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/perm-0.4.0/AlignmentsQ.cpp Examining data/perm-0.4.0/ChrIndex2GeneName.cpp Examining data/perm-0.4.0/ChromosomeInBits.cpp Examining data/perm-0.4.0/ColorSpaceRead.cpp Examining data/perm-0.4.0/FileInputBuffer.cpp Examining data/perm-0.4.0/FileOutputBuffer.cpp Examining data/perm-0.4.0/Filename.cpp Examining data/perm-0.4.0/Flags.cpp Examining data/perm-0.4.0/GenomeInBits.cpp Examining data/perm-0.4.0/GenomeNTdata.cpp Examining data/perm-0.4.0/Genome_Index.cpp Examining data/perm-0.4.0/Genome_Index_Table.cpp Examining data/perm-0.4.0/Genome_Index_TableQ.cpp Examining data/perm-0.4.0/HashIndexT.cpp Examining data/perm-0.4.0/Index_Table.cpp Examining data/perm-0.4.0/LongReadsSet.cpp Examining data/perm-0.4.0/MappingResult.cpp Examining data/perm-0.4.0/MismatchScores.cpp Examining data/perm-0.4.0/PairedReadsMapping.cpp Examining data/perm-0.4.0/PairedReadsSet.cpp Examining data/perm-0.4.0/ParseReadsOpts.cpp Examining data/perm-0.4.0/PerM.cpp Examining data/perm-0.4.0/PerMTest.cpp Examining data/perm-0.4.0/ReSeq_bits.cpp Examining data/perm-0.4.0/ReadInBits.cpp Examining data/perm-0.4.0/ReadInBitsSet.cpp Examining data/perm-0.4.0/ReadsFileParser.cpp Examining data/perm-0.4.0/ReadsMapping.cpp Examining data/perm-0.4.0/ReadsMappingFlags.cpp Examining data/perm-0.4.0/ReadsMappingStats.cpp Examining data/perm-0.4.0/ReadsQualScores.cpp Examining data/perm-0.4.0/SeedPattern.cpp Examining data/perm-0.4.0/ShortReadUtil.cpp Examining data/perm-0.4.0/TestChromosomeNTdata.cpp Examining data/perm-0.4.0/TestGenome_Index_TableQ.cpp Examining data/perm-0.4.0/bitsOperationUtil.cpp Examining data/perm-0.4.0/boolFlagArray.cpp Examining data/perm-0.4.0/chdir.cpp Examining data/perm-0.4.0/chromosomeNTdata.cpp Examining data/perm-0.4.0/minQ.cpp Examining data/perm-0.4.0/refInBinFile.cpp Examining data/perm-0.4.0/stdafx.cpp Examining data/perm-0.4.0/AlignmentsQ.h Examining data/perm-0.4.0/ChrIndex2GeneName.h Examining data/perm-0.4.0/ColorSpaceRead.h Examining data/perm-0.4.0/FileInputBuffer.h Examining data/perm-0.4.0/FileOutputBuffer.h Examining data/perm-0.4.0/Filename.h Examining data/perm-0.4.0/Flags.h Examining data/perm-0.4.0/GenomeInBits.h Examining data/perm-0.4.0/GenomeNTdata.h Examining data/perm-0.4.0/Genome_Index.h Examining data/perm-0.4.0/Genome_Index_Table.h Examining data/perm-0.4.0/Genome_Index_TableQ.h Examining data/perm-0.4.0/HashIndexT.h Examining data/perm-0.4.0/Index_Table.h Examining data/perm-0.4.0/LongReadsSet.h Examining data/perm-0.4.0/MismatchScores.h Examining data/perm-0.4.0/PairedReadsMapping.h Examining data/perm-0.4.0/PairedReadsSet.h Examining data/perm-0.4.0/ParameterList.h Examining data/perm-0.4.0/ParseReadsOpts.h Examining data/perm-0.4.0/ReadInBits.h Examining data/perm-0.4.0/ReadInBitsSet.h Examining data/perm-0.4.0/ReadsFileParser.h Examining data/perm-0.4.0/ReadsMapping.h Examining data/perm-0.4.0/ReadsMappingFlags.h Examining data/perm-0.4.0/ReadsMappingStats.h Examining data/perm-0.4.0/ReadsQualScores.h Examining data/perm-0.4.0/SeedPattern.h Examining data/perm-0.4.0/ShortReadUtil.h Examining data/perm-0.4.0/TestChromosomeNTdata.h Examining data/perm-0.4.0/TestGenome_Index_TableQ.h Examining data/perm-0.4.0/bitsOperationUtil.h Examining data/perm-0.4.0/boolFlagArray.h Examining data/perm-0.4.0/chdir.h Examining data/perm-0.4.0/chromosomeInBits.h Examining data/perm-0.4.0/chromosomeNTdata.h Examining data/perm-0.4.0/minQ.h Examining data/perm-0.4.0/refInBinFile.h Examining data/perm-0.4.0/refInBinary.h Examining data/perm-0.4.0/resource.h