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