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/abyss-2.2.5/ABYSS/abyss.cc
Examining data/abyss-2.2.5/AdjList/AdjList.cpp
Examining data/abyss-2.2.5/Align/Options.h
Examining data/abyss-2.2.5/Align/align.cc
Examining data/abyss-2.2.5/Align/alignGlobal.cc
Examining data/abyss-2.2.5/Align/alignGlobal.h
Examining data/abyss-2.2.5/Align/dialign.cpp
Examining data/abyss-2.2.5/Align/dialign.h
Examining data/abyss-2.2.5/Align/dna_diag_prob.cc
Examining data/abyss-2.2.5/Align/mergepairs.cc
Examining data/abyss-2.2.5/Align/smith_waterman.cpp
Examining data/abyss-2.2.5/Align/smith_waterman.h
Examining data/abyss-2.2.5/Assembly/AdjacencyAlgorithm.h
Examining data/abyss-2.2.5/Assembly/AssembleAlgorithm.h
Examining data/abyss-2.2.5/Assembly/AssemblyAlgorithms.cc
Examining data/abyss-2.2.5/Assembly/AssemblyAlgorithms.h
Examining data/abyss-2.2.5/Assembly/BranchGroup.h
Examining data/abyss-2.2.5/Assembly/BranchRecord.h
Examining data/abyss-2.2.5/Assembly/BranchRecordBase.h
Examining data/abyss-2.2.5/Assembly/BubbleAlgorithm.h
Examining data/abyss-2.2.5/Assembly/CoverageAlgorithm.h
Examining data/abyss-2.2.5/Assembly/DBG.h
Examining data/abyss-2.2.5/Assembly/DotWriter.h
Examining data/abyss-2.2.5/Assembly/ErodeAlgorithm.h
Examining data/abyss-2.2.5/Assembly/LoadAlgorithm.h
Examining data/abyss-2.2.5/Assembly/Options.cc
Examining data/abyss-2.2.5/Assembly/Options.h
Examining data/abyss-2.2.5/Assembly/SeqExt.h
Examining data/abyss-2.2.5/Assembly/SequenceCollection.h
Examining data/abyss-2.2.5/Assembly/SplitAlgorithm.h
Examining data/abyss-2.2.5/Assembly/TrimAlgorithm.h
Examining data/abyss-2.2.5/Assembly/VertexData.h
Examining data/abyss-2.2.5/Bloom/Bloom.h
Examining data/abyss-2.2.5/Bloom/BloomFilter.h
Examining data/abyss-2.2.5/Bloom/BloomFilterWindow.h
Examining data/abyss-2.2.5/Bloom/CascadingBloomFilter.h
Examining data/abyss-2.2.5/Bloom/CascadingBloomFilterWindow.h
Examining data/abyss-2.2.5/Bloom/ConcurrentBloomFilter.h
Examining data/abyss-2.2.5/Bloom/HashAgnosticCascadingBloom.h
Examining data/abyss-2.2.5/Bloom/RollingBloomDBGVisitor.h
Examining data/abyss-2.2.5/Bloom/bloom.cc
Examining data/abyss-2.2.5/BloomDBG/AssemblyCounters.h
Examining data/abyss-2.2.5/BloomDBG/AssemblyParams.h
Examining data/abyss-2.2.5/BloomDBG/AssemblyStreams.h
Examining data/abyss-2.2.5/BloomDBG/BloomIO.h
Examining data/abyss-2.2.5/BloomDBG/Checkpoint.h
Examining data/abyss-2.2.5/BloomDBG/LightweightKmer.h
Examining data/abyss-2.2.5/BloomDBG/MaskedKmer.h
Examining data/abyss-2.2.5/BloomDBG/RollingBloomDBG.h
Examining data/abyss-2.2.5/BloomDBG/RollingHash.h
Examining data/abyss-2.2.5/BloomDBG/RollingHashIterator.h
Examining data/abyss-2.2.5/BloomDBG/SpacedSeed.h
Examining data/abyss-2.2.5/BloomDBG/bloom-dbg.cc
Examining data/abyss-2.2.5/BloomDBG/bloom-dbg.h
Examining data/abyss-2.2.5/Common/Algorithms.h
Examining data/abyss-2.2.5/Common/Alignment.h
Examining data/abyss-2.2.5/Common/BitUtil.h
Examining data/abyss-2.2.5/Common/ConstString.h
Examining data/abyss-2.2.5/Common/ContigID.cpp
Examining data/abyss-2.2.5/Common/ContigID.h
Examining data/abyss-2.2.5/Common/ContigNode.h
Examining data/abyss-2.2.5/Common/ContigPath.h
Examining data/abyss-2.2.5/Common/ContigProperties.h
Examining data/abyss-2.2.5/Common/Dictionary.h
Examining data/abyss-2.2.5/Common/Estimate.h
Examining data/abyss-2.2.5/Common/Exception.h
Examining data/abyss-2.2.5/Common/Fcontrol.cpp
Examining data/abyss-2.2.5/Common/Fcontrol.h
Examining data/abyss-2.2.5/Common/Functional.h
Examining data/abyss-2.2.5/Common/Hash.h
Examining data/abyss-2.2.5/Common/HashFunction.h
Examining data/abyss-2.2.5/Common/Histogram.cpp
Examining data/abyss-2.2.5/Common/Histogram.h
Examining data/abyss-2.2.5/Common/IOUtil.h
Examining data/abyss-2.2.5/Common/InsOrderedMap.h
Examining data/abyss-2.2.5/Common/Iterator.h
Examining data/abyss-2.2.5/Common/Kmer.cpp
Examining data/abyss-2.2.5/Common/Kmer.h
Examining data/abyss-2.2.5/Common/KmerIterator.h
Examining data/abyss-2.2.5/Common/KmerSet.h
Examining data/abyss-2.2.5/Common/Log.cpp
Examining data/abyss-2.2.5/Common/Log.h
Examining data/abyss-2.2.5/Common/MemUtils.h
Examining data/abyss-2.2.5/Common/MemoryUtil.h
Examining data/abyss-2.2.5/Common/Options.cpp
Examining data/abyss-2.2.5/Common/Options.h
Examining data/abyss-2.2.5/Common/PMF.h
Examining data/abyss-2.2.5/Common/SAM.h
Examining data/abyss-2.2.5/Common/Sense.h
Examining data/abyss-2.2.5/Common/Sequence.cpp
Examining data/abyss-2.2.5/Common/Sequence.h
Examining data/abyss-2.2.5/Common/SignalHandler.cpp
Examining data/abyss-2.2.5/Common/SignalHandler.h
Examining data/abyss-2.2.5/Common/StringUtil.h
Examining data/abyss-2.2.5/Common/SuffixArray.h
Examining data/abyss-2.2.5/Common/Timer.cpp
Examining data/abyss-2.2.5/Common/Timer.h
Examining data/abyss-2.2.5/Common/Uncompress.cpp
Examining data/abyss-2.2.5/Common/Uncompress.h
Examining data/abyss-2.2.5/Common/UnorderedMap.h
Examining data/abyss-2.2.5/Common/UnorderedSet.h
Examining data/abyss-2.2.5/Common/VectorUtil.h
Examining data/abyss-2.2.5/Common/cholesky.hpp
Examining data/abyss-2.2.5/Common/city.cc
Examining data/abyss-2.2.5/Common/city.h
Examining data/abyss-2.2.5/Consensus/Consensus.cpp
Examining data/abyss-2.2.5/DAssembler/DAssembler.cpp
Examining data/abyss-2.2.5/DAssembler/RotatedRead.cpp
Examining data/abyss-2.2.5/DAssembler/RotatedRead.h
Examining data/abyss-2.2.5/DAssembler/Rotation.h
Examining data/abyss-2.2.5/DataBase/DB.cc
Examining data/abyss-2.2.5/DataBase/DB.h
Examining data/abyss-2.2.5/DataBase/Options.h
Examining data/abyss-2.2.5/DataBase/db-csv.cc
Examining data/abyss-2.2.5/DataLayer/FastaConcat.h
Examining data/abyss-2.2.5/DataLayer/FastaIndex.h
Examining data/abyss-2.2.5/DataLayer/FastaInterleave.h
Examining data/abyss-2.2.5/DataLayer/FastaReader.cpp
Examining data/abyss-2.2.5/DataLayer/FastaReader.h
Examining data/abyss-2.2.5/DataLayer/FastaWriter.cpp
Examining data/abyss-2.2.5/DataLayer/FastaWriter.h
Examining data/abyss-2.2.5/DataLayer/Options.h
Examining data/abyss-2.2.5/DataLayer/abyss-tofastq.cc
Examining data/abyss-2.2.5/DataLayer/fac.cc
Examining data/abyss-2.2.5/DistanceEst/DistanceEst.cpp
Examining data/abyss-2.2.5/DistanceEst/MLE.cpp
Examining data/abyss-2.2.5/DistanceEst/MLE.h
Examining data/abyss-2.2.5/FMIndex/BitArrays.h
Examining data/abyss-2.2.5/FMIndex/DAWG.h
Examining data/abyss-2.2.5/FMIndex/FMIndex.h
Examining data/abyss-2.2.5/FMIndex/abyss-dawg.cc
Examining data/abyss-2.2.5/FMIndex/bit_array.cc
Examining data/abyss-2.2.5/FMIndex/bit_array.h
Examining data/abyss-2.2.5/FMIndex/count.cc
Examining data/abyss-2.2.5/FilterGraph/FilterGraph.cc
Examining data/abyss-2.2.5/GapFiller/gapfill.cpp
Examining data/abyss-2.2.5/GapFiller/gapfill.h
Examining data/abyss-2.2.5/Graph/AdjIO.h
Examining data/abyss-2.2.5/Graph/AllPathsSearch.h
Examining data/abyss-2.2.5/Graph/AsqgIO.h
Examining data/abyss-2.2.5/Graph/Assemble.h
Examining data/abyss-2.2.5/Graph/BidirectionalBFS.h
Examining data/abyss-2.2.5/Graph/BidirectionalBFSVisitor.h
Examining data/abyss-2.2.5/Graph/BreadthFirstSearch.h
Examining data/abyss-2.2.5/Graph/ConstrainedBFSVisitor.h
Examining data/abyss-2.2.5/Graph/ConstrainedBidiBFSVisitor.h
Examining data/abyss-2.2.5/Graph/ConstrainedSearch.h
Examining data/abyss-2.2.5/Graph/ContigGraph.h
Examining data/abyss-2.2.5/Graph/ContigGraphAlgorithms.h
Examining data/abyss-2.2.5/Graph/DefaultColorMap.h
Examining data/abyss-2.2.5/Graph/DepthFirstSearch.h
Examining data/abyss-2.2.5/Graph/DirectedGraph.h
Examining data/abyss-2.2.5/Graph/DistIO.h
Examining data/abyss-2.2.5/Graph/DotIO.h
Examining data/abyss-2.2.5/Graph/ExtendPath.h
Examining data/abyss-2.2.5/Graph/FastaIO.h
Examining data/abyss-2.2.5/Graph/GfaIO.h
Examining data/abyss-2.2.5/Graph/GraphAlgorithms.h
Examining data/abyss-2.2.5/Graph/GraphIO.h
Examining data/abyss-2.2.5/Graph/GraphUtil.h
Examining data/abyss-2.2.5/Graph/HashGraph.h
Examining data/abyss-2.2.5/Graph/Options.h
Examining data/abyss-2.2.5/Graph/Path.h
Examining data/abyss-2.2.5/Graph/PopBubbles.h
Examining data/abyss-2.2.5/Graph/Properties.h
Examining data/abyss-2.2.5/Graph/SAMIO.h
Examining data/abyss-2.2.5/Graph/UndirectedGraph.h
Examining data/abyss-2.2.5/Graph/gc.cc
Examining data/abyss-2.2.5/Graph/todot.cc
Examining data/abyss-2.2.5/KAligner/Aligner.cpp
Examining data/abyss-2.2.5/KAligner/Aligner.h
Examining data/abyss-2.2.5/KAligner/KAligner.cpp
Examining data/abyss-2.2.5/KAligner/Options.h
Examining data/abyss-2.2.5/KAligner/Pipe.h
Examining data/abyss-2.2.5/KAligner/PipeMux.h
Examining data/abyss-2.2.5/KAligner/Semaphore.h
Examining data/abyss-2.2.5/Konnector/DBGBloom.h
Examining data/abyss-2.2.5/Konnector/DBGBloomAlgorithms.h
Examining data/abyss-2.2.5/Konnector/konnector.cc
Examining data/abyss-2.2.5/Konnector/konnector.h
Examining data/abyss-2.2.5/Layout/layout.cc
Examining data/abyss-2.2.5/LogKmerCount/CountingBloomFilter.h
Examining data/abyss-2.2.5/LogKmerCount/logcounter.cc
Examining data/abyss-2.2.5/LogKmerCount/plc.h
Examining data/abyss-2.2.5/LogKmerCount/plc_strand.h
Examining data/abyss-2.2.5/Map/index.cc
Examining data/abyss-2.2.5/Map/map.cc
Examining data/abyss-2.2.5/Map/overlap.cc
Examining data/abyss-2.2.5/MergePaths/MergeContigs.cpp
Examining data/abyss-2.2.5/MergePaths/MergePaths.cpp
Examining data/abyss-2.2.5/MergePaths/PathConsensus.cpp
Examining data/abyss-2.2.5/Overlap/Overlap.cpp
Examining data/abyss-2.2.5/PairedDBG/BranchRecord.h
Examining data/abyss-2.2.5/PairedDBG/Dinuc.h
Examining data/abyss-2.2.5/PairedDBG/KmerPair.cc
Examining data/abyss-2.2.5/PairedDBG/KmerPair.h
Examining data/abyss-2.2.5/PairedDBG/PairedDBGAlgorithms.h
Examining data/abyss-2.2.5/PairedDBG/SequenceCollection.h
Examining data/abyss-2.2.5/PairedDBG/abyss-paired-dbg.cc
Examining data/abyss-2.2.5/Parallel/CommLayer.cpp
Examining data/abyss-2.2.5/Parallel/CommLayer.h
Examining data/abyss-2.2.5/Parallel/MessageBuffer.cpp
Examining data/abyss-2.2.5/Parallel/MessageBuffer.h
Examining data/abyss-2.2.5/Parallel/Messages.cpp
Examining data/abyss-2.2.5/Parallel/Messages.h
Examining data/abyss-2.2.5/Parallel/NetworkSequenceCollection.cpp
Examining data/abyss-2.2.5/Parallel/NetworkSequenceCollection.h
Examining data/abyss-2.2.5/Parallel/SequenceCollection.h
Examining data/abyss-2.2.5/Parallel/parallelAbyss.cpp
Examining data/abyss-2.2.5/ParseAligns/ParseAligns.cpp
Examining data/abyss-2.2.5/ParseAligns/abyss-fixmate.cc
Examining data/abyss-2.2.5/PathOverlap/PathOverlap.cpp
Examining data/abyss-2.2.5/PopBubbles/PopBubbles.cpp
Examining data/abyss-2.2.5/RResolver/BloomFilters.cpp
Examining data/abyss-2.2.5/RResolver/BloomFilters.h
Examining data/abyss-2.2.5/RResolver/Contigs.cpp
Examining data/abyss-2.2.5/RResolver/Contigs.h
Examining data/abyss-2.2.5/RResolver/RAlgorithmsShort.cpp
Examining data/abyss-2.2.5/RResolver/RAlgorithmsShort.h
Examining data/abyss-2.2.5/RResolver/RResolverShort.cpp
Examining data/abyss-2.2.5/RResolver/RUtils.cpp
Examining data/abyss-2.2.5/RResolver/RUtils.h
Examining data/abyss-2.2.5/RResolver/SequenceTree.cpp
Examining data/abyss-2.2.5/RResolver/SequenceTree.h
Examining data/abyss-2.2.5/RResolver/btllib/extras/java/btllib_wrap.cxx
Examining data/abyss-2.2.5/RResolver/btllib/extras/python/btllib_wrap.cxx
Examining data/abyss-2.2.5/RResolver/btllib/include/btllib/bloom_filter.hpp
Examining data/abyss-2.2.5/RResolver/btllib/include/btllib/data_stream.hpp
Examining data/abyss-2.2.5/RResolver/btllib/include/btllib/graph.hpp
Examining data/abyss-2.2.5/RResolver/btllib/include/btllib/index_queue.hpp
Examining data/abyss-2.2.5/RResolver/btllib/include/btllib/nthash.hpp
Examining data/abyss-2.2.5/RResolver/btllib/include/btllib/seq.hpp
Examining data/abyss-2.2.5/RResolver/btllib/include/btllib/seq_reader.hpp
Examining data/abyss-2.2.5/RResolver/btllib/include/btllib/seq_writer.hpp
Examining data/abyss-2.2.5/RResolver/btllib/include/btllib/status.hpp
Examining data/abyss-2.2.5/RResolver/btllib/include/btllib/util.hpp
Examining data/abyss-2.2.5/RResolver/btllib/include/vendor/cpptoml.hpp
Examining data/abyss-2.2.5/RResolver/btllib/tests/bloom_filter.cpp
Examining data/abyss-2.2.5/RResolver/btllib/tests/data_stream.cpp
Examining data/abyss-2.2.5/RResolver/btllib/tests/helpers.hpp
Examining data/abyss-2.2.5/RResolver/btllib/tests/nthash.cpp
Examining data/abyss-2.2.5/RResolver/btllib/tests/seq.cpp
Examining data/abyss-2.2.5/RResolver/btllib/tests/seq_reader.cpp
Examining data/abyss-2.2.5/RResolver/btllib/tests/seq_writer.cpp
Examining data/abyss-2.2.5/Scaffold/drawgraph.cc
Examining data/abyss-2.2.5/Scaffold/junction.cc
Examining data/abyss-2.2.5/Scaffold/longseqdist.cpp
Examining data/abyss-2.2.5/Scaffold/scaffold.cc
Examining data/abyss-2.2.5/Sealer/sealer.cc
Examining data/abyss-2.2.5/SimpleGraph/SimpleGraph.cpp
Examining data/abyss-2.2.5/Unittest/BloomDBG/BloomDBGTest.cpp
Examining data/abyss-2.2.5/Unittest/BloomDBG/CountingBloomFilterTest.cpp
Examining data/abyss-2.2.5/Unittest/BloomDBG/HashAgnosticCascadingBloomTest.cpp
Examining data/abyss-2.2.5/Unittest/BloomDBG/LightweightKmerTest.cpp
Examining data/abyss-2.2.5/Unittest/BloomDBG/MaskedKmerTest.cpp
Examining data/abyss-2.2.5/Unittest/BloomDBG/RollingBloomDBGTest.cpp
Examining data/abyss-2.2.5/Unittest/BloomDBG/RollingHashIteratorTest.cpp
Examining data/abyss-2.2.5/Unittest/BloomDBG/RollingHashTest.cpp
Examining data/abyss-2.2.5/Unittest/BloomDBG/SpacedSeedTest.cpp
Examining data/abyss-2.2.5/Unittest/Common/BitUtilTest.cpp
Examining data/abyss-2.2.5/Unittest/Common/HistogramTest.cpp
Examining data/abyss-2.2.5/Unittest/Common/KmerIteratorTest.cpp
Examining data/abyss-2.2.5/Unittest/Common/KmerTest.cpp
Examining data/abyss-2.2.5/Unittest/Common/SAM.cc
Examining data/abyss-2.2.5/Unittest/Common/Sequence.cc
Examining data/abyss-2.2.5/Unittest/Common/StringUtilTest.cpp
Examining data/abyss-2.2.5/Unittest/DBG/LoadAlgorithmTest.cpp
Examining data/abyss-2.2.5/Unittest/Graph/AllPathsSearchTest.cpp
Examining data/abyss-2.2.5/Unittest/Graph/BidirectionalBFSTest.cpp
Examining data/abyss-2.2.5/Unittest/Graph/ConstrainedBFSVisitorTest.cpp
Examining data/abyss-2.2.5/Unittest/Graph/ConstrainedBidiBFSVisitorTest.cpp
Examining data/abyss-2.2.5/Unittest/Graph/DotIOTest.cpp
Examining data/abyss-2.2.5/Unittest/Graph/ExtendPathTest.cpp
Examining data/abyss-2.2.5/Unittest/Graph/HashGraphTest.cpp
Examining data/abyss-2.2.5/Unittest/Graph/UndirectedGraphTest.cpp
Examining data/abyss-2.2.5/Unittest/Konnector/BloomFilter.cc
Examining data/abyss-2.2.5/Unittest/Konnector/DBGBloomAlgorithmsTest.cpp
Examining data/abyss-2.2.5/Unittest/Konnector/DBGBloomTest.cpp
Examining data/abyss-2.2.5/Unittest/Konnector/konnectorTest.cpp
Examining data/abyss-2.2.5/Unittest/PairedDBG/BranchRecordTest.cpp
Examining data/abyss-2.2.5/Unittest/PairedDBG/DinucTest.cc
Examining data/abyss-2.2.5/Unittest/PairedDBG/KmerPairTest.cc
Examining data/abyss-2.2.5/Unittest/PairedDBG/LoadAlgorithmTest.cpp
Examining data/abyss-2.2.5/dialign/alig.c
Examining data/abyss-2.2.5/dialign/assemble.c
Examining data/abyss-2.2.5/dialign/diag.c
Examining data/abyss-2.2.5/dialign/io.c
Examining data/abyss-2.2.5/dialign/io.h
Examining data/abyss-2.2.5/dialign/museq.c
Examining data/abyss-2.2.5/dialign/orf.c
Examining data/abyss-2.2.5/dialign/orf.h
Examining data/abyss-2.2.5/dialign/parameters.c
Examining data/abyss-2.2.5/dialign/parameters.h