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