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/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Feature/Bed/BedGraphFeatureReader.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Feature/FeatureReader.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Feature/Gff/GffFeatureReader.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Feature/Gff/GffFeatureReader.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Feature/Gtf/GtfFeatureReader.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Feature/SequenceFeature.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Feature/SequenceFeature.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Feature/SequenceFeatureTools.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Feature/SequenceFeatureTools.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Fastq.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Fastq.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/BlockLengthMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/BlockMergerMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/BlockSizeMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/ChromosomeMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/ChromosomeMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/ConcatenateMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/CoordinateTranslatorMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/CoordinateTranslatorMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/CoordinatesOutputMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/DuplicateFilterMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/DuplicateFilterMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/EntropyFilterMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/EntropyFilterMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/FeatureExtractorMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/FeatureFilterMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/FeatureFilterMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/FullGapFilterMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/FullGapFilterMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/IterationListener.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/IterationListener.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/MafBlock.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/MafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/MafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/MafParser.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/MafParser.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/MafSequence.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/MafSequence.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/MafStatistics.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/MafStatistics.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/MaskFilterMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/MaskFilterMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/MsmcOutputMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/MsmcOutputMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/OrderFilterMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/OrderFilterMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/OrphanSequenceFilterMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputAlignmentMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/OutputMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/PlinkOutputMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/PlinkOutputMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/QualityFilterMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/QualityFilterMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/RemoveEmptySequencesMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/RemoveEmptySequencesMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/SequenceFilterMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/SequenceFilterMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/SequenceLDhotOutputMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/SequenceLDhotOutputMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/SequenceStatisticsMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/SequenceStreamToMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/TableOutputMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/TableOutputMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/VcfOutputMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.cpp
Examining data/libbpp-seq-omics-2.4.1/src/Bpp/Seq/Io/Maf/WindowSplitMafIterator.h
Examining data/libbpp-seq-omics-2.4.1/test/test_fastq.cpp
Examining data/libbpp-seq-omics-2.4.1/test/test_gff.cpp

FINAL RESULTS:


ANALYSIS SUMMARY:

No hits found.
Lines analyzed = 12050 in approximately 0.41 seconds (29343 lines/second)
Physical Source Lines of Code (SLOC) = 6335
Hits@level = [0]   0 [1]   0 [2]   0 [3]   0 [4]   0 [5]   0
Hits@level+ = [0+]   0 [1+]   0 [2+]   0 [3+]   0 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+]   0 [1+]   0 [2+]   0 [3+]   0 [4+]   0 [5+]   0
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.