename)) data/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:100:14: [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). file.open(toCString(illuminaOptions.probabilityMismatchFile), std::ios_base::in); data/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:167:14: [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). if (!open(vcfFileIn, toCString(vcfFileName))) data/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:192:10: [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). if (!open(faiIndex, toCString(fastaFileName))) data/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:206:14: [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). if (!open(methFaiIndex, toCString(methFastaFileName))) data/seqan2-2.4.0+dfsg/apps/micro_razers/micro_razers.cpp:55:7: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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.open(toCString(filename),ios_base::in | ios_base::binary); data/seqan2-2.4.0+dfsg/apps/micro_razers/micro_razers.cpp:414:19: [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). success = open(options.readFile, toCString(readFileNames[0])); data/seqan2-2.4.0+dfsg/apps/micro_razers/micro_razers.cpp:416:19: [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). success = open(options.readFile, std::cin); data/seqan2-2.4.0+dfsg/apps/micro_razers/outputFormat.h:361:19: [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). success = open(file, toCString(options.output)); data/seqan2-2.4.0+dfsg/apps/micro_razers/outputFormat.h:363:19: [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). success = open(file, std::cout, Nothing()); data/seqan2-2.4.0+dfsg/apps/micro_razers/outputFormat.h:565:8: [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). file.open(toCString(errorPrbFileName), ::std::ios_base::out | ::std::ios_base::trunc); data/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:307:10: [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). if (!open(bamFileIn, toCString(options.inputFileName))) data/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:318:10: [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). if (!open(roiFileOut, toCString(options.outputFileName))) data/seqan2-2.4.0+dfsg/apps/ngs_roi/png_canvas.h:422:18: [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. unsigned char const SIGNATURE[8] = {137, 80, 78, 71, 13, 10, 26, 10}; data/seqan2-2.4.0+dfsg/apps/ngs_roi/png_canvas.h:463:13: [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 nofilter[1] = {'\0'}; // filter 0 (no filter) data/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_builder.cpp:208:5: [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[100]; data/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:868:17: [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). inIntervals.open(toCString(options.inputIntervalsFile), std::ios::binary | std::ios::in); data/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:876:10: [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). if (!open(roiFileIn, toCString(options.inputRoiFile))) data/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:883:10: [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). if (!open(roiFileOut, toCString(options.outputRoiFile))) data/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:432:10: [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). if (!open(roiFileIn, toCString(options.inputFileName))) data/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:10: [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). if (!open(inFile, fileName)) data/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:198:10: [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). if (!open(outputFile, toCString(outfile))) data/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:210:10: [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). if (!open(bamFileIn, toCString(options.inputFile))) data/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:229:10: [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). if (!open(bamFileOut, toCString(options.outputFile))) data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1146:10: [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). if (!open(faiIndex, toCString(options.referencePath))) data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1175:10: [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). if (!open(inBam, toCString(options.inBamPath))) data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1220:40: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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 ((options.outGsiPath == "-" && !open(gsiStream, std::cout, Nothing())) || data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1221:10: [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). !open(gsiStream, toCString(options.outGsiPath))) data/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1295:10: [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). if (!open(faiIndex, toCString(options.referencePath))) data/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1342:10: [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). if (!open(inGsi, toCString(options.inGsiPath))) data/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1364:10: [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). if (!open(bamFileIn, toCString(options.inBamPath))) data/seqan2-2.4.0+dfsg/apps/rabema/rabema_stats.h:153:5: [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[1000]; data/seqan2-2.4.0+dfsg/apps/rabema/rabema_stats.h:209:5: [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[1000]; data/seqan2-2.4.0+dfsg/apps/razers/outputFormat.h:606:19: [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). success = open(file, toCString(options.output)); data/seqan2-2.4.0+dfsg/apps/razers/outputFormat.h:608:19: [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). success = open(file, std::cout, Nothing()); data/seqan2-2.4.0+dfsg/apps/razers/outputFormat.h:946:10: [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). if (!open(gFile, toCString(genomeFileNameList[filecount]))) data/seqan2-2.4.0+dfsg/apps/razers/outputFormat.h:1219:8: [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). file.open(toCString(errorPrbFileName), ::std::ios_base::out | ::std::ios_base::trunc); data/seqan2-2.4.0+dfsg/apps/razers/paramChooser.h:85:11: [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 * fname[2]; data/seqan2-2.4.0+dfsg/apps/razers/paramChooser.h:86:11: [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 * fprefix[1]; data/seqan2-2.4.0+dfsg/apps/razers/paramChooser.h:315:22: [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). filestrm.open(sstrm.str().c_str(), std::ios_base::in); data/seqan2-2.4.0+dfsg/apps/razers/paramChooser.h:334:22: [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). filestrm.open(sstrm.str().c_str(), std::ios_base::in); data/seqan2-2.4.0+dfsg/apps/razers/paramChooser.h:352:9: [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). out.open(avgOut.str().c_str(), std::ios_base::out); data/seqan2-2.4.0+dfsg/apps/razers/paramChooser.h:472:18: [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). filestrm.open(pm_options.shapeFile, std::ios_base::in); data/seqan2-2.4.0+dfsg/apps/razers/paramChooser.h:1222:18: [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). file.open(pm_options.fname[1], std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/apps/razers/paramChooser.h:1278:14: [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). file.open(paramsfile.str().c_str(), std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:77:10: [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). file.open(toCString(filename),ios_base::in | ios_base::binary); data/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:622:19: [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). success = open(options.readFile, toCString(readFileNames[0])); data/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:624:19: [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). success = open(options.readFile, std::cin); data/seqan2-2.4.0+dfsg/apps/razers/razers.h:108:12: [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 compMask[5]; data/seqan2-2.4.0+dfsg/apps/razers/razers.h:228:17: [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(verifications, "verification_tasks.bin", OPEN_WRONLY|OPEN_CREATE); data/seqan2-2.4.0+dfsg/apps/razers/razers.h:631:8: [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). if (!open(seqFile, toCString(fileNameList[i]))) data/seqan2-2.4.0+dfsg/apps/razers/razers.h:2015:8: [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). if (!open(file, toCString(genomeFileNameList[filecount]))) data/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:127:19: [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). success = open(rightMates, fileNameR); data/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:129:19: [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). success = open(rightMates, std::cin); data/seqan2-2.4.0+dfsg/apps/razers/razers_matepairs.h:751:8: [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). if (!open(file, toCString(genomeFileNameList[filecount]))) data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1662:8: [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). file.open(toCString(genomeFileNameList[filecount]), ::std::ios_base::in | ::std::ios_base::binary); data/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:561:23: [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). success = open(file, toCString(options.output)); data/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:563:23: [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). success = open(file, std::cout, Nothing()); data/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:654:5: [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 intBuf[40]; data/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1177:27: [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). success = open(bamFile, toCString(options.output)); data/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1179:27: [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). success = open(bamFile, std::cout, Sam()); data/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1237:22: [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). mismatchFile.open(toCString(options.mismatchFilename), std::ios_base::out | std::ios_base::trunc); data/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1248:14: [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). file.open(toCString(options.errorPrbFileName), std::ios_base::out | std::ios_base::trunc); data/seqan2-2.4.0+dfsg/apps/razers3/paramChooser.h:85:11: [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 * fname[2]; data/seqan2-2.4.0+dfsg/apps/razers3/paramChooser.h:86:11: [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 * fprefix[1]; data/seqan2-2.4.0+dfsg/apps/razers3/paramChooser.h:316:22: [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). filestrm.open(sstrm.str().c_str(), std::ios_base::in); data/seqan2-2.4.0+dfsg/apps/razers3/paramChooser.h:335:22: [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). filestrm.open(sstrm.str().c_str(), std::ios_base::in); data/seqan2-2.4.0+dfsg/apps/razers3/paramChooser.h:353:9: [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). out.open(avgOut.str().c_str(), std::ios_base::out); data/seqan2-2.4.0+dfsg/apps/razers3/paramChooser.h:473:18: [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). filestrm.open(pm_options.shapeFile, std::ios_base::in); data/seqan2-2.4.0+dfsg/apps/razers3/paramChooser.h:1223:18: [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). file.open(pm_options.fname[1], std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/apps/razers3/paramChooser.h:1279:14: [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). file.open(paramsfile.str().c_str(), std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/apps/razers3/profile_timeline.h:178:9: [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[30]; data/seqan2-2.4.0+dfsg/apps/razers3/profile_timeline.h:184:17: [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 * fp = fopen(pathBuffer, "w"); data/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:10: [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). if (!open(seqFileIn, toCString(readsFilename)) || !loadReads(store, seqFileIn, options)) data/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:19: [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). success = open(options.readFile, toCString(readFileNames[0])); data/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:787:19: [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). success = open(options.readFile, std::cin); data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:223:14: [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 compMask[5]; data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:632:7: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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.open(toCString(filename), std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:122:19: [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). success = open(rightMates, fileNameR); data/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:124:19: [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). success = open(rightMates, std::cin); data/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:155:10: [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). if (!open(strmReads, toCString(options.assembly))) data/seqan2-2.4.0+dfsg/apps/rep_sep/utils.h:220:12: [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). return atoi(toCString(groupId)); data/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:19: [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). openRes = open(inFile, toCString(options.inFastxPath)); data/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:339:19: [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). openRes = open(inFile, std::cin); data/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:347:19: [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). openRes = open(outFile, toCString(options.outPath)); data/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:349:19: [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). openRes = open(outFile, std::cout, seqan::Fastq()); data/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:89:23: [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). success = open(*readerPtr[i], toCString(inFiles[i])); data/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:92:23: [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). success = open(*readerPtr[i], std::cin); data/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:242:19: [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). success = open(writer, toCString(options.outFile)); data/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:247:23: [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). success = open(writer, std::cout, Bam()); data/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:250:23: [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). success = open(writer, std::cout, Sam()); data/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:484:40: [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). appendValue(parser.db.errors, std::atoi(toCString(parser._errors))); data/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:504:10: [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). if (!open(inputFile, toCString(fileName), OPEN_RDONLY)) data/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:270:10: [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). if (!open(writer, options.resultsFile)) data/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:121:27: [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). queries_available.open(QUERIES_AVAILABLE, std::ios::in); data/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:315:10: [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). if (!open(writer, options.resultsFile)) data/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:432:10: [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). if (!open(writer, options.resultsFile)) data/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:168:13: [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). inline bool open(Writer<TDb, TDbQuery, TSpec> & writer, TFileName const & fileName) data/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:170:10: [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). if (!open(writer.outputFile, toCString(fileName), OPEN_WRONLY | OPEN_CREATE)) data/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:10: [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). if (!open(inFile, fileName)) data/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:85:10: [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). if (!open(outStream, toCString(msaOpt.outfile))) data/seqan2-2.4.0+dfsg/apps/seqcons2/seqcons_app.cpp:116:10: [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). if (!open(seqFileOut, options.outputFileConsensus.c_str())) data/seqan2-2.4.0+dfsg/apps/seqcons2/seqcons_app.cpp:151:14: [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). if (!open(out, options.outputFileAlignment.c_str())) data/seqan2-2.4.0+dfsg/apps/seqcons2/seqcons_app.cpp:223:10: [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). if (!open(seqFileIn, fileName)) data/seqan2-2.4.0+dfsg/apps/seqcons2/seqcons_app.cpp:257:10: [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). if (!open(bamFileIn, fileName)) data/seqan2-2.4.0+dfsg/apps/sgip/sgip.h:77:8: [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). is.open(filename, std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:77:14: [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). if (!open(seqFileIn, toCString(fileNameList[filecount]))) data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:700:18: [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). if (!open(*bamFileIns.back(), toCString(options.readFNames[i]))) data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:729:23: [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). snpFileStream.open(toCString(options.outputSNP),::std::ios_base::out); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:748:25: [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). indelFileStream.open(toCString(options.outputIndel),::std::ios_base::out); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:770:23: [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). posFileStream.open(toCString(options.outputPosition),::std::ios_base::out); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:1040:13: [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). logfile.open(toCString(options.outputLog), ::std::ios_base::out | ::std::ios_base::trunc); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.h:144:18: [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. unsigned char compMask[5]; // for comparing nucleotides data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.h:564:10: [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). file.open(toCString(options.genomeFName), std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.h:1749:10: [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). file.open(filename,::std::ios_base::in | ::std::ios_base::binary); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.h:3818:17: [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). logfile.open(toCString(options.outputLog), ::std::ios_base::out | ::std::ios_base::app); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.h:3953:18: [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). tmpfile3.open("test.realigned.sam", ::std::ios_base::out); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.h:4604:17: [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). logfile.open(toCString(options.outputLog), ::std::ios_base::out | ::std::ios_base::app); data/seqan2-2.4.0+dfsg/apps/splazers/outputFormat.h:623:7: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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.open(toCString(fileName), ::std::ios_base::out | ::std::ios_base::trunc); data/seqan2-2.4.0+dfsg/apps/splazers/outputFormat.h:793:19: [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). success = open(file, toCString(options.output)); data/seqan2-2.4.0+dfsg/apps/splazers/outputFormat.h:795:19: [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). success = open(file, std::cout, Nothing()); data/seqan2-2.4.0+dfsg/apps/splazers/outputFormat.h:1124:10: [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). if (!open(gFile, toCString(genomeFileNameList[filecount]))) data/seqan2-2.4.0+dfsg/apps/splazers/outputFormat.h:1846:8: [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). file.open(toCString(errorPrbFileName), ::std::ios_base::out | ::std::ios_base::trunc); data/seqan2-2.4.0+dfsg/apps/splazers/paramChooser.h:88:8: [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. const char *fname[2]; data/seqan2-2.4.0+dfsg/apps/splazers/paramChooser.h:89:8: [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. const char *fprefix[1]; data/seqan2-2.4.0+dfsg/apps/splazers/paramChooser.h:313:22: [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). filestrm.open(sstrm.str().c_str(), std::ios_base::in); data/seqan2-2.4.0+dfsg/apps/splazers/paramChooser.h:332:22: [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). filestrm.open(sstrm.str().c_str(), std::ios_base::in); data/seqan2-2.4.0+dfsg/apps/splazers/paramChooser.h:350:9: [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). out.open(avgOut.str().c_str(), std::ios_base::out); data/seqan2-2.4.0+dfsg/apps/splazers/paramChooser.h:465:12: [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). filestrm.open(pm_options.shapeFile,::std::ios_base::in); data/seqan2-2.4.0+dfsg/apps/splazers/paramChooser.h:1048:9: [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). file.open(pm_options.fname[1],::std::ios_base::in | ::std::ios_base::binary); data/seqan2-2.4.0+dfsg/apps/splazers/paramChooser.h:1099:7: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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.open(paramsfile.str().c_str(),::std::ios_base::in | ::std::ios_base::binary); data/seqan2-2.4.0+dfsg/apps/splazers/razers.h:105:12: [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 compMask[5]; data/seqan2-2.4.0+dfsg/apps/splazers/razers.h:512:19: [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). success = open(seqFile, fileName); data/seqan2-2.4.0+dfsg/apps/splazers/razers.h:514:19: [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). success = open(seqFile, std::cin); data/seqan2-2.4.0+dfsg/apps/splazers/razers.h:604:7: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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(seqFile, fname) || atEnd(seqFile)) data/seqan2-2.4.0+dfsg/apps/splazers/razers.h:622:8: [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). if (!open(seqFile, toCString(fileNameList[i]))) data/seqan2-2.4.0+dfsg/apps/splazers/razers.h:1952:8: [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). if (!open(file, toCString(genomeFileNameList[filecount]))) data/seqan2-2.4.0+dfsg/apps/splazers/razers_matepairs.h:435:19: [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). success = open(leftMates, fileNameL); data/seqan2-2.4.0+dfsg/apps/splazers/razers_matepairs.h:437:19: [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). success = open(leftMates, std::cin); data/seqan2-2.4.0+dfsg/apps/splazers/razers_matepairs.h:442:19: [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). success = open(rightMates, fileNameR); data/seqan2-2.4.0+dfsg/apps/splazers/razers_matepairs.h:444:19: [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). success = open(rightMates, std::cin); data/seqan2-2.4.0+dfsg/apps/splazers/razers_matepairs.h:1000:8: [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). if (!open(file, toCString(genomeFileNameList[filecount]))) data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:210:7: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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, fileName)) return false; data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:2209:8: [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). if (!open(file, toCString(genomeFileNameList[filecount]))) data/seqan2-2.4.0+dfsg/apps/splazers/splazers.cpp:77:7: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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.open(toCString(filename),ios_base::in | ios_base::binary); data/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:241:10: [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). if (!open(inSeqs, (toCString(fileName)))) data/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:632:10: [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). file.open(toCString(options.outputFile)); data/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:643:16: [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). daFile.open(toCString(options.disabledQueriesFile)); data/seqan2-2.4.0+dfsg/apps/stellar/stellar_output.h:360:7: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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.open(toCString(fileName), ::std::ios_base::out | ::std::ios_base::app); data/seqan2-2.4.0+dfsg/apps/stellar/stellar_output.h:459:7: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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.open(toCString(fileName), ::std::ios_base::out | ::std::ios_base::app); data/seqan2-2.4.0+dfsg/apps/stellar/stellar_output.h:465:9: [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). daFile.open(toCString(disabledFile), ::std::ios_base::out | ::std::ios_base::app); data/seqan2-2.4.0+dfsg/apps/yara/file_pair.h:51:13: [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). inline bool open(Pair<FormattedFile<TFileType, TDirection, TSpec> > & me, const char * fileName1, const char * fileName2) data/seqan2-2.4.0+dfsg/apps/yara/file_pair.h:53:12: [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). return open(me.i1, fileName1) && open(me.i2, fileName2); data/seqan2-2.4.0+dfsg/apps/yara/file_pair.h:53:38: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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 open(me.i1, fileName1) && open(me.i2, fileName2); data/seqan2-2.4.0+dfsg/apps/yara/file_prefetched.h: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). inline bool open(PrefetchedFile<TFile, TRecords, TThreading> & me, const char * fileName) data/seqan2-2.4.0+dfsg/apps/yara/file_prefetched.h:99:12: [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). return open(me.file, fileName); data/seqan2-2.4.0+dfsg/apps/yara/file_prefetched.h:107:13: [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). inline bool open(PrefetchedFile<Pair<TFile>, TRecords, TThreading> & me, const char * fileName1, const char * fileName2) data/seqan2-2.4.0+dfsg/apps/yara/file_prefetched.h:109:12: [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). return open(me.file, fileName1, fileName2); data/seqan2-2.4.0+dfsg/apps/yara/file_prefetched.h:149:13: [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). inline bool open(PrefetchedFile<TFile, TRecords, Parallel> & me, const char * fileName) data/seqan2-2.4.0+dfsg/apps/yara/file_prefetched.h:151:9: [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). if (open(me.file, fileName)) data/seqan2-2.4.0+dfsg/apps/yara/file_prefetched.h:165:13: [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). inline bool open(PrefetchedFile<Pair<TFile>, TRecords, Parallel> & me, const char * fileName1, const char * fileName2) data/seqan2-2.4.0+dfsg/apps/yara/file_prefetched.h:167:9: [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). if (open(me.file, fileName1, fileName2)) data/seqan2-2.4.0+dfsg/apps/yara/index_fm.h:89:13: [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). inline bool open(Index<StringSet<TText, TSSetSpec>, FMIndex<TSpec, TConfig> > & index, data/seqan2-2.4.0+dfsg/apps/yara/index_fm.h:95:10: [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). if (!open(getFibre(index, FibreSA()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/apps/yara/index_fm.h:98:10: [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). if (!open(getFibre(index, FibreLF()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/apps/yara/indexer.cpp:195:10: [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). if (!open(me.contigsFile, toCString(me.options.contigsFile))) data/seqan2-2.4.0+dfsg/apps/yara/mapper.h:357:14: [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). if (!open(me.contigs, toCString(me.options.contigsIndexFile), OPEN_RDONLY)) data/seqan2-2.4.0+dfsg/apps/yara/mapper.h:381:14: [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). if (!open(me.index, toCString(me.options.contigsIndexFile), OPEN_RDONLY)) data/seqan2-2.4.0+dfsg/apps/yara/mapper.h:408:10: [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). if (!open(me.readsFile, toCString(me.options.readsFile.i1))) data/seqan2-2.4.0+dfsg/apps/yara/mapper.h:415:10: [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). if (!open(me.readsFile, toCString(me.options.readsFile.i1), toCString(me.options.readsFile.i2))) data/seqan2-2.4.0+dfsg/apps/yara/mapper.h:495:22: [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). opened = open(me.outputFile, std::cout, me.options.outputFormat); data/seqan2-2.4.0+dfsg/apps/yara/mapper.h:501:18: [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). opened = open(me.outputFile, toCString(me.options.outputFile), OPEN_WRONLY | OPEN_CREATE); data/seqan2-2.4.0+dfsg/apps/yara/misc_options.h:87:5: [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 cwd[1000]; data/seqan2-2.4.0+dfsg/apps/yara/misc_options.h:320:10: [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). if (!open(limits, toCString(contigsLimitFile), OPEN_RDONLY)) data/seqan2-2.4.0+dfsg/apps/yara/store_seqs.h:129:13: [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). inline bool open(SeqStore<TSpec, TConfig> & me, TFileName const & fileName, int openMode) data/seqan2-2.4.0+dfsg/apps/yara/store_seqs.h:134:10: [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). if (!open(me.seqs, toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/apps/yara/store_seqs.h:137:10: [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). if (!open(me.names, toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:13:10: [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). if (!open(bamFileIn, toCString(pathSam))) data/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:21:5: [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(bamFileOut, std::cout, Sam()); data/seqan2-2.4.0+dfsg/demos/dox/bed_io/UNUSED_bed_stream_read.cpp:21:10: [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). if (!open(bedIn, argv[1])) data/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:59:18: [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). if (!open(file, argv[arg])) data/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:131:29: [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). optMinLen = atoi(argv[arg]); data/seqan2-2.4.0+dfsg/demos/dox/index/open_save.cpp:24:18: [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). std::cout << open(openIndex, tempFileName) << std::endl; data/seqan2-2.4.0+dfsg/demos/dox/seq_io/fai_index_example.cpp:14:10: [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). if (!open(faiIndex, toCString(path))) data/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:18:10: [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). if (!open(seqFile, toCString(bgPath))) data/seqan2-2.4.0+dfsg/demos/dox/statistics/load_markov_model.cpp:17:21: [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). FILE * mmFile = fopen(toCString(mmPath), "rb"); data/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:40:12: [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 const * VALUE[1]; data/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:15:22: [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). if (argc < 2 || !open(seqFile, argv[1])) data/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:18:10: [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). if (!open(vcfFile, argv[1])) data/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:31:10: [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). if (!open(tabixIndex, tbiFileName.c_str())) data/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp:9:10: [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). if (!open(bedIn, toCString(getAbsolutePath("demos/tutorial/bed_io/example.bed")))) data/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp:10:10: [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). if (!open(bedIn, toCString(getAbsolutePath("demos/tutorial/bed_io/example.bed")))) data/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/example1.cpp:23:5: [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(openBamFileIn, toCString(bamFileInName)); data/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution1.cpp:13:10: [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). if (!open(bamFileIn, toCString(bamFileInName))) data/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:12:10: [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). if (!open(bamFileIn, toCString(bamFileInName))) data/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:11:10: [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). if (!open(bamFileIn, toCString(bamFileInName))) data/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution1.cpp:12:10: [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). if (!open(gffIn, toCString(file))) data/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:13:10: [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). if (!open(gffIn, toCString(file))) data/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:31:10: [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). if (!open(faiIndex, toCString(pathToFile))) data/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:36:10: [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). if (!open(faiIndex, toCString(pathToFile), toCString(pathToFaiFile))) data/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution2.cpp:18:10: [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). if (!open(faiIndex, argv[1])) data/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:78:5: [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(index, tempFileName); data/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:95:5: [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(external_index, tempFileName); data/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/assignment1.cpp:10:5: [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 const * strings[4] = data/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:11:5: [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 const * strings[4] = data/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:10:5: [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 const * strings[4] = data/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:14:10: [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). if (!open(inFile, toCString(bamFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:22:10: [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). if (!open(baiIndex, toCString(baiFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution1.cpp:11:10: [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). if (!open(bamFileIn, toCString(bamFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution2.cpp:11:10: [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). if (!open(bamFileIn, toCString(bamFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:11:10: [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). if (!open(bamFileIn, toCString(bamFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution2.cpp:12:10: [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). if (!open(seqFileIn, toCString(seqFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution3.cpp:10:10: [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). if (!open(seqFileIn, toCString(seqFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution4.cpp:10:10: [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). if (!open(seqFileIn, toCString(seqFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:25:10: [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). if (!open(alignmentFile, alignmentFileName.c_str())) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:36:10: [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). if (!open(annotationFile, toCString(annotationFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:25:10: [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). if (!open(alignmentFile, alignmentFileName.c_str())) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:36:10: [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). if (!open(annotationFile, toCString(annotationFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:28:10: [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). if (!open(alignmentFile, alignmentFileName.c_str())) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:39:10: [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). if (!open(annotationFile, toCString(annotationFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:29:10: [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). if (!open(alignmentFile, alignmentFileName.c_str())) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:40:10: [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). if (!open(annotationFile, toCString(annotationFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:19:10: [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). if (!open(alignmentFile, alignmentFileName.c_str())) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:30:10: [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). if (!open(annotationFile, toCString(annotationFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution2.cpp:22:10: [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). if (!open(alignmentFile, alignmentFileName.c_str())) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution2.cpp:33:10: [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). if (!open(annotationFile, toCString(annotationFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:23:10: [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). if (!open(alignmentFile, alignmentFileName.c_str())) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:34:10: [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). if (!open(annotationFile, toCString(annotationFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:25:10: [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). if (!open(alignmentFile, alignmentFileName.c_str())) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:36:10: [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). if (!open(annotationFile, toCString(annotationFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:25:10: [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). if (!open(alignmentFile, alignmentFileName.c_str())) data/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:36:10: [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). if (!open(annotationFile, toCString(annotationFileName))) data/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/example1.cpp:12:5: [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(vcfOut, std::cout, Vcf()); data/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp:12:5: [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(vcfOut, std::cout, Vcf()); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bam_library_size.cpp:221:10: [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). if (!open(bamFileIn, argv[1])) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bam_print_alignments.cpp:76:10: [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). if (!open(inSeq, argv[1])) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bam_print_alignments.cpp:88:10: [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). if (!open(bamFileIn, argv[2])) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:164:10: [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). if (!open(bamIndex, toCString(options.baiFile))) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:261:19: [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). success = open(reader, toCString(options.inFile)); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:263:19: [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). success = open(reader, std::cin); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:272:19: [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). success = open(writer, toCString(options.outFile)); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:278:23: [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). success = open(writer, std::cout, Bam()); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:281:19: [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). success = open(writer, std::cout, Sam()); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream.cpp:234:10: [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). if (!open(myString, filename, OPEN_RDONLY)) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream.cpp:255:20: [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 * f = fopen(filename, "rb"); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream.cpp:280:14: [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). if (!open(f, filename)) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream.cpp:293:14: [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). if (!open(f, filename)) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp:96:9: [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 filenameBuffer[1000]; data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp:114:9: [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 filenameBuffer[1000]; data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp:118:9: [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(mmapString, filenameBuffer); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp:146:9: [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 filenameBuffer[1000]; data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp:164:9: [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 filenameBuffer[1000]; data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp:168:9: [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(mmapString, filenameBuffer); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp:196:9: [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 filenameBuffer[1000]; data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_readwrite.cpp:7:1: [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 block1[512] = "This a test string"; data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_readwrite.cpp:8:1: [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 block2[512]; data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_readwrite.cpp:14:10: [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). if (!open(myFile1, "file_types.bin", OPEN_WRONLY | OPEN_CREATE)) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_readwrite.cpp:24:10: [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). if (!open(myFile2, "file_types.bin", OPEN_RDONLY)) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_speed.cpp:22:10: [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). if (!open(myFile, fileName, OPEN_WRONLY | OPEN_CREATE)) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_speed.cpp:53:10: [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). if (!open(myString, fileName, OPEN_WRONLY | OPEN_CREATE)) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_speed.cpp:76:10: [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). if (!open(myString, fileName, OPEN_RDWR /*| OPEN_CREATE*/)) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/filter_sam.cpp:139:9: [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(outFile, std::cout); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/filter_sam.cpp:141:9: [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(outFile, toCString(options.outputFilename)); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/gff2gtf.cpp:20:10: [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). if (!open(inFile, argv[1])) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/gff2gtf.cpp:28:10: [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). if (!open(outFile, argv[2])) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sam2svg.cpp:155:15: [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). ascii.open(options.fileOut.c_str(), std::ios_base::out | std::ios_base::trunc); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sam2svg.cpp:162:15: [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). else if (!open(svg, options.fileOut.c_str())) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sample_seqs.cpp:61:20: [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). unsigned num = atoi(argv[2]); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sample_seqs.cpp:66:10: [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). if (!open(seqFileIn, argv[1])) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_file_io/mmap_string_example.cpp:20:10: [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). if (!open(str2, argv[1], OPEN_RDONLY)) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_file_io/solution1.cpp:62:14: [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). if (!open(stream, argv[2])) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_file_io/solution1.cpp:72:14: [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). if (!open(stream, argv[2])) data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_file_io/stream_compression_formats.cpp:31:10: [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). if (!open(vin, argv[1])) data/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:500:9: [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[20]; data/seqan2-2.4.0+dfsg/include/seqan/alignment_free/af_n2.h:208:16: [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). myfile.open(toCString(score.outputFile)); data/seqan2-2.4.0+dfsg/include/seqan/arg_parse/arg_parse_ctd_support.h:578:13: [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). ctdfile.open(toCString(ctdfilename)); data/seqan2-2.4.0+dfsg/include/seqan/arg_parse/arg_parse_version_check.h:307:9: [2] (buffer) TCHAR: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. TCHAR tmp_path [MAX_PATH]; data/seqan2-2.4.0+dfsg/include/seqan/arg_parse/arg_parse_version_check.h:331:20: [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). timestamp_file.open(me._timestamp_filename.c_str()); data/seqan2-2.4.0+dfsg/include/seqan/arg_parse/arg_parse_version_check.h:368:12: [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). myfile.open(version_file.c_str()); data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:448:1: [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(BamIndex<Bai> & index, char const * filename) data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:554:1: [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(BamIndex<Bai> & index, char * filename) data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:556:12: [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). return open(index, static_cast<char const *>(filename)); data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:10: [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). if (!open(bamFile, bamFilename)) data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_sam_conversion.h:303:17: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char raw[4]; data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_tags_dict.h:301:17: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char raw[4]; data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_tags_dict.h:491:13: [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 raw[sizeof(Type)]; data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_tags_dict.h:666:13: [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 raw[sizeof(Type)]; data/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_bam.h: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. static char const * VALUE[1]; // default is one extension data/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_bam.h:74:21: [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. static unsigned char const VALUE[4]; data/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_sam.h:53:12: [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 const * VALUE[1]; // default is one extension data/seqan2-2.4.0+dfsg/include/seqan/bam_io/write_bam.h:160:21: [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. static unsigned char const MAP[256] = data/seqan2-2.4.0+dfsg/include/seqan/basic/allocator_chunkpool.h:73:5: [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 * data_recycled_blocks [MAX_COUNT]; data/seqan2-2.4.0+dfsg/include/seqan/basic/allocator_multipool.h:87:5: [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 * data_recycled_blocks [BLOCKING_COUNT]; data/seqan2-2.4.0+dfsg/include/seqan/basic/allocator_multipool.h:88:5: [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 * data_current_begin [BLOCKING_COUNT]; data/seqan2-2.4.0+dfsg/include/seqan/basic/allocator_multipool.h:89:5: [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 * data_current_free [BLOCKING_COUNT]; data/seqan2-2.4.0+dfsg/include/seqan/basic/alphabet_residue_tabs.h:53:12: [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 const VALUE[5]; data/seqan2-2.4.0+dfsg/include/seqan/basic/alphabet_residue_tabs.h:63:12: [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 const VALUE[5]; data/seqan2-2.4.0+dfsg/include/seqan/basic/alphabet_residue_tabs.h:72:12: [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 const VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/basic/alphabet_residue_tabs.h:109:12: [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 const VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/basic/alphabet_residue_tabs.h:145:12: [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 const VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/basic/alphabet_residue_tabs.h:172:12: [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 const VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/basic/alphabet_residue_tabs.h:203:12: [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 const VALUE[5]; data/seqan2-2.4.0+dfsg/include/seqan/basic/alphabet_residue_tabs.h:218:12: [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 const VALUE[16]; data/seqan2-2.4.0+dfsg/include/seqan/basic/alphabet_residue_tabs.h:245:12: [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 const VALUE[16]; data/seqan2-2.4.0+dfsg/include/seqan/basic/alphabet_residue_tabs.h:272:12: [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 const VALUE[16]; data/seqan2-2.4.0+dfsg/include/seqan/basic/alphabet_residue_tabs.h:299:12: [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 const VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/basic/alphabet_residue_tabs.h:331:12: [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 const VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/basic/alphabet_residue_tabs.h:362:12: [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 const VALUE[27]; data/seqan2-2.4.0+dfsg/include/seqan/basic/alphabet_residue_tabs.h:399:12: [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 const VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/basic/alphabet_residue_tabs.h:435:12: [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 const VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/basic/basic_exception.h:320:26: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (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 * const escapeCodes[14] = { data/seqan2-2.4.0+dfsg/include/seqan/basic/basic_exception.h:329:13: [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[6]; // 5 + 1, e.g. "\0xff" + trailing zero data/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:564:12: [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 const * VALUE[1]; data/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:975:10: [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(optr, iptr, n); data/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:984:10: [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(optr, iptr, n); data/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1119:5: [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[sizeof(TInteger) * 3 + 2]; data/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1147:5: [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[32]; data/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1161:5: [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[32]; data/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1175:5: [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[100]; data/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1203:10: [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(ptr, &val, sizeof(TValue)); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_helper.h:70:18: [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). FILE * fl1 = fopen(file1, "rb"); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_helper.h:73:18: [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). FILE * fl2 = fopen(file2, "rb"); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_helper.h:137:18: [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). FILE * fl1 = fopen(file1, "rb"); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_helper.h:140:18: [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). FILE * fl2 = fopen(file2, "rb"); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:411:5: [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[4096]; data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:412:5: [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 addr[20]; data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:413:5: [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 offset[20]; data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:616:16: [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 buffer[1024]; data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:671:12: [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 fileNameBuffer[1000]; data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:673:12: [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 filePathBuffer[1000]; data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:699:5: [2] (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). Risk is low because the source is a constant string. strcat(fileNameBuffer, "\\test_file"); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:703:5: [2] (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 string. strcpy(fileNameBuffer, "/tmp/SEQAN.XXXXXXXXXXXXXXXXXXXX"); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:705:16: [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 _tmp = mkstemp(fileNameBuffer); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:713:5: [2] (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). Risk is low because the source is a constant string. strcat(fileNameBuffer, "/test_file"); data/seqan2-2.4.0+dfsg/include/seqan/basic/profiling.h:278:23: [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). out = fopen(fname, "a"); data/seqan2-2.4.0+dfsg/include/seqan/basic/profiling.h:280:23: [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). out = fopen(fname, "w"); data/seqan2-2.4.0+dfsg/include/seqan/basic/profiling.h:308:18: [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(dst, ProfileData_<>::_proValue, 2 * sizeof(ProfileTimeValue_)); data/seqan2-2.4.0+dfsg/include/seqan/basic/profiling.h:312:18: [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(&(dst[2]), &(ProfileData_<>::_proValue[2]), sizeof(ProfileTStates_) - 2 * sizeof(ProfileTimeValue_)); data/seqan2-2.4.0+dfsg/include/seqan/basic/profiling.h:316:18: [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(dst, ProfileData_<>::_proValue, sizeof(ProfileTStates_)); data/seqan2-2.4.0+dfsg/include/seqan/bed_io/read_bed.h:70:12: [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 const * VALUE[1]; // default is one extension data/seqan2-2.4.0+dfsg/include/seqan/blast/blast_base.h:298:22: [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. static constexpr char const * const VALUE [6] = data/seqan2-2.4.0+dfsg/include/seqan/blast/blast_report_out.h:139:22: [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. static constexpr char const * VALUE[1] = data/seqan2-2.4.0+dfsg/include/seqan/blast/blast_report_out.h:455:5: [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[40] = ""; data/seqan2-2.4.0+dfsg/include/seqan/blast/blast_tabular.h:204:22: [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. static constexpr char const * VALUE[2] = data/seqan2-2.4.0+dfsg/include/seqan/file/file_base.h:80:17: [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). inline bool open(File<TSpec> &me, const char *fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/file/file_base.h:83:19: [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). return me.open(fileName, openMode); data/seqan2-2.4.0+dfsg/include/seqan/file/file_base.h:87:17: [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). inline bool open(File<TSpec> &me, const char *fileName) data/seqan2-2.4.0+dfsg/include/seqan/file/file_base.h:90:16: [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). return open(me, fileName, DefaultOpenMode<File<TSpec> >::VALUE); data/seqan2-2.4.0+dfsg/include/seqan/file/file_cstyle.h:120:5: [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* &me, const char *fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/file/file_cstyle.h:124:22: [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 (me = fopen(fileName, _getCStyleOpenMode(openMode))) != NULL; data/seqan2-2.4.0+dfsg/include/seqan/file/file_cstyle.h:128:5: [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* &me, const char *fileName) data/seqan2-2.4.0+dfsg/include/seqan/file/file_cstyle.h:131:16: [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). return open(me, fileName, DefaultOpenMode<FILE*>::VALUE); data/seqan2-2.4.0+dfsg/include/seqan/file/file_cstyle.h:139:22: [2] (tmpfile) tmpfile: Function tmpfile() has a security flaw on some systems (e.g., older System V systems) (CWE-377). return (me = tmpfile()) != NULL; data/seqan2-2.4.0+dfsg/include/seqan/file/file_mapping.h:363:1: [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(FileMapping<TSpec> &mapping, const char *filename, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/file/file_mapping.h:366:19: [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). bool result = open(mapping.file, filename, openMode); data/seqan2-2.4.0+dfsg/include/seqan/file/file_mapping.h:377:1: [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(FileMapping<TSpec> &mapping, TFile const &file) data/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1172:13: [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(*this, _file); data/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1179:13: [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(*this, fileName, openMode); data/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1796:5: [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(String<TValue, External<TConfig> > &me, const char *fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1803:28: [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). if ((me._ownFile = open(me.file, fileName, openMode))) data/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1820:5: [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(String<TValue, External<TConfig> > &me, const char *fileName) data/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1826:16: [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). return open(me, fileName, DefaultOpenMode<TFile>::VALUE); data/seqan2-2.4.0+dfsg/include/seqan/file/string_external.h:1831:5: [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(String<TValue, External<TConfig> > &me, typename TConfig::TFile file) data/seqan2-2.4.0+dfsg/include/seqan/file/string_mmap.h:165:13: [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(*this, _file); data/seqan2-2.4.0+dfsg/include/seqan/file/string_mmap.h:175:13: [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(*this, fileName, openMode); data/seqan2-2.4.0+dfsg/include/seqan/file/string_mmap.h:577:5: [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(String<TValue, MMap<TConfig> > &me, const char *fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/file/string_mmap.h:581:13: [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 (open(me.mapping, fileName, openMode)) data/seqan2-2.4.0+dfsg/include/seqan/file/string_mmap.h:588:5: [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(String<TValue, MMap<TConfig> > &me, const char *fileName) data/seqan2-2.4.0+dfsg/include/seqan/file/string_mmap.h:592:16: [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). return open(me, fileName, DefaultOpenMode<TFile>::VALUE); data/seqan2-2.4.0+dfsg/include/seqan/file/string_mmap.h:597:5: [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(String<TValue, MMap<TConfig> > &me, typename TConfig::TFile file) data/seqan2-2.4.0+dfsg/include/seqan/file/string_mmap.h:601:13: [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 (open(me.mapping, file)) data/seqan2-2.4.0+dfsg/include/seqan/find/find_wild_shiftand.h:190:17: [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). n = atoi(toCString(number)); data/seqan2-2.4.0+dfsg/include/seqan/find/find_wild_shiftand.h:206:21: [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). m = atoi(toCString(number)); data/seqan2-2.4.0+dfsg/include/seqan/find/find_wild_shiftand.h:261:17: [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). n = atoi(toCString(number)); data/seqan2-2.4.0+dfsg/include/seqan/find/find_wild_shiftand.h:270:21: [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). m = atoi(toCString(number)); data/seqan2-2.4.0+dfsg/include/seqan/find/find_wild_shiftand.h:402:17: [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). n = atoi(toCString(number)); data/seqan2-2.4.0+dfsg/include/seqan/find/find_wild_shiftand.h:410:21: [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). m = atoi(toCString(number)); data/seqan2-2.4.0+dfsg/include/seqan/gff_io/gff_io_base.h:92:12: [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 const * VALUE[2]; // default is one extension data/seqan2-2.4.0+dfsg/include/seqan/gff_io/gff_io_base.h:105:12: [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 const * VALUE[1]; // default is one extension data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:158:10: [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). strm.open(msaOpt.infile.c_str(), std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:171:14: [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). strm_lib.open(msaOpt.infile.c_str(), std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:378:22: [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). strm_lib.open((*begIt).c_str(), std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:438:22: [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). strm_lib.open((*begIt).c_str(), std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:453:22: [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). strm_lib.open((*begIt).c_str(), std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:468:22: [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). strm_lib.open((*begIt).c_str(), std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:500:19: [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). strm_tree.open(msaOpt.treefile.c_str(), std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional.h: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). inline bool open(Index<TText, BidirectionalIndex<TIndexSpec> > & index, const char * fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional.h:164:9: [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). if (open(index.fwd, toCString(name), openMode)) data/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional.h:167:16: [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). return open(index.rev, toCString(name), openMode); data/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:490:17: [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). inline bool open( data/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:498:15: [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 ((!open(getFibre(index, EsaText()), toCString(name), openMode)) && data/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:499:15: [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). (!open(getFibre(index, EsaText()), fileName, openMode))) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:502:14: [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). if (!open(getFibre(index, EsaSA()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:505:14: [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). if (!open(getFibre(index, EsaIsa()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:508:14: [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). if (!open(getFibre(index, EsaLcp()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:511:14: [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). if (!open(getFibre(index, EsaChildtab()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:514:14: [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). if (!open(getFibre(index, EsaBwt()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:519:17: [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). inline bool open( data/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:523:16: [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). return open(index, fileName, DefaultOpenMode<Index< TObject, IndexEsa<TSpec> > >::VALUE); data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:494:13: [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). inline bool open(Index<TText, FMIndex<TSpec, TConfig> > & index, const char * fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:499:10: [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). if (!open(getFibre(index, FibreText()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:502:10: [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). if (!open(getFibre(index, FibreSA()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:505:10: [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). if (!open(getFibre(index, FibreLF()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:514:13: [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). inline bool open(Index<TText, FMIndex<TSpec, TConfig> > & index, const char * fileName) data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:516:12: [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). return open(index, fileName, DefaultOpenMode<Index<TText, FMIndex<TSpec, TConfig> > >::VALUE); data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_compressed_sa.h:538:13: [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). inline bool open(CompressedSA<TText, TSpec, TConfig> & compressedSA, const char * fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_compressed_sa.h:540:12: [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). return open(getFibre(compressedSA, FibreSparseString()), fileName, openMode); data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_compressed_sa.h:544:13: [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). inline bool open(CompressedSA<TText, TSpec, TConfig> & compressedSA, const char * fileName) data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_compressed_sa.h:546:12: [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). return open(compressedSA, fileName, DefaultOpenMode<CompressedSA<TText, TSpec, TConfig> >::VALUE); data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_lf_table.h:782:13: [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). inline bool open(LF<TText, TSpec, TConfig> & lf, const char * fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_lf_table.h:788:10: [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). if (!open(lf.sums, toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_lf_table.h:792:10: [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). if (!open(lf.bwt, toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_lf_table.h:796:10: [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). if (!open(lf.sentinels, toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_lf_table.h:800:10: [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). if (!open(lf.sentinelSubstitute, toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_lf_table.h:806:13: [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). inline bool open(LF<TText, TSpec, TConfig> & lf, const char * fileName) data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_lf_table.h:808:12: [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). return open(lf, fileName, DefaultOpenMode<LF<TText, TSpec, TConfig> >::VALUE); data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_rank_dictionary_base.h:503:13: [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). inline bool open(RankDictionary<TValue, TSpec> & dict, const char * fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_rank_dictionary_base.h:505:12: [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). return open(getFibre(dict, FibreRanks()), fileName, openMode); data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_rank_dictionary_base.h:509:13: [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). inline bool open(RankDictionary<TValue, TSpec> & dict, const char * fileName) data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_rank_dictionary_base.h:511:12: [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). return open(dict, fileName, DefaultOpenMode<RankDictionary<TValue, TSpec> >::VALUE); data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_rank_dictionary_levels.h:1806:13: [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). inline bool open(RankDictionary<TValue, Levels<TSpec, TConfig> > & dict, const char * fileName, int const openMode) data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_rank_dictionary_levels.h:1813:15: [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). result &= open(getFibre(dict, FibreRanks()), toCString(name), openMode); data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_rank_dictionary_levels.h:1819:19: [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). result &= open(getFibre(dict, FibreSuperBlocks()), toCString(name), openMode); data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_rank_dictionary_levels.h:1826:19: [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). result &= open(getFibre(dict, FibreUltraBlocks()), toCString(name), openMode); data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_rank_dictionary_wt.h:491:13: [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). inline bool open(RankDictionary<TValue, WaveletTree<TSpec, TConfig> > & dict, const char * fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_rank_dictionary_wt.h:497:10: [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). if (!open(getFibre(dict, FibreRanks()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_rank_dictionary_wt.h:501:10: [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). if (!open(getFibre(dict, FibreTreeStructure()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_right_array_binary_tree.h:364:13: [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). inline bool open(RightArrayBinaryTree<TChar, TSpec> & treeStructure, const char * fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_right_array_binary_tree.h:370:10: [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). if (!open(getFibre(treeStructure, FibreTreeStructureEncoding()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_right_array_binary_tree.h:374:10: [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). if (!open(treeStructure.minCharValue, toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_right_array_binary_tree.h:380:13: [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). inline bool open(RightArrayBinaryTree<TChar, TSpec> & treeStructure, const char * fileName) data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_right_array_binary_tree.h:382:12: [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). return open(treeStructure, fileName, DefaultOpenMode<RightArrayBinaryTree<TChar, TSpec> >::VALUE); data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_sparse_string.h:515:13: [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). inline bool open(SparseString<TFibreValues, TSpec> & sparseString, const char * fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_sparse_string.h:522:10: [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). if (!open(sparseString._length, toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_sparse_string.h:527:10: [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). if (!open(getFibre(sparseString, FibreValues()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_sparse_string.h:532:10: [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). if (!open(getFibre(sparseString, FibreIndicators()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_sparse_string.h:538:13: [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). inline bool open(SparseString<TFibreValues, TSpec> & sparseString, const char * fileName) data/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_sparse_string.h:540:12: [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). return open(sparseString, fileName, DefaultOpenMode<SparseString<TFibreValues, TSpec> >::VALUE); data/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:357:13: [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). inline bool open( data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:2829:13: [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). inline bool open( data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:2837:11: [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). if ((!open(getFibre(index, QGramText()), toCString(name), openMode)) && data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:2838:11: [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). (!open(getFibre(index, QGramText()), fileName, openMode))) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:2841:10: [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). if (!open(getFibre(index, QGramSA()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:2844:10: [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). if (!open(getFibre(index, QGramDir()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:2849:13: [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). inline bool open( data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:2853:12: [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). return open(index, fileName, OPEN_RDONLY); data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_bucketrefinement.h:610:13: [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). inline bool open(Index<TText, IndexQGram<TShapeSpec, BucketRefinement> > & index, const char * fileName) data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_bucketrefinement.h:614:9: [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). if (open(static_cast<TBaseIndex &>(index), fileName)) data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:345:13: [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). inline bool open(Index<TText, IndexQGram<TShapeSpec, OpenAddressing> > &index, const char *fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:350:10: [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). if (!open(getFibre(index, QGramText()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:353:10: [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). if (!open(getFibre(index, QGramSA()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:356:10: [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). if (!open(getFibre(index, QGramDir()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:359:10: [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). if (!open(getFibre(index, QGramBucketMap()).qgramCode, toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h: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). inline bool open(Index<TText, IndexQGram<TShapeSpec, OpenAddressing> > &index, const char *fileName) data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:367:12: [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). return open(index, fileName, OPEN_RDONLY); data/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:656:13: [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). inline bool open(Index<TObject, IndexSa<TSpec> > & index, const char * fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:661:11: [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). if ((!open(getFibre(index, FibreText()), toCString(name), openMode)) && data/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:662:11: [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). (!open(getFibre(index, FibreText()), fileName, openMode))) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:665:10: [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). if (!open(getFibre(index, FibreSA()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:671:13: [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). inline bool open(Index<TObject, IndexSa<TSpec> > & index, const char * fileName) data/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:673:12: [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). return open(index, fileName, DefaultOpenMode<Index<TObject, IndexSa<TSpec> > >::VALUE); data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:787:17: [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). inline bool open(TValue & value, const char *fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:790:14: [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). if (!open(f, fileName, openMode & ~OPEN_CREATE)) data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:796:17: [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). inline bool open(TValue & value, const char *fileName) data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:798:16: [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). return open(value, fileName, OPEN_RDONLY); data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:802:17: [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). inline bool open(String<TValue, TSpec> &string, const char *fileName, int openMode) { data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:804:14: [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). if (!open(extString, fileName, openMode & ~OPEN_CREATE)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:809:17: [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). inline bool open(String<TValue, TSpec> &string, const char *fileName) { data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:810:16: [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). return open(string, fileName, OPEN_RDONLY); data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:814:17: [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). inline bool open(Segment<THost, TSpec> &string, const char *fileName, int openMode) { data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:816:14: [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). if (!open(extString, fileName, openMode & ~OPEN_CREATE)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:821:17: [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). inline bool open(Segment<THost, TSpec> &string, const char *fileName) { data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:822:16: [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). return open(string, fileName, OPEN_RDONLY); data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:829:17: [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). inline bool open(StringSet<TString, TSSSpec> &multi, const char *fileName, int openMode) { data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:830:9: [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 id[12]; // 2^32 has 10 decimal digits + 1 (0x00) data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:841:22: [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). if (!open(multi[i], toCString(name), (openMode & ~OPEN_CREATE) | OPEN_QUIET)) data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:853:21: [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). inline bool open(StringSet<String<TValue, TSpec>, Dependent<TSSSpec> > &, const char *, int) { data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:859:17: [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). inline bool open(StringSet<TString, Owner<ConcatDirect<TSSSpec> > > &multi, const char *fileName, int openMode) { data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:863:14: [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). if (!open(multi.concat, toCString(name), openMode | OPEN_QUIET)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:866:14: [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). if (!open(multi.limits, toCString(name), openMode | OPEN_QUIET) && !empty(multi.concat)) data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:878:17: [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). inline bool open(StringSet<String<TValue, TSpec>, TSSSpec> &multi, const char *fileName) { data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:879:16: [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). return open(multi, fileName, OPEN_RDONLY); data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:890:14: [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). if (!open(f, fileName, openMode)) data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:906:14: [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). if (!open(extString, fileName, openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:919:14: [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). if (!open(extString, fileName, openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:931:9: [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 id[12]; // 2^32 has 10 decimal digits + 2 ('.' and 0x00) data/seqan2-2.4.0+dfsg/include/seqan/index/index_wotd.h:2057:17: [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). inline bool open( data/seqan2-2.4.0+dfsg/include/seqan/index/index_wotd.h:2068:15: [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 ((!open(getFibre(index, WotdText()), toCString(name), openMode)) && data/seqan2-2.4.0+dfsg/include/seqan/index/index_wotd.h:2069:15: [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). (!open(getFibre(index, WotdText()), fileName, openMode))) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_wotd.h:2072:14: [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). if (!open(getFibre(index, WotdSA()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_wotd.h:2075:14: [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). if (!open(getFibre(index, WotdDir()), toCString(name), openMode)) return false; data/seqan2-2.4.0+dfsg/include/seqan/index/index_wotd.h:2086:17: [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). inline bool open( data/seqan2-2.4.0+dfsg/include/seqan/index/index_wotd.h:2090:16: [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). return open(index, fileName, OPEN_RDONLY); data/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:232:13: [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(&dst.i.i2, &src.i2, sizeof(T2)); data/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:233:13: [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(&dst.i.i3, &src.i3, sizeof(T3)); data/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:240:13: [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(&dst.i.i2, &src.i2, sizeof(T2)); data/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:377:13: [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(&dst.i.i1, &src.i1, sizeof(T1)); data/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:378:13: [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(&dst.i.i2, &src.i2, sizeof(T2)); data/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:379:13: [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(&dst.i.i3, &src.i3, sizeof(T3)); data/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:386:13: [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(&dst.i.i1, &src.i1, sizeof(T1)); data/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:387:13: [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(&dst.i.i2, &src.i2, sizeof(T2)); data/seqan2-2.4.0+dfsg/include/seqan/index/shape_threshold.h:145:16: [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 const VALUE[4]; data/seqan2-2.4.0+dfsg/include/seqan/map/sumlist_mini.h:54:27: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (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 unsigned char SIZES [4]; data/seqan2-2.4.0+dfsg/include/seqan/map/sumlist_mini.h:73:18: [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. unsigned char value_3[sizeof(TValue)+1]; data/seqan2-2.4.0+dfsg/include/seqan/map/sumlist_mini.h:174:14: [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 data_ [SIZE]; data/seqan2-2.4.0+dfsg/include/seqan/misc/svg.h:67:24: [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). friend inline bool open(SVGFile &svg, char const * fileName); data/seqan2-2.4.0+dfsg/include/seqan/misc/svg.h:82:9: [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(*this, fileName); data/seqan2-2.4.0+dfsg/include/seqan/misc/svg.h:181:13: [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). inline bool open(SVGFile &svg, char const * fileName) data/seqan2-2.4.0+dfsg/include/seqan/misc/svg.h:183:14: [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). svg.file.open(fileName, std::ios_base::out); data/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:166:12: [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 const VALUE[5]; data/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:175:12: [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 const VALUE[5]; data/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_functors.h:184:19: [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. static signed char const VALUE[16]; data/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:853:1: [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(ModifiedString<THost, TSpec> &, const char *, int) data/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:860:1: [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(StringSet<ModifiedString<THost, TSpec>, Owner<ConcatDirect<TSpec2> > > &, data/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_queue.h:95:45: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. mutable ReadWriteLock lock; char pad1[SEQAN_CACHE_LINE_SIZE - sizeof(ReadWriteLock)]; data/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_queue.h:99:45: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. TAtomicSize headPos; char pad4[SEQAN_CACHE_LINE_SIZE - sizeof(TAtomicSize)]; data/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_queue.h:100:45: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. TAtomicSize headReadPos; char pad5[SEQAN_CACHE_LINE_SIZE - sizeof(TAtomicSize)]; data/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_queue.h:101:45: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. TAtomicSize tailPos; char pad6[SEQAN_CACHE_LINE_SIZE - sizeof(TAtomicSize)]; data/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_queue.h:102:45: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. TAtomicSize tailWritePos; char pad7[SEQAN_CACHE_LINE_SIZE - sizeof(TAtomicSize)]; data/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_queue.h:103:45: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. TAtomicSize roundSize; char pad8[SEQAN_CACHE_LINE_SIZE - sizeof(TAtomicSize)]; data/seqan2-2.4.0+dfsg/include/seqan/parallel/parallel_queue.h:104:45: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. Atomic<bool>::Type virgin; char pad9[SEQAN_CACHE_LINE_SIZE - sizeof(Atomic < bool > ::Type)]; data/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:776:24: [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). _ownFile = open(file, fileName); data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_buchfink11_tables.h:57:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<Buchfink11> > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_buchfink11_tables.h:63:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_buchfink11_tables.h:69:18: [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 VALUE[27]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_buchfink11_tables.h:75:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cannata10_tables.h:57:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<Cannata10> > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cannata10_tables.h:63:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cannata10_tables.h:69:18: [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 VALUE[27]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cannata10_tables.h:75:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:60:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<19, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:66:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:72:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:78:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:85:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<18, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:91:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:97:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:103:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:110:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<17, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:116:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:122:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:128:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:135:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<16, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:141:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:147:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:153:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:160:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<15, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:166:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:172:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:178:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:185:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<14, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:191:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:197:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:203:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:210:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<13, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:216:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:222:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:228:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:235:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<12, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:241:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:247:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:253:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:260:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<11, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:266:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:272:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:278:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:285:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<10, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:291:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:297:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:303:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:310:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<9, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:316:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:322:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:328:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:335:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<8, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:341:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:347:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:353:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:360:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<7, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:366:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:372:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:378:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:385:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<6, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:391:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:397:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:403:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:410:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<5, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:416:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:422:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:428:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:435:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<4, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:441:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:447:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:453:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:460:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<3, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:466:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:472:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:478:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:485:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<2, 20, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:491:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:497:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h:503:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:60:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<21, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:66:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:72:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:78:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:85:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<20, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:91:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:97:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:103:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:110:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<19, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:116:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:122:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:128:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:135:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<18, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:141:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:147:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:153:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:160:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<17, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:166:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:172:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:178:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:185:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<16, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:191:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:197:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:203:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:210:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<15, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:216:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:222:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:228:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:235:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<14, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:241:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:247:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:253:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:260:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<13, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:266:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:272:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:278:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:285:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<12, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:291:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:297:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:303:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:310:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<11, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:316:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:322:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:328:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:335:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<10, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:341:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:347:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:353:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:360:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<9, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:366:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:372:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:378:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:385:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<8, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:391:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:397:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:403:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:410:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<7, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:416:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:422:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:428:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:435:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<6, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:441:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:447:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:453:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:460:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<5, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:466:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:472:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:478:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:485:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<4, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:491:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:497:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:503:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:510:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<3, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:516:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:522:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:528:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:535:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<2, 22, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:541:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:547:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h:553:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:60:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<23, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:66:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:72:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:78:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:85:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<22, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:91:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:97:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:103:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:110:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<21, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:116:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:122:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:128:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:135:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<20, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:141:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:147:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:153:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:160:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<19, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:166:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:172:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:178:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:185:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<18, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:191:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:197:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:203:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:210:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<17, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:216:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:222:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:228:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:235:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<16, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:241:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:247:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:253:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:260:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<15, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:266:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:272:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:278:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:285:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<14, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:291:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:297:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:303:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:310:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<13, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:316:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:322:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:328:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:335:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<12, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:341:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:347:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:353:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:360:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<11, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:366:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:372:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:378:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:385:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<10, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:391:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:397:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:403:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:410:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<9, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:416:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:422:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:428:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:435:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<8, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:441:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:447:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:453:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:460:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<7, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:466:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:472:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:478:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:485:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<6, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:491:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:497:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:503:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:510:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<5, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:516:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:522:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:528:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:535:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<4, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:541:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:547:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:553:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:560:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<3, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:566:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:572:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:578:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:585:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<ClusterReduction<2, 24, Blosum62> > > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:591:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:597:18: [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 VALUE[24]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h:603:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_li10_tables.h:57:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<Li10> > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_li10_tables.h:63:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_li10_tables.h:69:18: [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 VALUE[27]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_li10_tables.h:75:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h:57:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<Murphy10> > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h:63:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h:69:18: [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 VALUE[27]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h:75:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_murphy5_tables.h:57:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<Murphy5> > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_murphy5_tables.h:63:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_murphy5_tables.h:69:18: [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 VALUE[27]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_murphy5_tables.h:75:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_solis10_tables.h:57:18: [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 VALUE[ValueSize<SimpleType<unsigned char, ReducedAminoAcid_<Solis10> > >::VALUE]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_solis10_tables.h:63:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_solis10_tables.h:69:18: [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 VALUE[27]; data/seqan2-2.4.0+dfsg/include/seqan/reduced_aminoacid/reduced_aminoacid_solis10_tables.h:75:18: [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 VALUE[256]; data/seqan2-2.4.0+dfsg/include/seqan/rna_io/bpseq_read_write.h:80:12: [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 const * VALUE[1]; // default is one extension data/seqan2-2.4.0+dfsg/include/seqan/rna_io/connect_read_write.h:107:12: [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 const * VALUE[1]; data/seqan2-2.4.0+dfsg/include/seqan/rna_io/dot_bracket_read_write.h:98:12: [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 const * VALUE[1]; data/seqan2-2.4.0+dfsg/include/seqan/rna_io/dot_bracket_read_write.h:127:57: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). constexpr std::array<char, 30> const DotBracketArgs<T>::open; data/seqan2-2.4.0+dfsg/include/seqan/rna_io/dot_bracket_read_write.h:151:64: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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::stack<TCharStringSize> stack[length(DotBracketArgs<>::open)]; data/seqan2-2.4.0+dfsg/include/seqan/rna_io/dot_bracket_read_write.h:161:53: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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 open_idx = std::find(DotBracketArgs<>::open.begin(), DotBracketArgs<>::open.end(), bracketStr[idx]); data/seqan2-2.4.0+dfsg/include/seqan/rna_io/dot_bracket_read_write.h:161:85: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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 open_idx = std::find(DotBracketArgs<>::open.begin(), DotBracketArgs<>::open.end(), bracketStr[idx]); data/seqan2-2.4.0+dfsg/include/seqan/rna_io/dot_bracket_read_write.h:162:52: [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 (open_idx != std::end(DotBracketArgs<>::open)) data/seqan2-2.4.0+dfsg/include/seqan/rna_io/dot_bracket_read_write.h:164:67: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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::ptrdiff_t brIndex = open_idx - DotBracketArgs<>::open.begin(); data/seqan2-2.4.0+dfsg/include/seqan/rna_io/dot_bracket_read_write.h:190:44: [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). for (decltype(length(DotBracketArgs<>::open)) idx = 0; idx < length(DotBracketArgs<>::open); ++idx) data/seqan2-2.4.0+dfsg/include/seqan/rna_io/dot_bracket_read_write.h:190:91: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). for (decltype(length(DotBracketArgs<>::open)) idx = 0; idx < length(DotBracketArgs<>::open); ++idx) data/seqan2-2.4.0+dfsg/include/seqan/rna_io/dot_bracket_read_write.h:277:49: [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). bracketStr[idx] = DotBracketArgs<>::open[colors[idx]-1]; data/seqan2-2.4.0+dfsg/include/seqan/rna_io/ebpseq_read_write.h:84:12: [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 const * VALUE[1]; // default is one extension data/seqan2-2.4.0+dfsg/include/seqan/rna_io/stockholm_read_write.h:122:12: [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 const * VALUE[1]; data/seqan2-2.4.0+dfsg/include/seqan/rna_io/vienna_read_write.h:84:12: [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 const * VALUE[1]; data/seqan2-2.4.0+dfsg/include/seqan/roi_io/read_roi.h:72:12: [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 const * VALUE[1]; // default is one extension data/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:179:10: [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). if (!open(fin, toCString(filename))) data/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:194:10: [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). if (!open(fin, toCString(filename))) data/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:98:5: [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(bamIn, file.stream); data/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:494:13: [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). inline bool open(FaiIndex & index, char const * fastaFilename, char const * faiFilename) data/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:500:10: [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). if (!open(index.file, toCString(fastaFilename), OPEN_RDONLY)) data/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:524:13: [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). inline bool open(FaiIndex & index, char const * fastaFilename) data/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:528:12: [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). return open(index, fastaFilename, toCString(faiFilename)); data/seqan2-2.4.0+dfsg/include/seqan/seq_io/fai_index.h:661:10: [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). if (!open(index.file, toCString(fastaFilename), OPEN_RDONLY)) data/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:81:12: [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 const VALUE[1]; data/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:90:12: [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 const VALUE[1]; data/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:107:12: [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 const * VALUE[6]; data/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:124:12: [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 const * VALUE[2]; data/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h: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 const * VALUE[1]; data/seqan2-2.4.0+dfsg/include/seqan/seq_io/read_embl.h:70:12: [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 const VALUE[3]; data/seqan2-2.4.0+dfsg/include/seqan/seq_io/read_embl.h:82:12: [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 const * VALUE[1]; data/seqan2-2.4.0+dfsg/include/seqan/seq_io/read_genbank.h:79:12: [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 const VALUE[6]; data/seqan2-2.4.0+dfsg/include/seqan/seq_io/read_genbank.h:91:12: [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 const * VALUE[1]; data/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:2020:13: [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). inline bool open(String<TValue, Packed<THostspec> > & me, const char *fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:2022:12: [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). return open(host(me), fileName, openMode); data/seqan2-2.4.0+dfsg/include/seqan/simple_intervals_io/simple_intervals_file.h:99:12: [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 const * VALUE[1]; // default is one extension data/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:14: [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). if (!open(seqFile, toCString(fileNameList[f]))) data/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1261:10: [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). if (!open(seqFile, toCString(fileName))) data/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1279:10: [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). if (!open(seqFileL, toCString(fileNameL)) || !open(seqFileR, toCString(fileNameR))) data/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1279:51: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of 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(seqFileL, toCString(fileNameL)) || !open(seqFileR, toCString(fileNameR))) data/seqan2-2.4.0+dfsg/include/seqan/stream/adapt_ios.h:334:13: [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). inline bool open(std::basic_fstream<TValue, TTraits> & stream, const char *fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/stream/adapt_ios.h:337:12: [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). stream.open(fileName, _getSTLStyleOpenMode(openMode)); data/seqan2-2.4.0+dfsg/include/seqan/stream/adapt_ios.h:342:13: [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). inline bool open(std::basic_ifstream<TValue, TTraits> & stream, const char *fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/stream/adapt_ios.h:345:12: [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). stream.open(fileName, _getSTLStyleOpenMode(openMode)); data/seqan2-2.4.0+dfsg/include/seqan/stream/adapt_ios.h:350:13: [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). inline bool open(std::basic_ofstream<TValue, TTraits> & stream, const char *fileName, int openMode) data/seqan2-2.4.0+dfsg/include/seqan/stream/adapt_ios.h:353:12: [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). stream.open(fileName, _getSTLStyleOpenMode(openMode)); data/seqan2-2.4.0+dfsg/include/seqan/stream/adapt_ios.h:358:13: [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). inline bool open(std::basic_fstream<TValue, TTraits> & stream, const char *fileName) data/seqan2-2.4.0+dfsg/include/seqan/stream/adapt_ios.h:360:12: [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). return open(stream, fileName, DefaultOpenMode<std::basic_fstream<TValue, TTraits> >::VALUE); data/seqan2-2.4.0+dfsg/include/seqan/stream/adapt_ios.h:364:13: [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). inline bool open(std::basic_ifstream<TValue, TTraits> & stream, const char *fileName) data/seqan2-2.4.0+dfsg/include/seqan/stream/adapt_ios.h:366:12: [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). return open(stream, fileName, DefaultOpenMode<std::basic_ifstream<TValue, TTraits> >::VALUE); data/seqan2-2.4.0+dfsg/include/seqan/stream/adapt_ios.h:370:13: [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). inline bool open(std::basic_ofstream<TValue, TTraits> & stream, const char *fileName) data/seqan2-2.4.0+dfsg/include/seqan/stream/adapt_ios.h:372:12: [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). return open(stream, fileName, DefaultOpenMode<std::basic_ofstream<TValue, TTraits> >::VALUE); data/seqan2-2.4.0+dfsg/include/seqan/stream/file_stream.h:1154:9: [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(*this, fileName, openMode); data/seqan2-2.4.0+dfsg/include/seqan/stream/file_stream.h:1245:1: [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(FilePageTable<TValue, TDirection, TSpec> & pager, const char * fileName, int flags) data/seqan2-2.4.0+dfsg/include/seqan/stream/file_stream.h:1250:19: [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). bool result = open(pager.file, fileName, flags); data/seqan2-2.4.0+dfsg/include/seqan/stream/file_stream.h:1257:1: [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(FileStream<TValue, TDirection, TSpec> & stream, const char * fileName, int openMode = DefaultOpenMode<FileStream<TValue, TDirection, TSpec> >::VALUE) data/seqan2-2.4.0+dfsg/include/seqan/stream/file_stream.h:1259:12: [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). return open(stream.buffer.pager, fileName, openMode); data/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:277:24: [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). bool success = open(*this, ostream, format); data/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:318:24: [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). bool success = open(*this, ostream, format); data/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:651:10: [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). if (!open(file.stream, stream, compressionFormat)) data/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:670:1: [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(FormattedFile<TFileFormat, TDirection, TSpec> & file, data/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:677:13: [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). inline bool open(FormattedFile<TFileFormat, Output, TSpec> & file, data/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:686:13: [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). inline bool open(FormattedFile<TFileFormat, Output, TSpec> & file, data/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:704:10: [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). if (!open(file.stream, fileName, openMode)) data/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:735:13: [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). inline bool open(FormattedFile<TFileFormat, TDirection, TSpec> & file, data/seqan2-2.4.0+dfsg/include/seqan/stream/iostream_bgzf.h:68:9: [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[BGZF_MAX_BLOCK_SIZE]; data/seqan2-2.4.0+dfsg/include/seqan/stream/iostream_zutil.h:42:14: [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. extern const char *z_errmsg[10]; /* indexed by 2-zlib_error */ data/seqan2-2.4.0+dfsg/include/seqan/stream/iostream_zutil.h:104:6: [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). fopen((name), (mode), "mbc=60", "ctx=stm", "rfm=fix", "mrs=512") data/seqan2-2.4.0+dfsg/include/seqan/stream/iostream_zutil.h:150:30: [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). # define F_OPEN(name, mode) fopen((name), (mode)) data/seqan2-2.4.0+dfsg/include/seqan/stream/iostream_zutil.h:184:21: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. # define zmemcpy memcpy data/seqan2-2.4.0+dfsg/include/seqan/stream/stream_base.h:101:12: [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 const VALUE[3]; data/seqan2-2.4.0+dfsg/include/seqan/stream/stream_base.h:111:12: [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 const VALUE[3]; data/seqan2-2.4.0+dfsg/include/seqan/stream/stream_base.h:124:12: [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 const * VALUE[1]; data/seqan2-2.4.0+dfsg/include/seqan/stream/stream_base.h: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 const * VALUE[5]; data/seqan2-2.4.0+dfsg/include/seqan/stream/stream_base.h:154:12: [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 const * VALUE[1]; data/seqan2-2.4.0+dfsg/include/seqan/stream/stream_compressor.h:107:12: [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 const VALUE[18]; data/seqan2-2.4.0+dfsg/include/seqan/stream/stream_compressor.h:418:5: [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 putbackBuf[18]; data/seqan2-2.4.0+dfsg/include/seqan/stream/virtual_stream.h:285:9: [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(*this, stream); data/seqan2-2.4.0+dfsg/include/seqan/stream/virtual_stream.h:294:9: [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(*this, fileName, openMode); data/seqan2-2.4.0+dfsg/include/seqan/stream/virtual_stream.h:552:1: [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(VirtualStream<TValue, TDirection, TTraits> &stream, TStream &fileStream, TCompressionType & compressionType) data/seqan2-2.4.0+dfsg/include/seqan/stream/virtual_stream.h:568:20: [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). return open(stream, stream.bufferedStream, compressionType); data/seqan2-2.4.0+dfsg/include/seqan/stream/virtual_stream.h:593:1: [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(VirtualStream<TValue, TDirection, TTraits> &stream, TStream &fileStream, TCompressionType const & compressionType) data/seqan2-2.4.0+dfsg/include/seqan/stream/virtual_stream.h:596:12: [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). return open(stream, fileStream, stream.format); data/seqan2-2.4.0+dfsg/include/seqan/stream/virtual_stream.h:601:1: [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(VirtualStream<TValue, Input> &stream, TStream &fileStream) data/seqan2-2.4.0+dfsg/include/seqan/stream/virtual_stream.h:605:12: [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). return open(stream, fileStream, stream.format); data/seqan2-2.4.0+dfsg/include/seqan/stream/virtual_stream.h:610:1: [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(VirtualStream<TValue, TDirection, TTraits> &stream, data/seqan2-2.4.0+dfsg/include/seqan/stream/virtual_stream.h:618:10: [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). if (!open(stream.file, fileName, openMode)) data/seqan2-2.4.0+dfsg/include/seqan/stream/virtual_stream.h:625:9: [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(stream, stream.file, stream.format); // read from a pipe (without file extension) data/seqan2-2.4.0+dfsg/include/seqan/system/file_async.h:96:10: [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). bool open(char const * fileName, int openMode = DefaultOpenMode<File>::VALUE) data/seqan2-2.4.0+dfsg/include/seqan/system/file_async.h:147:9: [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 szTempName[MAX_PATH]; data/seqan2-2.4.0+dfsg/include/seqan/system/file_async.h:149:22: [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. static const char szTempPath[MAX_PATH] = SEQAN_DEFAULT_TMPDIR; data/seqan2-2.4.0+dfsg/include/seqan/system/file_async.h:151:9: [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 szTempPath[MAX_PATH]; data/seqan2-2.4.0+dfsg/include/seqan/system/file_async.h:165:16: [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). return open(szTempName, openMode | OPEN_TEMPORARY); data/seqan2-2.4.0+dfsg/include/seqan/system/file_async.h:393:9: [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(request.xmitDone); data/seqan2-2.4.0+dfsg/include/seqan/system/file_async.h:428:9: [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(request.xmitDone); data/seqan2-2.4.0+dfsg/include/seqan/system/file_async.h:745:10: [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). bool open(char const * fileName, int openMode = DefaultOpenMode<File>::VALUE) data/seqan2-2.4.0+dfsg/include/seqan/system/file_async.h:747:20: [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). handle = ::open(fileName, Base::_getOFlag(openMode & ~OPEN_ASYNC), S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH); data/seqan2-2.4.0+dfsg/include/seqan/system/file_async.h:758:29: [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). handleAsync = ::open(fileName, Base::_getOFlag(openMode | (OPEN_ASYNC & ~OPEN_CREATE)), S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH); data/seqan2-2.4.0+dfsg/include/seqan/system/file_directory.h:77:28: [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). friend inline bool open(Directory &dir, char const *dirName); data/seqan2-2.4.0+dfsg/include/seqan/system/file_directory.h:95:13: [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(*this, dirName); data/seqan2-2.4.0+dfsg/include/seqan/system/file_directory.h:122:5: [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(Directory &dir, char const *dirName) data/seqan2-2.4.0+dfsg/include/seqan/system/file_directory.h:196:28: [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). friend inline bool open(Directory &dir, char const *dirName); data/seqan2-2.4.0+dfsg/include/seqan/system/file_directory.h:215:13: [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(*this, dirName); data/seqan2-2.4.0+dfsg/include/seqan/system/file_directory.h:242:5: [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(Directory &dir, char const *dirName) data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:136:10: [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). bool open(char const * fileName, int openMode = DefaultOpenMode<File>::VALUE) data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:162:23: [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). bool result = open(fileName, openMode | OPEN_TEMPORARY); data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:285:18: [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). virtual bool open(char const * fileName, int openMode = DefaultOpenMode<File>::VALUE) data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:287:20: [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). handle = ::open(fileName, _getOFlag(openMode), S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH); data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:294:24: [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). handle = ::open(fileName, _getOFlag(openMode & ~OPEN_ASYNC), S_IRUSR | S_IWUSR | S_IRGRP | S_IWGRP | S_IROTH | S_IWOTH); data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:347:25: [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). if ((handle = ::mkstemp((char *)tmpDir.c_str())) == -1) data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:354:26: [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). if (!(close() && open(toCString(tmpDir), openMode))) data/seqan2-2.4.0+dfsg/include/seqan/system/system_event_win.h:62:23: [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). SEQAN_DO_SYS2(open(initial), "Could not create Event"); data/seqan2-2.4.0+dfsg/include/seqan/system/system_event_win.h:97:17: [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). inline bool open(BOOL initial = FALSE) data/seqan2-2.4.0+dfsg/include/seqan/system/system_event_win.h:191:13: [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). inline bool open(Event & e, bool initial) data/seqan2-2.4.0+dfsg/include/seqan/system/system_event_win.h:193:14: [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). return e.open(initial); data/seqan2-2.4.0+dfsg/include/seqan/system/system_event_win.h:196:13: [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). inline bool open(Event & e) data/seqan2-2.4.0+dfsg/include/seqan/system/system_event_win.h:198:12: [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). return open(e, false); data/seqan2-2.4.0+dfsg/include/seqan/system/system_forwards.h:63:13: [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). inline bool open(Event &e, bool initial); // "include/seqan/system/system_event.h"(101) data/seqan2-2.4.0+dfsg/include/seqan/system/system_forwards.h:64:13: [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). inline bool open(Event &e); // "include/seqan/system/system_event.h"(105) data/seqan2-2.4.0+dfsg/include/seqan/tabix_io/tabix_index_tbi.h:56:6: [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). bool open(TabixIndex & index, char const * filename); data/seqan2-2.4.0+dfsg/include/seqan/tabix_io/tabix_index_tbi.h:151:14: [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). if (!open(*this, fileName)) data/seqan2-2.4.0+dfsg/include/seqan/tabix_io/tabix_index_tbi.h:441:1: [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(TabixIndex & index, char const * filename) data/seqan2-2.4.0+dfsg/include/seqan/tabix_io/tabix_index_tbi.h:446:10: [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). if (!open(tbi, filename)) data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:200:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:211:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:246:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:281:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:316:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:351:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:386:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:421:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:456:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:491:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:526:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:562:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:598:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:634:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:670:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:706:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:742:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:778:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:814:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/translation/translation_tables.h:850:12: [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 const VALUE[4][4][4]; data/seqan2-2.4.0+dfsg/include/seqan/ucsc_io/ucsc_io.h:110:12: [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 const * VALUE[1]; // default is one extension data/seqan2-2.4.0+dfsg/include/seqan/ucsc_io/ucsc_io.h:123:12: [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 const * VALUE[1]; // default is one extension data/seqan2-2.4.0+dfsg/include/seqan/vcf_io/vcf_file.h:102:21: [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. static unsigned char const VALUE[16]; data/seqan2-2.4.0+dfsg/include/seqan/vcf_io/vcf_file.h:114:21: [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. static unsigned char const VALUE[5]; data/seqan2-2.4.0+dfsg/include/seqan/vcf_io/vcf_file.h:127:12: [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 const * VALUE[1]; // default is one extension data/seqan2-2.4.0+dfsg/include/seqan/vcf_io/vcf_file.h:139:12: [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 const * VALUE[1]; // default is one extension data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:167:11: [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 * argv[1] = {A_INT_0}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:187:11: [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 * argv[1] = {A_INT_0}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:207:11: [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 * argv[3] = {A_BOOL_ARG, A_BOOL_ARG_SHORT, A_BOOL_ARG_ON}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:228:11: [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 * argv[3] = {A_BOOL_ARG, A_BOOL_ARG_SHORT, A_BOOL_ARG_OFF}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:249:11: [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 * argv[3] = {A_INT_0, A_INT_1, A_INT_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h: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. const char * argv[3] = {A_INT_0, A_INT_2, A_INT_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:291:11: [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 * argv[3] = {A_INT_0, A_INT_1, A_INT_5}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:308:11: [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 * argv[3] = {A_INT64_0, A_INT64_1, A_INT64_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:329:11: [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 * argv[3] = {A_INT64_0, A_INT64_2, A_INT64_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:350:11: [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 * argv[3] = {A_INT64_0, A_INT64_1, A_INT64_5}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:367:11: [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 * argv[3] = {A_DOUBLE_0, A_DOUBLE_1, A_DOUBLE_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:388:11: [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 * argv[3] = {A_DOUBLE_0, A_DOUBLE_2, A_DOUBLE_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:409:11: [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 * argv[3] = {A_DOUBLE_0, A_DOUBLE_1, A_DOUBLE_5}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:426:11: [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 * argv[3] = {A_DOUBLE_0, A_DOUBLE_1, A_DOUBLE_6}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:447:11: [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 * argv[3] = {A_STRING_0, A_STRING_1, A_STRING_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:468:11: [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 * argv[3] = {A_STRING_0, A_STRING_2, A_STRING_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:488:11: [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 * argv[2] = {A_STRING_0, A_STRING_2}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:504:11: [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 * argv[7] = {A_STRING_0, A_STRING_1, A_STRING_3, A_STRING_2, A_STRING_3, A_STRING_1, A_STRING_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:532:11: [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 * argv[3] = {A_DOUBLE_0, A_DOUBLE_2, A_DOUBLE_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:553:11: [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 * argv[3] = {A_DOUBLE_0, A_DOUBLE_2, A_DOUBLE_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:571:11: [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 * argv[3] = {A_DOUBLE_0, A_DOUBLE_2, A_DOUBLE_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:590:11: [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 * argv[3] = {A_INT_0, A_INT_2, A_INT_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:612:11: [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 * argv[3] = {A_INT_0, A_INT_2, A_INT_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:630:11: [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 * argv[3] = {A_INT_0, A_INT_2, A_INT_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:648:11: [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 * argv[3] = {A_STRING_0, A_STRING_2, A_STRING_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:670:11: [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 * argv[3] = {A_STRING_0, A_STRING_2, A_STRING_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:686:11: [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 * argv[3] = {A_IN_FILE_0, A_IN_FILE_1, A_IN_FILE_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:706:11: [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 * argv[3] = {A_IN_FILE_0, A_IN_FILE_2, A_IN_FILE_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:726:11: [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 * argv[2] = {A_IN_FILE_0, A_IN_FILE_1}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:744:11: [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 * argv[3] = {A_IN_FILE_0, A_IN_FILE_2, A_IN_FILE_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:762:11: [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 * argv[3] = {A_IN_FILE_0, A_IN_FILE_2, A_IN_FILE_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:784:11: [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 * argv[3] = {A_IN_FILE_0, A_IN_FILE_2, A_IN_FILE_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:865:11: [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 * argv[3] = {A_OUT_FILE_0, A_OUT_FILE_1, A_OUT_FILE_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:885:11: [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 * argv[3] = {A_OUT_FILE_0, A_OUT_FILE_2, A_OUT_FILE_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:905:11: [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 * argv[2] = {A_OUT_FILE_0, A_OUT_FILE_1}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:923:11: [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 * argv[3] = {A_OUT_FILE_0, A_OUT_FILE_2, A_OUT_FILE_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:941:11: [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 * argv[3] = {A_OUT_FILE_0, A_OUT_FILE_2, A_OUT_FILE_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:963:11: [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 * argv[3] = {A_OUT_FILE_0, A_OUT_FILE_2, A_OUT_FILE_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:985:11: [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 * argv[3] = {A_OUT_FILE_0, A_OUT_FILE_2, A_OUT_FILE_4}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1008:11: [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 * argv[5] = {A_OUT_FILE_0, A_OUT_FILE_2, A_OUT_FILE_5, A_OUT_FILE_6, A_OUT_FILE_7}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1031:11: [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 * argv[5] = {A_OUT_FILE_0, A_OUT_FILE_2, A_OUT_FILE_3, A_OUT_FILE_6, A_OUT_FILE_8}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1048:11: [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 * argv[3] = {A_ARGUMENT_0, A_ARGUMENT_1, A_ARGUMENT_2}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1065:11: [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 * argv[2] = {A_ARGUMENT_0, A_ARGUMENT_1}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1081:11: [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 * argv[2] = {A_ARGUMENT_0, A_ARGUMENT_DOUBLE_5}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1101:11: [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 * argv[2] = {A_ARGUMENT_0, A_ARGUMENT_1}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1202:11: [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 * argv[7] = {A_TUPLE_LIST, A_TUPLE_LIST_L, A_TUPLE_LIST_L_1, A_TUPLE_LIST_L_2, A_TUPLE_LIST_L, A_TUPLE_LIST_L_3, A_TUPLE_LIST_L_4}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1231:11: [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 * argv[9] = {A_TUPLE_LIST, A_TUPLE_LIST_DL, A_TUPLE_LIST_DL_1, A_TUPLE_LIST_DL_2, A_TUPLE_LIST_DL_3, A_TUPLE_LIST_DL, A_TUPLE_LIST_DL_4, A_TUPLE_LIST_DL_5, A_TUPLE_LIST_DL_6}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1265:11: [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 * argv[8] = {A_TUPLE_LIST, A_TUPLE_LIST_DL, A_TUPLE_LIST_DL_1, A_TUPLE_LIST_DL_2, A_TUPLE_LIST_DL_3, A_TUPLE_LIST_DL, A_TUPLE_LIST_DL_4, A_TUPLE_LIST_DL_5}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1288:11: [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 * argv[3] = { A_BOOL, A_BOOL_1, A_BOOL_2 }; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1316:11: [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 * argv[2] = { A_BOOL, A_BOOL_3 }; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1345:11: [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 * argv[2] = { A_BOOL, A_BOOL_3 }; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1374:11: [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 * argv[3] = {A_STRING_0, A_STRING_1, A_STRING_3}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1401:5: [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 buffer1[100]; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1403:5: [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 buffer2[100]; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1405:5: [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 buffer3[100]; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1408:5: [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 * argv[3] = {&buffer1[0], &buffer2[0], &buffer3[0]}; data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse_version_check.h:142:11: [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 * argv[3] = {TestVersionCheck_::APP_NAME.c_str(), TestVersionCheck_::OPTION_VERSION_CHECK, data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse_version_check.h:162:11: [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 * argv[3] = {TestVersionCheck_::APP_NAME.c_str(), TestVersionCheck_::OPTION_VERSION_CHECK, data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse_version_check.h:182:11: [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 * argv[3] = {TestVersionCheck_::APP_NAME.c_str(), TestVersionCheck_::OPTION_VERSION_CHECK, data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse_version_check.h:206:11: [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 * argv[3] = {TestVersionCheck_::APP_NAME.c_str(), TestVersionCheck_::OPTION_VERSION_CHECK, data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse_version_check.h:233:11: [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 * argv[3] = {TestVersionCheck_::APP_NAME.c_str(), TestVersionCheck_::OPTION_VERSION_CHECK, data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse_version_check.h:259:11: [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 * argv[3] = {TestVersionCheck_::APP_NAME.c_str(), TestVersionCheck_::OPTION_VERSION_CHECK, data/seqan2-2.4.0+dfsg/tests/bam_io/test_bam_file.h:521:5: [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(bamI, toCString(filePath)); data/seqan2-2.4.0+dfsg/tests/bam_io/test_bam_file.h:540:5: [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(bamO, toCString(filePath)); data/seqan2-2.4.0+dfsg/tests/bam_io/test_bam_index.h:67:18: [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). SEQAN_ASSERT(open(baiIndex, toCString(baiFilename))); data/seqan2-2.4.0+dfsg/tests/bam_io/test_bam_index.h:106:18: [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). SEQAN_ASSERT(open(baiIndex, toCString(baiFilename))); data/seqan2-2.4.0+dfsg/tests/bam_io/test_read_bam.h:57:5: [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(in, toCString(bamFilename)); data/seqan2-2.4.0+dfsg/tests/bam_io/test_read_bam.h:111:5: [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(in, toCString(bamFilename)); data/seqan2-2.4.0+dfsg/tests/bam_io/test_write_bam.h:81:5: [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(EXPECTED, toCString(bamFilename)); data/seqan2-2.4.0+dfsg/tests/bam_io/test_write_bam.h:141:5: [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(EXPECTED, toCString(bamFilename)); data/seqan2-2.4.0+dfsg/tests/basic/test_basic_alphabet.h:120:9: [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 c_buf1[200 * sizeof(Test1)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_alphabet.h:123:9: [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 c_buf2[200 * sizeof(Test1)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:205:9: [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 space[sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:226:9: [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 space[sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:270:9: [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 space[sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:292:9: [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 space[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:311:9: [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 space[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:340:5: [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 space[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.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 space2[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:372:5: [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 space[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:379:5: [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 space2[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:410:5: [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 space[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:432:5: [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 space[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:461:5: [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 source[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:465:5: [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 target[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:493:5: [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 source[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:497:5: [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 target[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:525:5: [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 source[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:529:5: [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 target[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:561:5: [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 source[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:565:5: [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 target[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:593:5: [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 source[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:597:5: [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 target[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:625:5: [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 source[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:629:5: [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 target[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:662:9: [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 arr[6 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:680:9: [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 arr[6 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:698:9: [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 arr[6 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:722:9: [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 arr[6 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:744:9: [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 arr[6 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_array_construct_destruct.h:771:9: [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 arr[6 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:178:9: [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 space[sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:199:9: [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 space[sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:221:9: [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 space[sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:261:9: [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 space[sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:281:9: [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 space[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:300:9: [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 space[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:327:5: [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 space[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:334:5: [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 space2[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:357:5: [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 space[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:364:5: [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 space2[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:394:5: [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 space[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:414:5: [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 space[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:441:5: [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 source[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:445:5: [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 target[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:471:5: [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 source[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:475:5: [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 target[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:501:5: [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 source[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:505:5: [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 target[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:535:5: [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 source[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:539:5: [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 target[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:565:5: [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 source[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:569:5: [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 target[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:595:5: [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 source[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:599:5: [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 target[2 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:630:9: [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 arr[6 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:648:9: [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 arr[6 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:666:9: [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 arr[6 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:690:9: [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 arr[6 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:712:9: [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 arr[6 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_construct_destruct.h:738:9: [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 arr[6 * sizeof(CDStruct)]; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_proxy.h:72:5: [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 s1[100] = ""; data/seqan2-2.4.0+dfsg/tests/basic/test_basic_proxy.h:93:5: [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 data[10] = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 }; data/seqan2-2.4.0+dfsg/tests/bed_io/test_bed_io.cpp:448:5: [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(bedI, toCString(filePath)); data/seqan2-2.4.0+dfsg/tests/bed_io/test_bed_io.cpp:467:5: [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(bedO, toCString(filePath)); data/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:490:5: [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 filenameBuffer[1000]; data/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:50:5: [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(inString, toCString(gffPath)); data/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:107:5: [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(inString, toCString(gffPath)); data/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:128:5: [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(goldString, toCString(goldPath)); data/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:139:5: [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(inString, toCString(gffPath)); data/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:197:5: [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(inString, toCString(gtfPath)); data/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:263:5: [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(inString, toCString(gtfPath)); data/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:319:5: [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(inString, toCString(gtfPath)); data/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:344:5: [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(goldString, toCString(goldPath)); data/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:510:5: [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(gffI, toCString(filePath)); data/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:529:5: [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(gffO, toCString(filePath)); data/seqan2-2.4.0+dfsg/tests/graph_align/test_graph_match_refinement.h:188:18: [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). bool f = open(str[i], s.str().c_str()); data/seqan2-2.4.0+dfsg/tests/graph_align/test_graph_match_refinement.h:304:5: [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(matches, strstream.str().c_str()); data/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_tcoffee.h:191:10: [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). strm.open(fileName.c_str(), std::ios_base::out | std::ios_base::trunc); data/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_tcoffee.h:201:14: [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). strmRead.open(fileName.c_str(), std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_tcoffee.h:212:11: [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). strm2.open(fileName.c_str(), std::ios_base::out | std::ios_base::trunc); data/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_tcoffee.h:218:15: [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). strmRead2.open(fileName.c_str(), std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_tcoffee.h:239:15: [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). strmBlast.open(fileName.c_str(), std::ios_base::out | std::ios_base::trunc); data/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_tcoffee.h:249:18: [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). strmBlastLib.open(fileName.c_str(), std::ios_base::in | std::ios_base::binary); data/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:109:18: [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). SEQAN_ASSERT(open(this->index, fileName)); data/seqan2-2.4.0+dfsg/tests/index/test_stree_iterators.h:130:22: [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). std::cout << open(gen1, "corpus/NC_000117.txt"); data/seqan2-2.4.0+dfsg/tests/index/test_stree_iterators.h:131:22: [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). std::cout << open(gen2, "corpus/NC_002620.txt"); data/seqan2-2.4.0+dfsg/tests/index/test_stree_iterators.h:132:22: [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). std::cout << open(gen3, "corpus/NC_007429.txt"); data/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:179:5: [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(roiI, toCString(filePath)); data/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:198:5: [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(roiO, toCString(filePath)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_fai_index.h:74:21: [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). SEQAN_ASSERT_EQ(open(faiIndex, toCString(filePath)), true); data/seqan2-2.4.0+dfsg/tests/seq_io/test_fai_index.h:88:21: [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). SEQAN_ASSERT_EQ(open(faiIndex, toCString(filePath)), true); data/seqan2-2.4.0+dfsg/tests/seq_io/test_fai_index.h:103:25: [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). SEQAN_ASSERT_EQ(open(faiIndex, toCString(filePath)), true); data/seqan2-2.4.0+dfsg/tests/seq_io/test_fai_index.h:114:25: [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). SEQAN_ASSERT_EQ(open(faiIndex, toCString(filePath)), true); data/seqan2-2.4.0+dfsg/tests/seq_io/test_fai_index.h:125:25: [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). SEQAN_ASSERT_EQ(open(faiIndex, toCString(filePath)), true); data/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io_generic.h:47:5: [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 filenameBuffer[1000]; data/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io_generic.h:74:5: [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 filenameBuffer[1000]; data/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io_generic.h:101:5: [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 filenameBuffer[1000]; data/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io_generic.h:128:5: [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 filenameBuffer[1000]; data/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io_generic.h:162:5: [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 filenameBuffer[1000]; data/seqan2-2.4.0+dfsg/tests/seq_io/test_sequence_file.h:352:5: [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(seqI, toCString(filePath)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_sequence_file.h:371:5: [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(seqO, toCString(filePath)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_stream_record_reader_fasta.h:215:5: [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(mmapString, toCString(filename)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_stream_record_reader_fasta.h:233:5: [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(mmapString, toCString(filename)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_stream_record_reader_fasta.h:251:5: [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(mmapString, toCString(filename)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_stream_record_reader_fasta.h:269:5: [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(mmapString, toCString(filename)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_stream_record_reader_fasta.h:287:5: [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(mmapString, toCString(filename)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_stream_record_reader_fasta.h:305:5: [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(mmapString, toCString(filename)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_tag_select_intersect.h:64:5: [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(inputFile, toCString(filePath)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_tag_select_intersect.h:73:5: [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(inputFile, toCString(filePath)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_tag_select_intersect.h:81:5: [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(inputFile, toCString(filePath)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_tag_select_intersect.h:89:5: [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(inputFile, toCString(filePath)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_tag_select_intersect.h:98:5: [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(inputFile, toCString(filePath)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_write_bam.h:82:10: [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). if (!open(bamFileIn, toCString(tmpPath))) data/seqan2-2.4.0+dfsg/tests/sequence/test_string.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 str[100] = "hallo"; data/seqan2-2.4.0+dfsg/tests/sequence/test_string.h:620:5: [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 str1[200] = "hello"; data/seqan2-2.4.0+dfsg/tests/sequence/test_string.h:683:5: [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 strq [200] = "hello seqan"; data/seqan2-2.4.0+dfsg/tests/sequence/test_string.h:1204:5: [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 str7[800] = "hello again"; data/seqan2-2.4.0+dfsg/tests/statistics/test_statistics_base.h:163:16: [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 *fd = fopen(buffer.c_str(), "r"); data/seqan2-2.4.0+dfsg/tests/store/test_store_io_bam.h:119:5: [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 fastaBuffer[1023]; data/seqan2-2.4.0+dfsg/tests/store/test_store_io_bam.h:121:5: [2] (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). Risk is low because the source is a constant string. strcat(fastaBuffer, "/projects/tests/store/toy.fa"); data/seqan2-2.4.0+dfsg/tests/store/test_store_io_bam.h:124:5: [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 samBuffer[1023]; data/seqan2-2.4.0+dfsg/tests/store/test_store_io_bam.h:126:5: [2] (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). Risk is low because the source is a constant string. strcat(samBuffer, "/projects/tests/store/toy.sam"); data/seqan2-2.4.0+dfsg/tests/store/test_store_io_bam.h: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 tmpBuffer[1023]; data/seqan2-2.4.0+dfsg/tests/store/test_store_io_bam.h:135:20: [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 * samFp = fopen(samBuffer, "rb"); data/seqan2-2.4.0+dfsg/tests/store/test_store_io_bam.h:141:20: [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 * outFb = fopen(tmpBuffer, "wb"); data/seqan2-2.4.0+dfsg/tests/stream/test_stream.cpp:186:10: [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). file.open(toCString(ctx.inputFilename), std::ios_base::out | std::ios_base::trunc | std::ios_base::binary); data/seqan2-2.4.0+dfsg/tests/stream/test_stream.cpp:228:18: [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). SEQAN_ASSERT(open(this->stream, toCString(ctx.inputFilename), OPEN_RDONLY)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream.cpp:245:5: [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(this->stream, toCString(ctx.inputFilename)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream.cpp:264:5: [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(this->stream, toCString(ctx.inputFilename), OPEN_RDONLY); data/seqan2-2.4.0+dfsg/tests/stream/test_stream.cpp:285:18: [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). SEQAN_ASSERT(open(this->stream, toCString(ctx.outputFilename), OPEN_WRONLY)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream.cpp:291:18: [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). SEQAN_ASSERT(open(this->stream, toCString(ctx.inputFilename), OPEN_WRONLY|OPEN_APPEND)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream.cpp:308:5: [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(this->stream, toCString(ctx.outputFilename), OPEN_WRONLY); data/seqan2-2.4.0+dfsg/tests/stream/test_stream.cpp:331:5: [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(this->stream, toCString(ctx.inputFilename), DefaultOpenMode<TStream>::VALUE | OPEN_APPEND); data/seqan2-2.4.0+dfsg/tests/stream/test_stream.cpp:347:5: [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(this->stream, toCString(ctx.inputFilename), DefaultOpenMode<TStream>::VALUE | OPEN_APPEND); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:87:18: [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). SEQAN_ASSERT(open(stream, toCString(tempFilename))); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:93:5: [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, toCString(tempFilename)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:98:18: [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). SEQAN_ASSERT(open(stream2, toCString(tempFilename))); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:110:18: [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). SEQAN_ASSERT(open(stream, toCString(tempFilename))); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:116:5: [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, toCString(tempFilename)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:121:18: [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). SEQAN_ASSERT(open(stream2, toCString(tempFilename))); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:132:18: [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). SEQAN_ASSERT(open(stream, toCString(tempFilename))); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:140:18: [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). SEQAN_ASSERT(open(stream2, toCString(tempFilename))); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:141:5: [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[100] = "__________"; data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:156:18: [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). SEQAN_ASSERT(open(stream, toCString(tempFilename))); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:163:18: [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). SEQAN_ASSERT(open(stream2, toCString(tempFilename))); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:164:5: [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[100] = "__________"; data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:182:18: [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). SEQAN_ASSERT(open(stream, toCString(tempFilename))); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.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 buffer[100]; data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:189:18: [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). SEQAN_ASSERT(open(stream2, toCString(tempFilename))); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:217:18: [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). SEQAN_ASSERT(open(stream, toCString(tempFilename))); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:225:18: [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). SEQAN_ASSERT(open(stream2, toCString(tempFilename))); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:240:18: [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). SEQAN_ASSERT(open(stream, toCString(tempFilename), OPEN_RDWR | OPEN_CREATE | OPEN_APPEND)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:248:18: [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). SEQAN_ASSERT(open(stream2, toCString(tempFilename), OPEN_RDWR | OPEN_CREATE | OPEN_APPEND)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:278:18: [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). SEQAN_ASSERT(open(stream, toCString(tempFilename))); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:302:18: [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). SEQAN_ASSERT(open(stream, toCString(tempFilename))); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:341:18: [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). SEQAN_ASSERT(open(stream, toCString(tempFilename))); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:342:5: [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[13]; data/seqan2-2.4.0+dfsg/tests/stream/test_stream_generic.h: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 buffer[100]; data/seqan2-2.4.0+dfsg/tests/stream/test_stream_tokenization.h:133:9: [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(file, toCString(fileName)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_tokenization.h:149:9: [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(file, toCString(fileName)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_tokenization.h:165:9: [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(file, toCString(fileName)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_virtual_stream.h:95:18: [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). SEQAN_ASSERT(open(vstream, toCString(fileName), OPEN_RDONLY)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_virtual_stream.h:99:18: [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). SEQAN_ASSERT(open(vstream, toCString(fileName), OPEN_RDONLY)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_virtual_stream.h:104:22: [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). SEQAN_ASSERT_NOT(open(vstream, toCString(fileName), OPEN_RDONLY)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_virtual_stream.h:125:5: [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(vstream, toCString(toCString(fileName)), OPEN_RDONLY); data/seqan2-2.4.0+dfsg/tests/ucsc_io/test_ucsc_io.cpp:54:18: [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). SEQAN_ASSERT(open(mmapString, toCString(ucscPath))); data/seqan2-2.4.0+dfsg/tests/ucsc_io/test_ucsc_io.cpp:109:18: [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). SEQAN_ASSERT(open(mmapString, toCString(ucscPath))); data/seqan2-2.4.0+dfsg/tests/ucsc_io/test_ucsc_io.cpp:140:18: [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). SEQAN_ASSERT(open(mmapString, toCString(ucscPath))); data/seqan2-2.4.0+dfsg/tests/ucsc_io/test_ucsc_io.cpp:160:18: [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). SEQAN_ASSERT(open(mmapString, toCString(ucscPath))); data/seqan2-2.4.0+dfsg/tests/ucsc_io/test_ucsc_io.cpp:259:18: [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). SEQAN_ASSERT(open(mmapString, toCString(ucscPath))); data/seqan2-2.4.0+dfsg/tests/ucsc_io/test_ucsc_io.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). SEQAN_ASSERT(open(mmapString, toCString(ucscPath))); data/seqan2-2.4.0+dfsg/tests/vcf_io/test_vcf_io.h:50:18: [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). SEQAN_ASSERT(open(mmapString, toCString(vcfPath))); data/seqan2-2.4.0+dfsg/tests/vcf_io/test_vcf_io.h:111:5: [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(mmapString, toCString(vcfPath)); data/seqan2-2.4.0+dfsg/tests/vcf_io/test_vcf_io.h:501:5: [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(vcfI, toCString(vcfPath)); data/seqan2-2.4.0+dfsg/tests/vcf_io/test_vcf_io.h:520:5: [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(vcfO, toCString(vcfPath)); data/seqan2-2.4.0+dfsg/util/cmake/GetCurrentDate.cpp:44:5: [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 date[100]; data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:317:40: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). for(unsigned i = 0; i < length(read); ++i) data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:318:44: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). avgRQ += (int) getQualityValue(read[i]); data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:321:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if((char)(avgRQ/length(read))<(fragmentStore.alignQualityStore[(*it).id]).score) data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:323:85: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). (fragmentStore.alignQualityStore[(*it).id]).score = (char)(avgRQ/length(read)); data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:398:45: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if(clipLeft+clipRight > (int)length(read) || clipLeft > (int)length(read) || clipRight > (int)length(read)) data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:398:77: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if(clipLeft+clipRight > (int)length(read) || clipLeft > (int)length(read) || clipRight > (int)length(read)) data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:398:110: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if(clipLeft+clipRight > (int)length(read) || clipLeft > (int)length(read) || clipRight > (int)length(read)) data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:402:52: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::cout << "readlength = "<<length(read)<< " \n"; data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:405:39: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::cout << "read=" << read << std::endl; data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:409:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). clipLeft = length(read); data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:413:52: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::cout << "readlength = "<<length(read)<< " \n"; data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:416:39: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::cout << "read=" << read << std::endl; data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:423:28: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if((int)length(read)-clipLeft-clipRight < options.minClippedLength) data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:426:51: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::cout << "Discarded: "<<read<<" at position "<< beginPos <<"\n"; data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:433:26: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read = infix(read,clipLeft,length(read)-clipRight); data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:433:47: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read = infix(read,clipLeft,length(read)-clipRight); data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:437:44: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). for(unsigned i = 0; i < length(read); ++i) data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:438:48: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). avgRQ += (int) getQualityValue(read[i]); data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:439:46: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). aliQ.score = (char)(avgRQ/length(read)); data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:444:41: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). assignSource(row(align, 0), read); data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:461:82: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). unsigned viewPosReadLast = toViewPosition(row(align, 0), length(read) - 1); data/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:526:43: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::cout << "read=" << read << std::endl; data/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.cpp:84:28: [1] (access) umask: Ensure that umask is given most restrictive possible setting (e.g., 066 or 077) (CWE-732). mode_t cur_umask = umask(S_IRWXO | S_IRWXG); // to silence Coverity warning data/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.cpp:87:9: [1] (access) umask: Ensure that umask is given most restrictive possible setting (e.g., 066 or 077) (CWE-732). umask(cur_umask); data/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:971:75: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). fragmentIdSplitter.files[rID * haplotypeCount + hID]->read( data/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:187:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void _simulateSequence(TRead & read, TRng & rng, TFrag const & frag, data/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:190:11: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). clear(read); data/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:201:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). appendValue(read, *it); data/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:223:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). appendValue(read, seqan::Dna5(num)); data/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:225:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). appendValue(read, seqan::Dna5(num + (num == ordValue(*it)))); data/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:53:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void _simulateSequence(TRead & read, TRng & rng, TFrag const & frag, data/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:56:11: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). clear(read); data/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:67:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). appendValue(read, *it); data/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:89:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). appendValue(read, seqan::Dna5(num)); data/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:91:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). appendValue(read, seqan::Dna5(num + (num == ordValue(*it)))); data/seqan2-2.4.0+dfsg/apps/micro_razers/outputFormat.h:171:59: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). for (unsigned i = 0; i < length(posError) && i < length(read); ++i) data/seqan2-2.4.0+dfsg/apps/micro_razers/outputFormat.h:172:75: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if ((options.compMask[ordValue(genome[i])] & options.compMask[ordValue(read[i])]) == 0) data/seqan2-2.4.0+dfsg/apps/ngs_roi/png_canvas.h:535:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void read(char const * /*filename*/) data/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:27:52: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). Pattern<Dna5String, MyersUkkonenReads> pattern(read, -static_cast<int>(length(read))); data/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:27:83: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). Pattern<Dna5String, MyersUkkonenReads> pattern(read, -static_cast<int>(length(read))); data/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:33:42: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if (endPosition(finder) < length(read)) data/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:44:41: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). assignSource(row(ali, 1), infix(read, 0, length(read))); data/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:44:57: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). assignSource(row(ali, 1), infix(read, 0, length(read))); data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:388:49: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadSeq /*const*/ & read, data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:403:49: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). Pattern<TReadSeq, TPatternSpec> pattern(read, -(int)length(read) * 40); data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:403:68: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). Pattern<TReadSeq, TPatternSpec> pattern(read, -(int)length(read) * 40); data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:433:77: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). int relativeMinScore = (int)ceilAwayFromZero(100.0 * -maxError / length(read)); data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:437:45: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). Pattern<TReadSeq, TPatternSpec> pattern(read, -(int)length(read) * 40); data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:437:64: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). Pattern<TReadSeq, TPatternSpec> pattern(read, -(int)length(read) * 40); data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:447:36: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). << " read = " << read << std::endl; data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:456:52: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). << infix(contig, endPos - length(read), endPos) << std::endl; data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:477:86: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). int relativeScore = (int)ceilAwayFromZero(100.0 * getScore(pattern) / length(read)); data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:486:102: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::cerr << __FILE__ << ":" << __LINE__ << " -- infix " << infix(finder) << " read " << read data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:508:90: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). int relativeScore = (int)ceilAwayFromZero(100.0 * getScore(pattern) / length(read)); data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:516:42: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). << " read " << read << std::endl; data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:527:102: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). relativeScore = static_cast<int>(ceilAwayFromZero(100.0 * getScore(pattern) / length(read))); data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:536:74: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). for (unsigned i = 0; find(finder, pattern) && i < length(read); ++i) data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:543:94: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). relativeScore = (int)ceilAwayFromZero(100.0 * getScore(pattern) / length(read)); data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:551:50: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). << " read " << read << std::endl; data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:567:45: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TPosition kIntervalLen = length(read) + maxError; data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:613:94: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). int relativeScore = (int)ceilAwayFromZero(100.0 * getScore(pattern) / length(read)); data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:621:34: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). << read << std::endl; data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:629:94: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). relativeScore = (int)ceilAwayFromZero(100.0 * getScore(pattern) / length(read)); data/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:639:38: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). << read << std::endl; data/seqan2-2.4.0+dfsg/apps/razers/outputFormat.h:175:59: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). for (unsigned i = 0; i < length(posError) && i < length(read); ++i) data/seqan2-2.4.0+dfsg/apps/razers/outputFormat.h:176:75: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if ((options.compMask[ordValue(genome[i])] & options.compMask[ordValue(read[i])]) == 0) data/seqan2-2.4.0+dfsg/apps/razers/razers.h:1274:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritBeg = begin(read, Standard()); data/seqan2-2.4.0+dfsg/apps/razers/razers.h:1275:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritEnd = end(read, Standard()); data/seqan2-2.4.0+dfsg/apps/razers/razers.h:1378:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritBeg = begin(read, Standard()); data/seqan2-2.4.0+dfsg/apps/razers/razers.h:1379:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritEnd = end(read, Standard()); data/seqan2-2.4.0+dfsg/apps/razers/razers.h:1522:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritBeg = begin(read, Standard()); data/seqan2-2.4.0+dfsg/apps/razers/razers.h:1523:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritEnd = end(read, Standard()); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:737:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritBeg = begin(read, Standard()); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:738:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritEnd = end(read, Standard()); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:740:64: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TGenomeIterator gitEnd = end(genomeInf, Standard()) - (length(read) - 1); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:744:46: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). unsigned maxTotalErrors = (unsigned)(length(read) * options.errorRate); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:848:59: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::cout << "genome=" << genomeInf << "\nread =" << read <<"\n"; data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:851:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritEnd = end(read, Standard())-1; data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:852:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritBeg = begin(read, Standard()); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:858:46: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). unsigned maxTotalErrors = (unsigned)(length(read) * options.errorRate); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1025:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TRead & read, data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1040:30: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TGenomeInf readInfL = infix(read,options.minMatchLen,mL.mScore); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1042:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TGenomeInfRev readInfR(infix(read,length(read)-mR.mScore,length(read)-options.minMatchLen)); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1042:43: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TGenomeInfRev readInfR(infix(read,length(read)-mR.mScore,length(read)-options.minMatchLen)); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1042:66: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TGenomeInfRev readInfR(infix(read,length(read)-mR.mScore,length(read)-options.minMatchLen)); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1057:26: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). int readLength = length(read); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1070:37: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). assignSource(row(align, 0), infix(read,0,readLength)); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1301:26: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). int readLength = length(read); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1336:35: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if ((options.compMask[ordValue(read[i])] & options.compMask[ordValue(genomeInf[i])]) == 0) data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1348:23: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). mR.mScore = length(read)- halfReadLen; data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1376:39: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). bool result = findBestSplitPosition(read,genomeInf,mL.mScore,mR.mScore,mL.editDist,mR.editDist, options, orientation, SwiftSemiGlobalHamming()); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1395:49: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). bool result = findBestSplitPosition(genomeInf,read,mL.mScore,mR.mScore,mL.editDist,mR.editDist, options, orientation,SwiftSemiGlobalHamming()); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1687:4: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(file, genome, Fasta()); // read Fasta sequence data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1877:46: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TGPos maxEndPos = (*it).i2.gEnd + length(read)-2*options.minMatchLen + floor(options.errorRate*length(read)); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1877:107: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TGPos maxEndPos = (*it).i2.gEnd + length(read)-2*options.minMatchLen + floor(options.errorRate*length(read)); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1920:35: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if((int)minBeginPos - length(read)+2*options.minMatchLen - floor(options.errorRate*length(read)) > 0) data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1920:96: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if((int)minBeginPos - length(read)+2*options.minMatchLen - floor(options.errorRate*length(read)) > 0) data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1921:42: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). minBeginPos = minBeginPos - length(read)+2*options.minMatchLen - floor(options.errorRate*length(read)); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1921:103: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). minBeginPos = minBeginPos - length(read)+2*options.minMatchLen - floor(options.errorRate*length(read)); data/seqan2-2.4.0+dfsg/apps/razers/razers_spliced.h:1972:39: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if(!combineLeftRight(mRtmp,mLtmp,read,genome,options,orientation,TSwiftSpec())) data/seqan2-2.4.0+dfsg/apps/razers/readSimulator.h:224:11: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TGenome read; data/seqan2-2.4.0+dfsg/apps/razers/readSimulator.h:225:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). resize(read,readLength); data/seqan2-2.4.0+dfsg/apps/razers/readSimulator.h:270:30: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if(currOp == SEQAN_MATCH) read[trueLength] = readTemplate[pos]; data/seqan2-2.4.0+dfsg/apps/razers/readSimulator.h:275:6: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read[trueLength] = sample(currOp,readTemplate[pos]); data/seqan2-2.4.0+dfsg/apps/razers/readSimulator.h:422:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). resize(read,trueLength); data/seqan2-2.4.0+dfsg/apps/razers/readSimulator.h:435:26: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). appendValue(readSet, read, Generous()); data/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:201:65: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). for (unsigned i = 0; i < length(posError) && i < length(read); ++i) data/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:202:84: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if ((options.compMask[ordValue(genome[i])] & options.compMask[ordValue(read[i])]) == 0) data/seqan2-2.4.0+dfsg/apps/razers3/profile_timeline.h:169:34: [1] (buffer) strlen: Does not handle 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 * pathBuffer = new char[strlen(path) + 30]; data/seqan2-2.4.0+dfsg/apps/razers3/profile_timeline.h:180:9: [1] (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). Risk is low because the source is a constant character. strcat(pathBuffer, "."); data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1841:19: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TRead const & read, // read data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1856:37: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritBeg = begin(read, Standard()); data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1857:35: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritEnd = end(read, Standard()); data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1965:19: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TRead const & read, // reads data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1976:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::cout << "Read: " << read << std::endl; data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1995:74: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). scoreInit = scoreMatch(verifier.options->scoringScheme) * length(read); data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:1999:37: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritBeg = begin(read, Standard()); data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2000:35: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritEnd = end(read, Standard()); data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2111:19: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TRead const & read, // reads data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2139:33: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). unsigned ndlLength = length(read); data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2158:37: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadPrefix readPrefix = prefix(read, ndlLength); data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2160:22: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TRead readPrefix(read); // here only infixes (no sequence) is copied data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2172:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::cout << "Read: " << read << "(id: " << readId << ")" << std::endl; data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2193:112: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if ((verifier.options->compMask[ordValue(origInf[pos + 1])] & verifier.options->compMask[ordValue(back(read))]) == 0) data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2234:127: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if ((verifier.options->compMask[ordValue(origInf[maxPos + 1])] & verifier.options->compMask[ordValue(back(read))]) == 0) data/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2337:119: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if ((verifier.options->compMask[ordValue(origInf[maxPos + 1])] & verifier.options->compMask[ordValue(back(read))]) == 0) data/seqan2-2.4.0+dfsg/apps/razers3/readSimulator.h:221:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TGenome read; data/seqan2-2.4.0+dfsg/apps/razers3/readSimulator.h:222:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). resize(read, readLength); data/seqan2-2.4.0+dfsg/apps/razers3/readSimulator.h:271:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read[trueLength] = readTemplate[pos]; data/seqan2-2.4.0+dfsg/apps/razers3/readSimulator.h:276:21: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read[trueLength] = sample(currOp, readTemplate[pos]); data/seqan2-2.4.0+dfsg/apps/razers3/readSimulator.h:425:24: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). resize(read, trueLength); data/seqan2-2.4.0+dfsg/apps/razers3/readSimulator.h:443:38: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). appendValue(readSet, read, Generous()); data/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:160:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(fragStore, strmReads, Amos()); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:319:40: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). for(unsigned i = 0; i < length(read); ++i) data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:320:44: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). avgRQ += (int) getQualityValue(read[i]) ; data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:322:90: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if((fragmentStore.alignQualityStore[(*it).id]).score == 0 || (char)(avgRQ/length(read))<(fragmentStore.alignQualityStore[(*it).id]).score) data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:323:85: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). (fragmentStore.alignQualityStore[(*it).id]).score = (char)(avgRQ/length(read)); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:399:45: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if(clipLeft+clipRight > (int)length(read) || clipLeft > (int)length(read) || clipRight > (int)length(read)) data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:399:77: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if(clipLeft+clipRight > (int)length(read) || clipLeft > (int)length(read) || clipRight > (int)length(read)) data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:399:110: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if(clipLeft+clipRight > (int)length(read) || clipLeft > (int)length(read) || clipRight > (int)length(read)) data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:403:52: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::cout << "readlength = "<<length(read)<< " \n"; data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:406:39: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::cout << "read=" << read << std::endl; data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:410:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). clipLeft = length(read); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:414:52: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::cout << "readlength = "<<length(read)<< " \n"; data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:417:39: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::cout << "read=" << read << std::endl; data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:424:28: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if((int)length(read)-clipLeft-clipRight < options.minClippedLength) data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:427:51: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::cout << "Discarded: "<<read<<" at position "<< beginPos <<"\n"; data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:434:26: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read = infix(read,clipLeft,length(read)-clipRight); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:434:47: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read = infix(read,clipLeft,length(read)-clipRight); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:438:44: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). for(unsigned i = 0; i < length(read); ++i) data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:439:48: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). avgRQ += (int) getQualityValue(read[i]) ; data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:440:46: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). aliQ.score = (char)(avgRQ/length(read)); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:445:41: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). assignSource(row(align, 0), read); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:462:82: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). unsigned viewPosReadLast = toViewPosition(row(align, 0), length(read) - 1); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:527:43: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::cout << "read=" << read << std::endl; data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.h:3745:26: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). calibrateQuality(TRead & read, TMatchQuality & matchQuality, int originalQuality,TOptions & options) data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.h:3747:59: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). double epsilon = (double)(matchQuality.errors)/length(read); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.h:5014:30: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). int readLen = length(read); data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.h:5019:50: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if(extraV) ::std::cout << "read=" << read << " beg,end="<<(*matchIt).beginPos << ","<<(*matchIt).endPos <<::std::endl; data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.h:5131:34: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). rInf = infix(read, data/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.h:5139:34: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). rInf = infix(read, data/seqan2-2.4.0+dfsg/apps/splazers/outputFormat.h:171:59: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). for (unsigned i = 0; i < length(posError) && i < length(read); ++i) data/seqan2-2.4.0+dfsg/apps/splazers/outputFormat.h:172:75: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if ((options.compMask[ordValue(genome[i])] & options.compMask[ordValue(read[i])]) == 0) data/seqan2-2.4.0+dfsg/apps/splazers/razers.h:1233:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritBeg = begin(read, Standard()); data/seqan2-2.4.0+dfsg/apps/splazers/razers.h:1234:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritEnd = end(read, Standard()); data/seqan2-2.4.0+dfsg/apps/splazers/razers.h:1337:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritBeg = begin(read, Standard()); data/seqan2-2.4.0+dfsg/apps/splazers/razers.h:1338:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritEnd = end(read, Standard()); data/seqan2-2.4.0+dfsg/apps/splazers/razers.h:1481:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritBeg = begin(read, Standard()); data/seqan2-2.4.0+dfsg/apps/splazers/razers.h:1482:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritEnd = end(read, Standard()); data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:899:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritBeg = begin(read, Standard()); data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:900:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritEnd = end(read, Standard()); data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:902:64: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TGenomeIterator gitEnd = end(genomeInf, Standard()) - (length(read) - 1); data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:1013:59: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::cout << "genome=" << genomeInf << "\nread =" << read <<"\n"; data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:1017:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritEnd = end(read, Standard())-1; data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:1018:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TReadIterator ritBeg = begin(read, Standard()); data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:1524:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TRead & read, data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:1539:30: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TGenomeInf readInfL = infix(read,options.minMatchLen,mL.mScore); data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:1541:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TGenomeInfRev readInfR(infix(read,length(read)-mR.mScore,length(read)-options.minMatchLen)); data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:1541:43: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TGenomeInfRev readInfR(infix(read,length(read)-mR.mScore,length(read)-options.minMatchLen)); data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:1541:66: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TGenomeInfRev readInfR(infix(read,length(read)-mR.mScore,length(read)-options.minMatchLen)); data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:1556:26: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). int readLength = length(read); data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:1569:37: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). assignSource(row(align, 0), infix(read,0,readLength)); data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:1824:26: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). int readLength = length(read); data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:1859:35: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if ((options.compMask[ordValue(read[i])] & options.compMask[ordValue(genomeInf[i])]) == 0) data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:1871:23: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). mR.mScore = length(read)- halfReadLen; data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:1899:39: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). bool result = findBestSplitPosition(read,genomeInf,mL.mScore,mR.mScore,mL.editDist,mR.editDist, traceExt, options, orientation, SwiftSemiGlobalHamming()); data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:1921:49: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). bool result = findBestSplitPosition(genomeInf,read,mL.mScore,mR.mScore,mL.editDist,mR.editDist, traceExt, options, orientation,SwiftSemiGlobalHamming()); data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:2463:40: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TSignedGPos extensionOffset = length(read)-2*options.minMatchLen; data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:2465:73: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). extensionOffset += static_cast<TGPos>(floor(options.errorRate*length(read))); data/seqan2-2.4.0+dfsg/apps/splazers/razers_spliced.h:2701:38: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). !combineLeftRight(mRtmp,mLtmp,read,genome,options,orientation,TSwiftSpec())) data/seqan2-2.4.0+dfsg/apps/splazers/readSimulator.h:225:11: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TGenome read; data/seqan2-2.4.0+dfsg/apps/splazers/readSimulator.h:226:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). resize(read,readLength); data/seqan2-2.4.0+dfsg/apps/splazers/readSimulator.h:273:30: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if(currOp == SEQAN_MATCH) read[trueLength] = readTemplate[pos]; data/seqan2-2.4.0+dfsg/apps/splazers/readSimulator.h:278:6: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read[trueLength] = sample(rng, currOp,readTemplate[pos]); data/seqan2-2.4.0+dfsg/apps/splazers/readSimulator.h:425:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). resize(read,trueLength); data/seqan2-2.4.0+dfsg/apps/splazers/readSimulator.h:438:26: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). appendValue(readSet, read, Generous()); data/seqan2-2.4.0+dfsg/demos/dox/align_split/split_alignment.cpp:28:34: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). assignSource(row(alignL, 1), read); data/seqan2-2.4.0+dfsg/demos/dox/align_split/split_alignment.cpp:32:34: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). assignSource(row(alignR, 1), read); data/seqan2-2.4.0+dfsg/demos/dox/align_split/split_alignment.cpp:63:47: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). << "Read Left " << prefix(read, readSplitLPosition) << "\n" data/seqan2-2.4.0+dfsg/demos/dox/align_split/split_alignment.cpp:64:46: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). << "Read Center " << infix(read, readSplitLPosition, readSplitRPosition) << "\n" data/seqan2-2.4.0+dfsg/demos/dox/align_split/split_alignment.cpp:65:47: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). << "Read Right " << suffix(read, readSplitRPosition) << "\n"; data/seqan2-2.4.0+dfsg/demos/dox/parallel/queue_example.cpp:24:17: [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. equal &= (i == popFront(queue)); data/seqan2-2.4.0+dfsg/demos/dox/parallel/queue_example.cpp:25:27: [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. std::cout << (equal ? "SUCCESS" : "FAILURE") << std::endl; data/seqan2-2.4.0+dfsg/demos/dox/statistics/load_markov_model.cpp:26:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(mmFile, mm); data/seqan2-2.4.0+dfsg/demos/tutorial/alignment/scoring_scheme_simple.cpp:27:66: [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 score = globalAlignment(align, Score<int, Simple>(match, mismatch, gap)); data/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_3_workshop.cpp:8:63: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void printAlign(TText1 const & genomeFragment, TText2 const & read) data/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_3_workshop.cpp:12:35: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::cout << " read : " << read << std::endl; data/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_3_workshop_solution.cpp:8:63: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void printAlign(TText1 const & genomeFragment, TText2 const & read) data/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_3_workshop_solution.cpp:12:35: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::cout << " read : " << read << std::endl; data/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_4_workshop_solution.cpp:8:63: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void printAlign(TText1 const & genomeFragment, TText2 const & read) data/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_4_workshop_solution.cpp:12:35: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::cout << " read : " << read << std::endl; data/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_2_solution.cpp:12:63: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void printAlign(TText1 const & genomeFragment, TText2 const & read) data/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_2_solution.cpp:16:35: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::cout << " read : " << read << std::endl; data/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_5_solution.cpp:14:63: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void printAlign(TText1 const & genomeFragment, TText2 const & read) data/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_5_solution.cpp:20:18: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::cout << read << std::endl; data/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_5_solution.cpp:34:98: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). Infix<Dna5String>::Type genomeFragment = infix(genome, beginPosition, beginPosition + length(read)); data/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_5_solution.cpp:38:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). printAlign(genomeFragment, read); data/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_6_solution.cpp:8:63: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void printAlign(TText1 const & genomeFragment, TText2 const & read) data/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_6_solution.cpp:12:35: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::cout << " read : " << read << std::endl; data/seqan2-2.4.0+dfsg/demos/tutorial/sequences/base.cpp:52:37: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). for (unsigned i = 0; i < length(read); ++i) data/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/assignment_3_workshop_solution.cpp:9:63: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void printAlign(TText1 const & genomeFragment, TText2 const & read) data/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/assignment_3_workshop_solution.cpp:13:35: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::cout << " read : " << read << std::endl; data/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/assignment_4_workshop_solution.cpp:8:63: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void printAlign(TText1 const & genomeFragment, TText2 const & read) data/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/assignment_4_workshop_solution.cpp:12:35: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::cout << " read : " << read << std::endl; data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp:97:9: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(filenameBuffer, toCString(tempFilename), 999); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp:115:9: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(filenameBuffer, toCString(tempFilename), 999); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp:147:9: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(filenameBuffer, toCString(tempFilename), 999); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp:165:9: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(filenameBuffer, toCString(tempFilename), 999); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp:197:9: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(filenameBuffer, toCString(tempFilename), 999); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_readwrite.cpp:29:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(myFile2, block2, sizeof(block2)); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_file_io/example1.cpp:25:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(buffer, reader, capacity(buffer)); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_file_io/solution1.cpp:24:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(buffer, reader, capacity(buffer)); data/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_file_io/stream_compression_formats.cpp:47:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(buffer, reader, capacity(buffer)); data/seqan2-2.4.0+dfsg/include/seqan/arg_parse/arg_parse_parse.h:116:29: [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). size_t argLen = strlen(argv[argi]); data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:457:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). fin.read(&buffer[0], 4); data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:464:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). fin.read(reinterpret_cast<char *>(&nRef), 4); data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:476:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). fin.read(reinterpret_cast<char *>(&nBin), 4); data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:487:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). fin.read(reinterpret_cast<char *>(&bin), 4); data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:493:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). fin.read(reinterpret_cast<char *>(&nChunk), 4); data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:502:21: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). fin.read(reinterpret_cast<char *>(&chunkBeg), 8); data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:503:21: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). fin.read(reinterpret_cast<char *>(&chunkEnd), 8); data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:517:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). fin.read(reinterpret_cast<char *>(&nIntv), 4); data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:526:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). fin.read(reinterpret_cast<char *>(&ioffset), 8); data/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:539:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). fin.read(reinterpret_cast<char *>(&nNoCoord), 8); data/seqan2-2.4.0+dfsg/include/seqan/bam_io/read_bam.h:102:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(magic, iter, 4); data/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1279:1: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(TTarget &target, TFwdIterator &iter, TSize n) data/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1293:1: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(TTarget &target, TContainer &cont) data/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1296:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). return read(target, iter, length(cont)); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_helper.h:83:13: [1] (buffer) fgetc: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if (fgetc(fl1) != fgetc(fl2)) goto End; data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_helper.h:83:27: [1] (buffer) fgetc: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if (fgetc(fl1) != fgetc(fl2)) goto End; data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_helper.h:107:9: [1] (buffer) fgetc: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). c = fgetc(fl); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_helper.h:113:17: [1] (buffer) fgetc: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). c = fgetc(fl); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_helper.h:119:25: [1] (buffer) fgetc: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). c = fgetc(fl); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_helper.h:126:17: [1] (buffer) fgetc: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). c = fgetc(fl); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:600:32: [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). for (size_t i = 0; i < strlen(file) - strlen("include"); ++i) data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:600:47: [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). for (size_t i = 0; i < strlen(file) - strlen("include"); ++i) data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:602:46: [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). if (strncmp(file + i, "include", strlen("include")) == 0) data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:617:9: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(&buffer[0], file, pos); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:704:24: [1] (access) umask: Ensure that umask is given most restrictive possible setting (e.g., 066 or 077) (CWE-732). mode_t cur_umask = umask(S_IRWXO | S_IRWXG); // to silence Coverity warning data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:707:5: [1] (access) umask: Ensure that umask is given most restrictive possible setting (e.g., 066 or 077) (CWE-732). umask(cur_umask); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:741:9: [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(StaticData::basePath(), "."); data/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:747:9: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(StaticData::basePath(), argv0, len); data/seqan2-2.4.0+dfsg/include/seqan/file/file_base.h:178:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). inline bool read(File<TSpec> & me, TValue *memPtr, TSize const count) data/seqan2-2.4.0+dfsg/include/seqan/file/file_base.h:183:19: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). return me.read(memPtr, nbytes) == nbytes; data/seqan2-2.4.0+dfsg/include/seqan/file/file_base.h:232:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). return read(me, memPtr, count); data/seqan2-2.4.0+dfsg/include/seqan/file/file_cstyle.h:182:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(FILE* me, TValue *memPtr, TSize const count) data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_io.h:119:1: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(TFile & file, data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_io.h:260:1: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(TFile & file, data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_io.h:388:1: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(TFile & file, data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_io.h:503:1: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(TFile & file, data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_io.h:607:1: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(TFile & file, data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_io.h:820:1: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(TFile & file, data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_io.h:908:1: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(TFile & file, data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:159:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(strm, origStrSet, names, FastaAlign()); data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:172:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(strm_lib, matches, scores, names, FastaAlign()); data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:379:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(strm_lib, matches, scores, sequenceNames, FastaAlign()); data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:439:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(strm_lib, matches, scores, sequenceNames, TCoffeeLib()); data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:454:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(strm_lib, matches, scores, seqSet, sequenceNames, MummerLib()); data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:469:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(strm_lib, matches, scores, sequenceNames, BlastLib()); data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:501:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(strm_tree, guideTree, sequenceNames, NewickFormat()); // Read newick tree data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_refinement.h: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. Score(TValue match, TValue mismatch, TValue gap_extend, TValue gap_open) data/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_refinement.h:123:28: [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. _mismatchScore(sc, mismatch); data/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:1530:13: [1] (buffer) strlen: Does not handle 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 > q1) { data/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:792:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). return read(f, &value, 1); data/seqan2-2.4.0+dfsg/include/seqan/journaled_set/score_biaffine.h:70:42: [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. Score(TScoreValue match, TScoreValue mismatch, TScoreValue gap) : data/seqan2-2.4.0+dfsg/include/seqan/journaled_set/score_biaffine.h:72:47: [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/seqan2-2.4.0+dfsg/include/seqan/journaled_set/score_biaffine.h:78:42: [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. Score(TScoreValue match, TScoreValue mismatch, TScoreValue gapExtend, TScoreValue gapOpen) : data/seqan2-2.4.0+dfsg/include/seqan/journaled_set/score_biaffine.h:80:47: [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/seqan2-2.4.0+dfsg/include/seqan/journaled_set/score_biaffine.h:86:42: [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. Score(TScoreValue match, TScoreValue mismatch, TScoreValue gapExtendHorizontal, TScoreValue gapOpenHorizontal, data/seqan2-2.4.0+dfsg/include/seqan/journaled_set/score_biaffine.h:88:83: [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. _mismatch(mismatch), data/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:814:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(it, target); data/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:95:1: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc, data/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:152:1: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(Score<TValue, ScoreMatrix<TSequenceValue, TSpec> > & sc, data/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:155:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(sc, iter, ScoreMatrixFile()); data/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:183:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(sc, reader); data/seqan2-2.4.0+dfsg/include/seqan/score/score_matrix_io.h:199:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(sc, reader, ScoreMatrixFile()); data/seqan2-2.4.0+dfsg/include/seqan/sequence/adapt_array_pointer.h:335:17: [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). return std::strlen(me); data/seqan2-2.4.0+dfsg/include/seqan/sequence/adapt_array_pointer.h:341:17: [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). return std::strlen(me); data/seqan2-2.4.0+dfsg/include/seqan/sequence/adapt_array_pointer.h:618:33: [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). if (static_cast<TSize>(std::strlen(me)) > new_length) data/seqan2-2.4.0+dfsg/include/seqan/sequence/adapt_array_pointer.h:620:17: [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). return std::strlen(me); data/seqan2-2.4.0+dfsg/include/seqan/sequence/adapt_array_pointer.h:631:29: [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). TSize old_length = std::strlen(me); data/seqan2-2.4.0+dfsg/include/seqan/sequence/adapt_array_pointer.h:635:17: [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). return std::strlen(me); data/seqan2-2.4.0+dfsg/include/seqan/sequence/adapt_stl_container.h:1304:37: [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). std::copy(source, source + std::strlen(source), me.begin()); data/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:801:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(it, target); data/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:810:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(it, target); data/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:2071:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(it, target); data/seqan2-2.4.0+dfsg/include/seqan/statistics/statistics_markov_model.h:453:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void read(FILE *file) data/seqan2-2.4.0+dfsg/include/seqan/statistics/statistics_markov_model.h:860:6: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void read(FILE *file, data/seqan2-2.4.0+dfsg/include/seqan/statistics/statistics_markov_model.h:864:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). mm.read(file); data/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1046:18: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TRead const &read, data/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1056:34: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). appendValue(me.readSeqStore, read, Generous()); data/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1064:18: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TRead const &read, data/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1075:34: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). appendValue(me.readSeqStore, read, Generous()); data/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1084:18: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TRead const &read) data/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1089:27: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). return appendRead(me, read, TReadStoreElement::INVALID_ID); data/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1096:18: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). TRead const &read, data/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1102:27: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). return appendRead(me, read, name, TReadStoreElement::INVALID_ID); data/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:162:1: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(FragmentStore<TSpec, TConfig>& fragStore, data/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:805:63: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). _fillBamSeqAndQual(TSeq &bamSeq, TQual &bamQual, TRead const &read) data/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:807:14: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). bamSeq = read; data/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:809:28: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). resize(bamQual, length(read)); data/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:811:67: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). typename Iterator<TRead const, Standard>::Type sIt = begin(read, Standard()); data/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:812:65: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). typename Iterator<TRead const, Standard>::Type sItEnd = end(read, Standard()); data/seqan2-2.4.0+dfsg/include/seqan/stream/iostream_bgzf.h:422:55: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). streamBuf->serializer.istream.read( data/seqan2-2.4.0+dfsg/include/seqan/stream/iostream_bgzf.h:447:55: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). streamBuf->serializer.istream.read( data/seqan2-2.4.0+dfsg/include/seqan/stream/iostream_bzip2_impl.h:302:19: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). m_istream.read( data/seqan2-2.4.0+dfsg/include/seqan/stream/iostream_zip_impl.h:362:15: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). m_istream.read((char_type *)(&(m_input_buffer[0])), data/seqan2-2.4.0+dfsg/include/seqan/system/file_async.h:183:18: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). inline DWORD read(void * memPtr, SizeType_ count) const data/seqan2-2.4.0+dfsg/include/seqan/system/file_forwards.h:140:73: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). template <typename TSpec, typename TValue, typename TSize > inline bool read(File<Sync<TSpec> > & me, TValue *memPtr, TSize const count); // "include/seqan/file/file_sync.h"(226) data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:177:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). inline int read(void * buffer, SizeType_ count) const data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:346:23: [1] (access) umask: Ensure that umask is given most restrictive possible setting (e.g., 066 or 077) (CWE-732). int oldMode = umask(077); // Create with restrictive permissions. data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:349:13: [1] (access) umask: Ensure that umask is given most restrictive possible setting (e.g., 066 or 077) (CWE-732). umask(oldMode); // Reset umask mode. data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:356:13: [1] (access) umask: Ensure that umask is given most restrictive possible setting (e.g., 066 or 077) (CWE-732). umask(oldMode); // Reset umask mode. data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:359:9: [1] (access) umask: Ensure that umask is given most restrictive possible setting (e.g., 066 or 077) (CWE-732). umask(oldMode); // Reset umask mode. data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:378:20: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). inline ssize_t read(void * buffer, SizeType_ count) const data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:382:28: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ssize_t result = ::read(handle, buffer, count); data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:476:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). inline bool read(File<Sync<TSpec> > & me, TValue * memPtr, TSize const count) data/seqan2-2.4.0+dfsg/include/seqan/system/file_sync.h:478:23: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). return (size_t)me.read(memPtr, count * sizeof(TValue)) == (size_t)(count * sizeof(TValue)); data/seqan2-2.4.0+dfsg/include/seqan/tabix_io/tabix_index_tbi.h:453:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(magic, iter, 4); data/seqan2-2.4.0+dfsg/include/seqan/tabix_io/tabix_index_tbi.h:471:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(tmp, iter, lNm); data/seqan2-2.4.0+dfsg/tests/align_split/test_align_split.h:506:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). setSource(readGapsLeft, read); data/seqan2-2.4.0+dfsg/tests/align_split/test_align_split.h:507:30: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). setSource(readGapsRight, read); data/seqan2-2.4.0+dfsg/tests/align_split/test_align_split.h:527:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). setSource(readGapsLeft, read); data/seqan2-2.4.0+dfsg/tests/align_split/test_align_split.h:528:30: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). setSource(readGapsRight, read); data/seqan2-2.4.0+dfsg/tests/align_split/test_align_split.h:547:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). setSource(readGapsLeft, read); data/seqan2-2.4.0+dfsg/tests/align_split/test_align_split.h:548:30: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). setSource(readGapsRight, read); data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1402:5: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). Risk is low because the source is a constant string. strncpy(buffer1, "program_name", 100); data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1404:5: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). Risk is low because the source is a constant string. strncpy(buffer2, "-i", 100); data/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.h:1406:5: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). Risk is low because the source is a constant character. strncpy(buffer3, "1", 100); data/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:502:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). fstream.read(&contents[0], contents.size()); data/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1191:32: [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). const int kNeedleLen = strlen(kNeedleStr); data/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1209:32: [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). const int kNeedleLen = strlen(kNeedleStr); data/seqan2-2.4.0+dfsg/tests/find/test_find_myers_banded.h:158:9: [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) return true; data/seqan2-2.4.0+dfsg/tests/find/test_find_myers_banded.h:173:12: [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 equal; data/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_tcoffee.h:202:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(strmRead,seqSet,nameSet,TCoffeeLib()); data/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_tcoffee.h:222:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(strmRead2, matches, scores, nameSet,BlastLib()); data/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_tcoffee.h:252:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(strmBlastLib, matches, scores, nameSet,BlastLib()); data/seqan2-2.4.0+dfsg/tests/parallel/test_parallel_algorithms.h:57:22: [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. SEQAN_ASSERT_MSG(equal, "Sequences differ!"); data/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io_generic.h:48:5: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(filenameBuffer, toCString(tempFilename), 999); data/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io_generic.h:63:22: [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). file->write(STR, strlen(STR)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io_generic.h:75:5: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(filenameBuffer, toCString(tempFilename), 999); data/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io_generic.h:90:22: [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). file->write(STR, strlen(STR)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io_generic.h:102:5: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(filenameBuffer, toCString(tempFilename), 999); data/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io_generic.h:117:22: [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). file->write(STR, strlen(STR)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io_generic.h:129:5: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(filenameBuffer, toCString(tempFilename), 999); data/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io_generic.h:150:22: [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). file->write(STR, strlen(STR)); data/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io_generic.h:163:5: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(filenameBuffer, toCString(tempFilename), 999); data/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io_generic.h:177:22: [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). file->write(STR, strlen(STR)); data/seqan2-2.4.0+dfsg/tests/sequence/test_string.h:687:21: [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). SEQAN_ASSERT_EQ(strlen(str2), strlen(strq)); data/seqan2-2.4.0+dfsg/tests/sequence/test_string.h:687:35: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). SEQAN_ASSERT_EQ(strlen(str2), strlen(strq)); data/seqan2-2.4.0+dfsg/tests/statistics/test_statistics_base.h:164:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(fd, mm); data/seqan2-2.4.0+dfsg/tests/store/test_store_io.h:693:15: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). int res = read(store, fAmosIn, seqan::Amos()); data/seqan2-2.4.0+dfsg/tests/store/test_store_io.h:757:15: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). int res = read(store, fAmosIn, seqan::Amos()); data/seqan2-2.4.0+dfsg/tests/store/test_store_io_bam.h:136:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read(samFp, samStore, Sam()); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:88:23: [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). stream.write(STR, strlen(STR)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:111:23: [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). stream.write(STR, strlen(STR)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:142:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream2.read(buffer, 10); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:165:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream2.read(buffer, 10); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:183:23: [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). stream.write(STR, strlen(STR)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:190:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream2.read(buffer, strlen(STR)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:190:26: [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). stream2.read(buffer, strlen(STR)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:219:23: [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). stream.write(STR, strlen(STR)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:242:23: [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). stream.write(STR, strlen(STR));; data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:281:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(begin(buffer, Standard()), FILE_SIZE); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:316:7: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). f.read(begin(buffer, Standard()), FILE_SIZE); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:347:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(buffer, 13); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_file_stream.h:356:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(buffer, 13); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_generic.h:132:24: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). size_t charsRead = read(buffer, iter, 20); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_generic.h:148:21: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). SEQAN_ASSERT_EQ(read(buffer, iter, 5), 5); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_tokenization.h:65:22: [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). file.write(text, strlen(text)); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_tokenization.h:193:36: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). SEQAN_TYPED_TEST(TokenizationTest, read) data/seqan2-2.4.0+dfsg/tests/stream/test_stream_tokenization.h:200:21: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). SEQAN_ASSERT_EQ(read(buf, ctx.iter, 16), 16); data/seqan2-2.4.0+dfsg/tests/stream/test_stream_tokenization.h:209:21: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). SEQAN_ASSERT_EQ(read(buf,ctx.iter, 3), 1); ANALYSIS SUMMARY: Hits = 1722 Lines analyzed = 591596 in approximately 14.47 seconds (40894 lines/second) Physical Source Lines of Code (SLOC) = 348765 Hits@level = [0] 101 [1] 393 [2] 1259 [3] 25 [4] 45 [5] 0 Hits@level+ = [0+] 1823 [1+] 1722 [2+] 1329 [3+] 70 [4+] 45 [5+] 0 Hits/KSLOC@level+ = [0+] 5.22702 [1+] 4.93742 [2+] 3.81059 [3+] 0.200708 [4+] 0.129027 [5+] 0 Dot directories skipped = 1 (--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.