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/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/allocators.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/document.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/encodedstream.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/encodings.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/error/en.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/error/error.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/filereadstream.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/filewritestream.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/fwd.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/biginteger.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/diyfp.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/dtoa.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/ieee754.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/itoa.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/meta.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/pow10.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/regex.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/stack.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/strfunc.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/strtod.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/swap.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/istreamwrapper.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/memorybuffer.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/memorystream.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/msinttypes/inttypes.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/msinttypes/stdint.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/ostreamwrapper.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/pointer.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/prettywriter.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/rapidjson.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/schema.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/stream.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/stringbuffer.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/writer.h
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml.hpp
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml_iterators.hpp
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml_print.hpp
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml_utils.hpp
Examining data/toppic-1.3.0+dfsg1/ext/xml2json/xml2json.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/activation.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/activation.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/activation_base.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/activation_base.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/activation_data.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/amino_acid.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/amino_acid.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/amino_acid_base.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/amino_acid_base.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/amino_acid_data.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/base_data.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/base_data.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/ion.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/ion.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/ion_type.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/ion_type.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/ion_type_base.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/ion_type_base.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/ion_type_data.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/mass_constant.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/mod.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/mod.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/mod_base.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/mod_base.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/mod_data.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/mod_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/mod_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/neutral_loss.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/neutral_loss.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/neutral_loss_base.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/neutral_loss_base.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/neutral_loss_data.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/prot_mod.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/prot_mod.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/prot_mod_base.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/prot_mod_base.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/prot_mod_data.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/prot_mod_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/prot_mod_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/ptm.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/ptm.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/ptm_base.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/ptm_base.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/ptm_data.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/ptm_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/ptm_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/residue.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/residue.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/residue_base.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/residue_base.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/residue_data.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/residue_freq.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/residue_freq.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/residue_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/residue_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/support_peak_type.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/support_peak_type.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/support_peak_type_base.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/support_peak_type_base.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/support_peak_type_data.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/trunc.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/trunc.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/trunc_base.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/trunc_base.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/trunc_data.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/trunc_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/base/trunc_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/thread/simple_thread_pool.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/thread/simple_thread_pool.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/util/logger.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/util/logger.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/util/str_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/util/str_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/util/time_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/util/time_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/util/version.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/util/file_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/util/file_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/xml/xml_dom_document.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/xml/xml_dom_document.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/xml/xml_dom_element.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/xml/xml_dom_err_handler.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/xml/xml_dom_err_handler.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/xml/xml_dom_impl.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/xml/xml_dom_impl.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/xml/xml_dom_parser.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/xml/xml_dom_parser.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/xml/xml_dom_str.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/xml/xml_dom_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/xml/xml_dom_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/common/xml/xml_writer.cpp
Examining data/toppic-1.3.0+dfsg1/src/common/xml/xml_writer.hpp
Examining data/toppic-1.3.0+dfsg1/src/console/topdiff.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/topdiff_argument.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/topdiff_argument.hpp
Examining data/toppic-1.3.0+dfsg1/src/console/topdiff_process.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/topdiff_process.hpp
Examining data/toppic-1.3.0+dfsg1/src/console/topfd.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/topfd_argument.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/topfd_argument.hpp
Examining data/toppic-1.3.0+dfsg1/src/console/topfd_single.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/topfd_single_argument.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/topfd_single_argument.hpp
Examining data/toppic-1.3.0+dfsg1/src/console/topfd_single_process.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/topfd_single_process.hpp
Examining data/toppic-1.3.0+dfsg1/src/console/topfd_train.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/topmg.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/topmg_argument.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/topmg_argument.hpp
Examining data/toppic-1.3.0+dfsg1/src/console/topmg_process.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/topmg_process.hpp
Examining data/toppic-1.3.0+dfsg1/src/console/toppic.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/toppic_argument.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/toppic_argument.hpp
Examining data/toppic-1.3.0+dfsg1/src/console/toppic_match_peak.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/toppic_process.cpp
Examining data/toppic-1.3.0+dfsg1/src/console/toppic_process.hpp
Examining data/toppic-1.3.0+dfsg1/src/filter/diag/diag_filter_mng.cpp
Examining data/toppic-1.3.0+dfsg1/src/filter/diag/diag_filter_mng.hpp
Examining data/toppic-1.3.0+dfsg1/src/filter/diag/diag_filter_processor.cpp
Examining data/toppic-1.3.0+dfsg1/src/filter/diag/diag_filter_processor.hpp
Examining data/toppic-1.3.0+dfsg1/src/filter/diag/mass_diag_filter.cpp
Examining data/toppic-1.3.0+dfsg1/src/filter/diag/mass_diag_filter.hpp
Examining data/toppic-1.3.0+dfsg1/src/filter/massmatch/filter_protein.cpp
Examining data/toppic-1.3.0+dfsg1/src/filter/massmatch/filter_protein.hpp
Examining data/toppic-1.3.0+dfsg1/src/filter/massmatch/mass_match.cpp
Examining data/toppic-1.3.0+dfsg1/src/filter/massmatch/mass_match.hpp
Examining data/toppic-1.3.0+dfsg1/src/filter/massmatch/mass_match_factory.cpp
Examining data/toppic-1.3.0+dfsg1/src/filter/massmatch/mass_match_factory.hpp
Examining data/toppic-1.3.0+dfsg1/src/filter/massmatch/mass_match_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/filter/massmatch/mass_match_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/filter/oneptm/mass_one_ptm_filter.cpp
Examining data/toppic-1.3.0+dfsg1/src/filter/oneptm/mass_one_ptm_filter.hpp
Examining data/toppic-1.3.0+dfsg1/src/filter/oneptm/one_ptm_filter_mng.cpp
Examining data/toppic-1.3.0+dfsg1/src/filter/oneptm/one_ptm_filter_mng.hpp
Examining data/toppic-1.3.0+dfsg1/src/filter/oneptm/one_ptm_filter_processor.cpp
Examining data/toppic-1.3.0+dfsg1/src/filter/oneptm/one_ptm_filter_processor.hpp
Examining data/toppic-1.3.0+dfsg1/src/filter/zeroptm/mass_zero_ptm_filter.cpp
Examining data/toppic-1.3.0+dfsg1/src/filter/zeroptm/mass_zero_ptm_filter.hpp
Examining data/toppic-1.3.0+dfsg1/src/filter/zeroptm/zero_ptm_filter_mng.cpp
Examining data/toppic-1.3.0+dfsg1/src/filter/zeroptm/zero_ptm_filter_mng.hpp
Examining data/toppic-1.3.0+dfsg1/src/filter/zeroptm/zero_ptm_filter_processor.cpp
Examining data/toppic-1.3.0+dfsg1/src/filter/zeroptm/zero_ptm_filter_processor.hpp
Examining data/toppic-1.3.0+dfsg1/src/gui/topdiff/threadtopdiff.cpp
Examining data/toppic-1.3.0+dfsg1/src/gui/topdiff/threadtopdiff.h
Examining data/toppic-1.3.0+dfsg1/src/gui/topdiff/topdiff_gui.cpp
Examining data/toppic-1.3.0+dfsg1/src/gui/topdiff/topdiffdialog.cpp
Examining data/toppic-1.3.0+dfsg1/src/gui/topdiff/topdiffdialog.h
Examining data/toppic-1.3.0+dfsg1/src/gui/topfd/threadtopfd.cpp
Examining data/toppic-1.3.0+dfsg1/src/gui/topfd/threadtopfd.hpp
Examining data/toppic-1.3.0+dfsg1/src/gui/topfd/topfd_gui.cpp
Examining data/toppic-1.3.0+dfsg1/src/gui/topfd/topfddialog.cpp
Examining data/toppic-1.3.0+dfsg1/src/gui/topfd/topfddialog.hpp
Examining data/toppic-1.3.0+dfsg1/src/gui/topmg/threadtopmg.cpp
Examining data/toppic-1.3.0+dfsg1/src/gui/topmg/threadtopmg.h
Examining data/toppic-1.3.0+dfsg1/src/gui/topmg/topmg_gui.cpp
Examining data/toppic-1.3.0+dfsg1/src/gui/topmg/topmgwindow.cpp
Examining data/toppic-1.3.0+dfsg1/src/gui/topmg/topmgwindow.h
Examining data/toppic-1.3.0+dfsg1/src/gui/toppic/threadtoppic.cpp
Examining data/toppic-1.3.0+dfsg1/src/gui/toppic/threadtoppic.h
Examining data/toppic-1.3.0+dfsg1/src/gui/toppic/toppic_gui.cpp
Examining data/toppic-1.3.0+dfsg1/src/gui/toppic/toppicwindow.cpp
Examining data/toppic-1.3.0+dfsg1/src/gui/toppic/toppicwindow.h
Examining data/toppic-1.3.0+dfsg1/src/merge/feature_prsm.cpp
Examining data/toppic-1.3.0+dfsg1/src/merge/feature_prsm.hpp
Examining data/toppic-1.3.0+dfsg1/src/merge/feature_prsm_reader.cpp
Examining data/toppic-1.3.0+dfsg1/src/merge/feature_prsm_reader.hpp
Examining data/toppic-1.3.0+dfsg1/src/merge/feature_sample_merge.cpp
Examining data/toppic-1.3.0+dfsg1/src/merge/feature_sample_merge.hpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/charge_cmp.cpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/charge_cmp.hpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/env_assign.cpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/env_assign.hpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/env_base.cpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/env_base.hpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/env_detect.cpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/env_detect.hpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/env_filter.cpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/env_filter.hpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/env_para.cpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/env_para.hpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/env_peak_pair.cpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/env_peak_pair.hpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/env_rescore.cpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/env_rescore.hpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/envelope.cpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/envelope.hpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/match_env.cpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/match_env.hpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/match_env_filter.cpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/match_env_filter.hpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/match_env_refine.cpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/match_env_refine.hpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/match_env_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/ms/env/match_env_util.hpp
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Examining data/toppic-1.3.0+dfsg1/src/seq/alter_type.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/bp_spec.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/bp_spec.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/break_point.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/break_point.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/db_block.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/db_block.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/fasta_index_reader.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/fasta_index_reader.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/fasta_reader.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/fasta_reader.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/fasta_seq.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/fasta_seq.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/fasta_sub_seq.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/fasta_sub_seq.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/fasta_sub_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/fasta_sub_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/fasta_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/fasta_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/local_anno.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/local_anno.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/mass_shift.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/mass_shift.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/proteoform.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/proteoform.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/proteoform_factory.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/proteoform_factory.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/proteoform_type.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/proteoform_type.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/proteoform_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/proteoform_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/residue_seq.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/residue_seq.hpp
Examining data/toppic-1.3.0+dfsg1/src/seq/seq_segment.cpp
Examining data/toppic-1.3.0+dfsg1/src/seq/seq_segment.hpp
Examining data/toppic-1.3.0+dfsg1/src/stat/local/local_mng.hpp
Examining data/toppic-1.3.0+dfsg1/src/stat/local/local_processor.cpp
Examining data/toppic-1.3.0+dfsg1/src/stat/local/local_processor.hpp
Examining data/toppic-1.3.0+dfsg1/src/stat/local/local_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/stat/local/local_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/stat/mcmc/comp_pvalue_mcmc.cpp
Examining data/toppic-1.3.0+dfsg1/src/stat/mcmc/comp_pvalue_mcmc.hpp
Examining data/toppic-1.3.0+dfsg1/src/stat/mcmc/mcmc_dpr_processor.cpp
Examining data/toppic-1.3.0+dfsg1/src/stat/mcmc/mcmc_dpr_processor.hpp
Examining data/toppic-1.3.0+dfsg1/src/stat/mcmc/mcmc_mass_table_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/stat/mcmc/mcmc_mass_table_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/stat/mcmc/mcmc_mng.hpp
Examining data/toppic-1.3.0+dfsg1/src/stat/tdgf/comp_prob_value.cpp
Examining data/toppic-1.3.0+dfsg1/src/stat/tdgf/comp_prob_value.hpp
Examining data/toppic-1.3.0+dfsg1/src/stat/tdgf/comp_pvalue_array.cpp
Examining data/toppic-1.3.0+dfsg1/src/stat/tdgf/comp_pvalue_array.hpp
Examining data/toppic-1.3.0+dfsg1/src/stat/tdgf/comp_pvalue_lookup_table.cpp
Examining data/toppic-1.3.0+dfsg1/src/stat/tdgf/comp_pvalue_lookup_table.hpp
Examining data/toppic-1.3.0+dfsg1/src/stat/tdgf/count_test_num.cpp
Examining data/toppic-1.3.0+dfsg1/src/stat/tdgf/count_test_num.hpp
Examining data/toppic-1.3.0+dfsg1/src/stat/tdgf/evalue_processor.cpp
Examining data/toppic-1.3.0+dfsg1/src/stat/tdgf/evalue_processor.hpp
Examining data/toppic-1.3.0+dfsg1/src/stat/tdgf/tdgf_mng.hpp
Examining data/toppic-1.3.0+dfsg1/src/stat/tdgf/tdgf_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/stat/tdgf/tdgf_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/suffix/db_file_handler.cpp
Examining data/toppic-1.3.0+dfsg1/src/suffix/db_file_handler.hpp
Examining data/toppic-1.3.0+dfsg1/src/suffix/edge.cpp
Examining data/toppic-1.3.0+dfsg1/src/suffix/edge.hpp
Examining data/toppic-1.3.0+dfsg1/src/suffix/node.cpp
Examining data/toppic-1.3.0+dfsg1/src/suffix/node.hpp
Examining data/toppic-1.3.0+dfsg1/src/suffix/protein_db.hpp
Examining data/toppic-1.3.0+dfsg1/src/suffix/suffix.cpp
Examining data/toppic-1.3.0+dfsg1/src/suffix/suffix.hpp
Examining data/toppic-1.3.0+dfsg1/src/suffix/suffix_position.hpp
Examining data/toppic-1.3.0+dfsg1/src/suffix/suffix_tree.cpp
Examining data/toppic-1.3.0+dfsg1/src/suffix/suffix_tree.hpp
Examining data/toppic-1.3.0+dfsg1/src/test/activation_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/amino_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/base_data_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/catch.hpp
Examining data/toppic-1.3.0+dfsg1/src/test/fasta_reader_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/file_util_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/ion_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/mod_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/neutral_loss_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/prot_mod_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/prot_mod_util_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/ptm_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/residue_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/str_util_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/suffix_tree/suffix_tree_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/support_peak_type_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/toppic_suite_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/test/trunc_test.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/common/topfd_para.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/common/topfd_para.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/common/topfd_process.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/common/topfd_process.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/deconv/deconv_one_sp.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/deconv/deconv_one_sp.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/deconv/deconv_process.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/deconv/deconv_process.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/co_table.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/co_table.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/dp.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/dp.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/dp_a.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/dp_a.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/dp_b.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/dp_b.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/dp_para.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/vertex.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/vertex.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/vertex_a.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/vertex_a.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/vertex_b.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/vertex_b.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/vertex_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/dp/vertex_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/feature_detect/feature_detect.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/feature_detect/feature_detect.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/feature_detect/feature_para.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/feature_detect/feature_para.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/msreader/pw_ms_reader.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/msreader/pw_ms_reader.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/msreader/raw_ms_group_reader.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/msreader/raw_ms_group_reader.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/msreader/raw_ms_reader.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/msreader/raw_ms_reader.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/msreader/raw_ms_writer.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/msreader/raw_ms_writer.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/spec/deconv_data.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/spec/deconv_data.hpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/spec/deconv_data_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/topfd/spec/deconv_data_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_cleavage.cpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_cleavage.hpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_file_list.cpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_file_list.hpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_mass_shift.cpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_mass_shift.hpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_proteoform.cpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_proteoform.hpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_prsm.cpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_prsm.hpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_ptm.cpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_ptm.hpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_ptm_position.cpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_ptm_position.hpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_residue.cpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_residue.hpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_xml_util.cpp
Examining data/toppic-1.3.0+dfsg1/src/visual/anno_xml_util.hpp
Examining data/toppic-1.3.0+dfsg1/src/visual/json_transformer.cpp
Examining data/toppic-1.3.0+dfsg1/src/visual/json_transformer.hpp
Examining data/toppic-1.3.0+dfsg1/src/visual/prsm_view_mng.hpp
Examining data/toppic-1.3.0+dfsg1/src/visual/xml_generator.cpp
Examining data/toppic-1.3.0+dfsg1/src/visual/xml_generator.hpp

FINAL RESULTS:

data/toppic-1.3.0+dfsg1/src/common/util/file_util.cpp:58:16:  [5] (race) readlink:
  This accepts filename arguments; if an attacker can move those files or
  change the link content, a race condition results. Also, it does not
  terminate with ASCII NUL. (CWE-362, CWE-20). Reconsider approach.
  size_t len = readlink("/proc/self/exe", buffer, buffer_size);
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:4621:1:  [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(T a, T b) {
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:4630:1:  [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(T a, T b) {
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:12879:18:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
            std::srand(config.rngSeed());
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/allocators.h:217:22:  [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(newBuffer, originalPtr, originalSize);
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/document.h:1060:20:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-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[sizeof(GenericValue)];
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/document.h:1847:9:  [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 payload[sizeof(SizeType) * 2 + 6];     // 2 x SizeType + lower 48-bit pointer
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/document.h:1849:9:  [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 payload[sizeof(SizeType) * 2 + sizeof(void*) + 6]; // 6 padding bytes
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/document.h:1851:9:  [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 payload[sizeof(SizeType) * 2 + sizeof(void*) + 2]; // 2 padding bytes
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/document.h:1884:13:  [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 padding[4];
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/document.h:1888:13:  [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 padding2[4];
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/document.h:1892:13:  [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 padding[4];
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/document.h:1896:13:  [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 padding2[4];
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/document.h:1939:18:  [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(e, values, count * sizeof(GenericValue));
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/document.h:1952:18:  [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(m, members, count * sizeof(Member));
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/document.h:1979:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        std::memcpy(str, s, s.length * sizeof(Ch));
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/biginteger.h:33:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        std::memcpy(digits_, rhs.digits_, count_ * sizeof(Type));
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/biginteger.h:59:18:  [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(digits_, rhs.digits_, count_ * sizeof(Type));
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/itoa.h:24:18:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static const char cDigitsLut[200] = {
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/internal/regex.h:474:9:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        memcpy(s, &GetState(src.minIndex), count * sizeof(State));
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/pointer.h:215:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        std::memcpy(p, token.name, (token.length + 1) * sizeof(Ch));
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/pointer.h:265:9:  [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[21];
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/pointer.h:771:18:  [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(tokens_, rhs.tokens_, rhs.tokenCount_ * sizeof(Token));
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/pointer.h:774:18:  [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(nameBuffer_, rhs.nameBuffer_, nameBufferSize * sizeof(Ch));
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/pointer.h:1030:26:  [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 hexDigits[16] = { '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'A', 'B', 'C', 'D', 'E', 'F' };
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.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 whitespace[16] = " \n\r\t";
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h:323:18:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static const char whitespace[16] = " \n\r\t";
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h:363:18:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static const char whitespaces[4][16] = { C16(' '), C16('\n'), C16('\r'), C16('\t') };
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h:399:18:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static const char whitespaces[4][16] = { C16(' '), C16('\n'), C16('\r'), C16('\t') };
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h:843:22:  [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 escape[256] = {
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h:928:22:  [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 dquote[16] = { '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"' };
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h:929:22:  [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 bslash[16] = { '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\' };
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h:930:22:  [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 space[16]  = { 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19 };
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h:989:22:  [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 dquote[16] = { '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"' };
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h:990:22:  [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 bslash[16] = { '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\' };
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h:991:22:  [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 space[16] = { 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19 };
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h:1037:22:  [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 dquote[16] = { '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"' };
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h:1038:22:  [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 bslash[16] = { '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\' };
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h:1039:22:  [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 space[16] = { 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19 };
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h:1461:31:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        static const unsigned char tokenMap[256] = {
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/reader.h:1484:22:  [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 G[cIterativeParsingStateCount][kTokenCount] = {
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/schema.h:403:21:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
                    char buffer[256 + 24];
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/schema.h:1267:9:  [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[21];
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/writer.h:288:9:  [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[11];
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/writer.h:297:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buffer[10];
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/writer.h:306:9:  [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[21];
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/writer.h:315:9:  [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/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/writer.h:343:9:  [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[25];
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/writer.h:353:22:  [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 escape[256] = {
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/writer.h:568:18:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static const char dquote[16] = { '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"' };
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/writer.h:569:18:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static const char bslash[16] = { '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\' };
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidjson/writer.h:570:18:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    static const char space[16]  = { 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19, 0x19 };
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml.hpp:311:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            static const unsigned char lookup_whitespace[256];              // Whitespace table
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml.hpp:312:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            static const unsigned char lookup_node_name[256];               // Node name table
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml.hpp:313:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            static const unsigned char lookup_element_name[256];            // Element name table
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml.hpp:314:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            static const unsigned char lookup_text[256];                    // Text table
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml.hpp:315:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            static const unsigned char lookup_text_pure_no_ws[256];         // Text table
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml.hpp:316:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            static const unsigned char lookup_text_pure_with_ws[256];       // Text table
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml.hpp:317:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            static const unsigned char lookup_attribute_name[256];          // Attribute name table
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml.hpp:318:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            static const unsigned char lookup_attribute_data_1[256];        // Attribute data table with single quote
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml.hpp:319:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            static const unsigned char lookup_attribute_data_1_pure[256];   // Attribute data table with single quote
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml.hpp:320:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            static const unsigned char lookup_attribute_data_2[256];        // Attribute data table with double quotes
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml.hpp:321:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            static const unsigned char lookup_attribute_data_2_pure[256];   // Attribute data table with double quotes
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml.hpp:322:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            static const unsigned char lookup_digits[256];                  // Digits
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml.hpp:323:35:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            static const unsigned char lookup_upcase[256];                  // To uppercase conversion table for ASCII characters
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml.hpp:688:9:  [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 m_static_memory[RAPIDXML_STATIC_POOL_SIZE];    // Static raw memory
data/toppic-1.3.0+dfsg1/src/common/util/file_util.cpp:53:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char file_name[MAX_PATH];
data/toppic-1.3.0+dfsg1/src/common/util/time_util.cpp:26:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[50];
data/toppic-1.3.0+dfsg1/src/common/xml/xml_writer.cpp:24:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  file_.open(file_name.c_str());
data/toppic-1.3.0+dfsg1/src/console/topfd_single_process.cpp:63:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  input.open(file_name.c_str(), std::ios::in);
data/toppic-1.3.0+dfsg1/src/console/topmg_process.cpp:150:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[50];
data/toppic-1.3.0+dfsg1/src/console/topmg_process.cpp:348:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[50];
data/toppic-1.3.0+dfsg1/src/console/topmg_process.cpp:429:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[50];
data/toppic-1.3.0+dfsg1/src/console/toppic_match_peak.cpp:34:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[50];
data/toppic-1.3.0+dfsg1/src/console/toppic_process.cpp:152:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buf[50];
data/toppic-1.3.0+dfsg1/src/console/toppic_process.cpp: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 buf[50];
data/toppic-1.3.0+dfsg1/src/console/toppic_process.cpp:496:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buf[50];
data/toppic-1.3.0+dfsg1/src/merge/feature_prsm_reader.cpp:23:14:  [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).
      input_.open(file_name.c_str(), std::ios::in);
data/toppic-1.3.0+dfsg1/src/merge/feature_sample_merge.cpp:328:8:  [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(output_file_name_.c_str());
data/toppic-1.3.0+dfsg1/src/ms/env/env_base.cpp:29:13:  [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).
      input.open(file_name.c_str(), std::ios::in);
data/toppic-1.3.0+dfsg1/src/ms/feature/frac_feature_reader.cpp:23:14:  [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).
      input_.open(file_name.c_str(), std::ios::in);
data/toppic-1.3.0+dfsg1/src/ms/feature/frac_feature_writer.cpp:143:8:  [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(output_file_name.c_str());
data/toppic-1.3.0+dfsg1/src/ms/feature/frac_xml_feature_reader.cpp:23:14:  [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).
      input_.open(file_name.c_str(), std::ios::in);
data/toppic-1.3.0+dfsg1/src/ms/feature/peak_cluster_score.cpp:27:10:  [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).
  input_.open(file_name.c_str(), std::ios::in);
data/toppic-1.3.0+dfsg1/src/ms/feature/sample_feature_reader.cpp:23:14:  [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).
      input_.open(file_name.c_str(), std::ios::in);
data/toppic-1.3.0+dfsg1/src/ms/feature/spec_feature_reader.cpp:23:14:  [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).
      input_.open(file_name.c_str(), std::ios::in);
data/toppic-1.3.0+dfsg1/src/ms/spec/msalign_frac_merge.cpp:58:11:  [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).
  outfile.open(output_file);
data/toppic-1.3.0+dfsg1/src/ms/spec/msalign_reader.cpp:29:14:  [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).
      input_.open(file_name.c_str(), std::ios::in);
data/toppic-1.3.0+dfsg1/src/ms/spec/msalign_reader.cpp:53:14:  [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).
      input_.open(file_name.c_str(), std::ios::in);
data/toppic-1.3.0+dfsg1/src/ms/spec/msalign_util.cpp:39:16:  [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).
  index_output.open(index_file_name.c_str(), std::ios::out);
data/toppic-1.3.0+dfsg1/src/ms/spec/msalign_util.cpp:47:15:  [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).
  index_input.open(index_file_name.c_str(), std::ios::in);
data/toppic-1.3.0+dfsg1/src/ms/spec/msalign_writer.cpp:24:15:  [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).
      output_.open(file_name);
data/toppic-1.3.0+dfsg1/src/prsm/prsm_coverage.cpp:57:14:  [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).
  out_stream.open(output_file_name.c_str());
data/toppic-1.3.0+dfsg1/src/prsm/prsm_reader.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).
  input_.open(file_name.c_str(), std::ios::in);
data/toppic-1.3.0+dfsg1/src/prsm/prsm_sample_merge.cpp:85:8:  [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(output_file_name_.c_str());
data/toppic-1.3.0+dfsg1/src/prsm/prsm_stat.cpp:230:8:  [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(output_file_name.c_str());
data/toppic-1.3.0+dfsg1/src/prsm/prsm_table_writer.cpp:41:8:  [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(output_file_name.c_str());
data/toppic-1.3.0+dfsg1/src/prsm/prsm_xml_writer.cpp:24:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  file_.open(file_name.c_str());
data/toppic-1.3.0+dfsg1/src/prsm/simple_prsm_reader.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).
  input_.open(file_name.c_str(), std::ios::in);
data/toppic-1.3.0+dfsg1/src/prsm/simple_prsm_table_writer.cpp:36:9:  [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(output_file_name.c_str());
data/toppic-1.3.0+dfsg1/src/prsm/simple_prsm_xml_writer.cpp:25:9:  [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(file_name.c_str());
data/toppic-1.3.0+dfsg1/src/seq/db_block.cpp:33:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  input.open(index_file_name.c_str(), std::ios::in);
data/toppic-1.3.0+dfsg1/src/seq/fasta_reader.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).
  input_.open(file_name.c_str(), std::ios::in);
data/toppic-1.3.0+dfsg1/src/seq/fasta_util.cpp:52:10:  [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).
  output.open(target_decoy_file_name.c_str(), std::ios::out);
data/toppic-1.3.0+dfsg1/src/seq/fasta_util.cpp:86:15:  [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).
  standard_db.open(st_file_name.c_str(), std::ios::out);
data/toppic-1.3.0+dfsg1/src/seq/fasta_util.cpp:103:16:  [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).
  index_output.open(index_file_name.c_str(), std::ios::out);
data/toppic-1.3.0+dfsg1/src/seq/fasta_util.cpp:106:16:  [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).
  block_output.open(block_file_name.c_str(), std::ios::out);
data/toppic-1.3.0+dfsg1/src/seq/fasta_util.cpp:124:20:  [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).
      block_output.open(block_file_name.c_str(), std::ios::out);
data/toppic-1.3.0+dfsg1/src/stat/tdgf/comp_pvalue_lookup_table.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).
  input_.open(
data/toppic-1.3.0+dfsg1/src/stat/tdgf/comp_pvalue_lookup_table.cpp:59:10:  [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).
  input_.open(
data/toppic-1.3.0+dfsg1/src/stat/tdgf/comp_pvalue_lookup_table.cpp:72:10:  [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).
  input_.open(
data/toppic-1.3.0+dfsg1/src/suffix/db_file_handler.cpp:27:7:  [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).
  fis.open(db_file.c_str());
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:2150:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char timeStamp[timeStampSize];
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:4435:29:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        alignas(alignof(T)) char storage[sizeof(T)];
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:5942:16:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        static char line[CATCH_CONFIG_CONSOLE_WIDTH] = {0};
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:7463:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        void open();
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:11276:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        std::memcpy(&i, &f, sizeof(f));
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:11283:14:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
        std::memcpy(&i, &d, sizeof(d));
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:11825:9:  [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 m_buffer[L_tmpnam] = { 0 };
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:11912:13:  [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[100];
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:11921:23:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
        m_file = std::tmpfile();
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:11945:9:  [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[100] = {};
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:12408:30:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
                    tracker->open();
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:13208:31:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char **utf8Argv = new char *[ argc ];
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:13367:13:  [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 data[bufferSize];
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:13416:23:  [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).
                m_ofs.open( filename.c_str() );
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:13667:13:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            memcpy( m_data, m_start, m_size );
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:14153:23:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    void TrackerBase::open() {
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:14253:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            open();
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:14667:21:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
                    char asChar[sizeof (int)];
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:15334:9:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        char buffer[maxDoubleSize];
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:15341:14:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
        std::sprintf(buffer, "%.3f", duration);
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:15934:10:  [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/toppic-1.3.0+dfsg1/src/test/catch.hpp:15968:12:  [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).
        tp.open();
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:16369:13:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            char timeStamp[timeStampSize];
data/toppic-1.3.0+dfsg1/src/test/fasta_reader_test.cpp:28:13:  [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).
  test_file.open("test.fa");
data/toppic-1.3.0+dfsg1/src/test/suffix_tree/suffix_tree_test.cpp:28:13:  [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).
  test_file.open("test.fa");
data/toppic-1.3.0+dfsg1/src/topfd/msreader/raw_ms_writer.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).
  output.open(file_name.c_str());
data/toppic-1.3.0+dfsg1/ext/xml2json/rapidxml/rapidxml_utils.hpp:45:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            stream.read(&m_data.front(), static_cast<streamsize>(size));
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:3695:29:  [1] (buffer) is_permutation:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
                return std::is_permutation(m_target.begin(), m_target.end(), vec.begin());
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:13237:36:  [1] (buffer) getchar:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            static_cast<void>(std::getchar());
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:13242:36:  [1] (buffer) getchar:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            static_cast<void>(std::getchar());
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:13539:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        return s.size() >= prefix.size() && std::equal(prefix.begin(), prefix.end(), s.begin());
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:13545:50:  [1] (buffer) equal:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
        return s.size() >= suffix.size() && std::equal(suffix.rbegin(), suffix.rend(), s.rbegin());
data/toppic-1.3.0+dfsg1/src/test/catch.hpp:13637:67:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    : StringRef( rawChars, static_cast<StringRef::size_type>(std::strlen(rawChars) ) )

ANALYSIS SUMMARY:

Hits = 145
Lines analyzed = 93032 in approximately 2.06 seconds (45191 lines/second)
Physical Source Lines of Code (SLOC) = 62374
Hits@level = [0]  10 [1]   7 [2] 134 [3]   3 [4]   0 [5]   1
Hits@level+ = [0+] 155 [1+] 145 [2+] 138 [3+]   4 [4+]   1 [5+]   1
Hits/KSLOC@level+ = [0+] 2.48501 [1+] 2.32469 [2+] 2.21246 [3+] 0.0641293 [4+] 0.0160323 [5+] 0.0160323
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.