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/trinityrnaseq-2.11.0+dfsg/Inchworm/src/MaskedKmerCounter.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_reader.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/cigar_tweaker.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/KmerCounter.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/fastaToKmerCoverageStats.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/SAM_entry.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/SAM_reader.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/DeBruijnGraph.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Cigar.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/stacktrace.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/string_util.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/stacktrace.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/SAM_entry.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/SNP_stomper.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/IRKE_run.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Ktree.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/pull_reads_with_kmers.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/argProcessor.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/KtreeNode.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Ktree.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/string_util.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/argProcessor.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/mpi_deprecated/MPIinchworm.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Cigar.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_entry.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/DeBruijnGraph.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/irke_common.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/SAM_reader.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/sequenceUtil.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_entry.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/FastaToDeBruijn.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/common.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/Fasta_reader.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/MaskedKmerCounter.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/IRKE.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/KmerCounter.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/KtreeNode.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/IRKE.hpp
Examining data/trinityrnaseq-2.11.0+dfsg/Inchworm/src/sequenceUtil.cpp
Examining data/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.h
Examining data/trinityrnaseq-2.11.0+dfsg/Chrysalis/aligns/KmerAlignCore.cc
Examining data/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.h
Examining data/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/checkLock.c
Examining data/trinityrnaseq-2.11.0+dfsg/Chrysalis/util/mutil.cc