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/pbbam-1.6.0+dfsg/include/pbbam/Accuracy.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/AlignmentPrinter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/BaiIndexCache.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/BaiIndexedBamReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/BamFile.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/BamFileMerger.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/BamHeader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/BamReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/BamRecord.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/BamRecordImpl.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/BamRecordTag.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/BamRecordView.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/BamTagCodec.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/BamWriter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/BgzipFastaWriter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/BgzipFastqWriter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/BgzipWriter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/Cigar.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/CigarOperation.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/ClipType.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/CollectionMetadata.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/Compare.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/CompositeBamReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/CompositeFastaReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/Config.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/DataSet.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/DataSetTypes.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/DataSetXsd.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/Deleters.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/EntireFileQuery.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/FaiIndex.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/FastaCache.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/FastaReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/FastaSequence.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/FastaSequenceQuery.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/FastaWriter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/FastqReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/FastqSequence.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/FastqWriter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/FormatUtils.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/FrameEncodingType.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/Frames.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/GenomicInterval.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/GenomicIntervalQuery.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/IFastaWriter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/IFastqWriter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/IRecordWriter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/IndexedBamWriter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/IndexedFastaReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/IndexedFastqReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/Interval.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/LibraryInfo.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/LocalContextFlags.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/MD5.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/MoveAppend.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/Orientation.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/PbbamVersion.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/PbiBasicTypes.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/PbiBuilder.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/PbiFile.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/PbiFilter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/PbiFilterQuery.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/PbiFilterTypes.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/PbiIndexedBamReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/PbiRawData.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/Position.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/ProgramInfo.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/PulseBehavior.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/PulseExclusionReason.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/QualityValue.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/QualityValues.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/RecordType.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/RunMetadata.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/SNR.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/SamReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/SamTagCodec.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/SamWriter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/SequenceInfo.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/Strand.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/StringUtilities.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/Tag.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/TagCollection.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/TextFileReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/TextFileWriter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/Validator.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/ZmwChunkedFastaReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/ZmwChunkedFastqReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/ZmwGroupQuery.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/ZmwQuery.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/ZmwType.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/ZmwTypeMap.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/bed/BedReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/bed/BedWriter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSHeader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSPbiBuilder.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecord.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecordFormat.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecordReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/ccs/CCSRecordWriter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/exception/BundleChemistryMappingException.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/exception/InvalidSequencingChemistryException.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/exception/ValidationException.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/internal/DataSetBaseTypes.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/internal/DataSetElement.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/internal/QueryBase.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfFile.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfFormat.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfHeader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfHeaderTypes.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfQuery.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfSort.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfVariant.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/vcf/VcfWriter.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualPolymeraseBamRecord.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualPolymeraseCompositeReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualPolymeraseReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualRegion.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualRegionType.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualRegionTypeMap.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/virtual/VirtualZmwBamRecord.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/virtual/WhitelistedZmwReadStitcher.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/virtual/ZmwReadStitcher.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/virtual/ZmwWhitelistVirtualReader.h
Examining data/pbbam-1.6.0+dfsg/include/pbbam/ReadGroupInfo.h
Examining data/pbbam-1.6.0+dfsg/src/AlignmentPrinter.cpp
Examining data/pbbam-1.6.0+dfsg/src/Autovalidate.h
Examining data/pbbam-1.6.0+dfsg/src/BaiIndexCache.cpp
Examining data/pbbam-1.6.0+dfsg/src/BaiIndexedBamReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/BamFile.cpp
Examining data/pbbam-1.6.0+dfsg/src/BamFileMerger.cpp
Examining data/pbbam-1.6.0+dfsg/src/BamHeader.cpp
Examining data/pbbam-1.6.0+dfsg/src/BamReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/BamRecord.cpp
Examining data/pbbam-1.6.0+dfsg/src/BamRecordImpl.cpp
Examining data/pbbam-1.6.0+dfsg/src/BamRecordTags.cpp
Examining data/pbbam-1.6.0+dfsg/src/BamRecordTags.h
Examining data/pbbam-1.6.0+dfsg/src/BamRecordView.cpp
Examining data/pbbam-1.6.0+dfsg/src/BamTagCodec.cpp
Examining data/pbbam-1.6.0+dfsg/src/BamWriter.cpp
Examining data/pbbam-1.6.0+dfsg/src/BgzipFastaWriter.cpp
Examining data/pbbam-1.6.0+dfsg/src/BgzipFastqWriter.cpp
Examining data/pbbam-1.6.0+dfsg/src/BgzipWriter.cpp
Examining data/pbbam-1.6.0+dfsg/src/ChemistryTable.cpp
Examining data/pbbam-1.6.0+dfsg/src/ChemistryTable.h
Examining data/pbbam-1.6.0+dfsg/src/CollectionMetadata.cpp
Examining data/pbbam-1.6.0+dfsg/src/Compare.cpp
Examining data/pbbam-1.6.0+dfsg/src/CompositeBamReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/CompositeFastaReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/Config.cpp
Examining data/pbbam-1.6.0+dfsg/src/DataSet.cpp
Examining data/pbbam-1.6.0+dfsg/src/DataSetBaseTypes.cpp
Examining data/pbbam-1.6.0+dfsg/src/DataSetElement.cpp
Examining data/pbbam-1.6.0+dfsg/src/DataSetIO.cpp
Examining data/pbbam-1.6.0+dfsg/src/DataSetIO.h
Examining data/pbbam-1.6.0+dfsg/src/DataSetTypes.cpp
Examining data/pbbam-1.6.0+dfsg/src/DataSetUtils.h
Examining data/pbbam-1.6.0+dfsg/src/DataSetXsd.cpp
Examining data/pbbam-1.6.0+dfsg/src/EntireFileQuery.cpp
Examining data/pbbam-1.6.0+dfsg/src/ErrnoReason.cpp
Examining data/pbbam-1.6.0+dfsg/src/ErrnoReason.h
Examining data/pbbam-1.6.0+dfsg/src/FaiIndex.cpp
Examining data/pbbam-1.6.0+dfsg/src/FaiZmwChunker.cpp
Examining data/pbbam-1.6.0+dfsg/src/FaiZmwChunker.h
Examining data/pbbam-1.6.0+dfsg/src/FastaCache.cpp
Examining data/pbbam-1.6.0+dfsg/src/FastaReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/FastaSequence.cpp
Examining data/pbbam-1.6.0+dfsg/src/FastaSequenceQuery.cpp
Examining data/pbbam-1.6.0+dfsg/src/FastaWriter.cpp
Examining data/pbbam-1.6.0+dfsg/src/FastqReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/FastqSequence.cpp
Examining data/pbbam-1.6.0+dfsg/src/FastqWriter.cpp
Examining data/pbbam-1.6.0+dfsg/src/FileProducer.cpp
Examining data/pbbam-1.6.0+dfsg/src/FileProducer.h
Examining data/pbbam-1.6.0+dfsg/src/FileUtils.cpp
Examining data/pbbam-1.6.0+dfsg/src/FileUtils.h
Examining data/pbbam-1.6.0+dfsg/src/FofnReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/FofnReader.h
Examining data/pbbam-1.6.0+dfsg/src/FormatUtils.cpp
Examining data/pbbam-1.6.0+dfsg/src/GenomicIntervalQuery.cpp
Examining data/pbbam-1.6.0+dfsg/src/IFastaWriter.cpp
Examining data/pbbam-1.6.0+dfsg/src/IFastqWriter.cpp
Examining data/pbbam-1.6.0+dfsg/src/IRecordWriter.cpp
Examining data/pbbam-1.6.0+dfsg/src/IndexedBamWriter.cpp
Examining data/pbbam-1.6.0+dfsg/src/IndexedFastaReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/IndexedFastqBgzfReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/IndexedFastqBgzfReader.h
Examining data/pbbam-1.6.0+dfsg/src/IndexedFastqReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/IndexedFastqReaderImpl.cpp
Examining data/pbbam-1.6.0+dfsg/src/IndexedFastqReaderImpl.h
Examining data/pbbam-1.6.0+dfsg/src/IndexedFastqTextReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/IndexedFastqTextReader.h
Examining data/pbbam-1.6.0+dfsg/src/KSeqReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/KSeqReader.h
Examining data/pbbam-1.6.0+dfsg/src/LibraryInfo.cpp
Examining data/pbbam-1.6.0+dfsg/src/MD5.cpp
Examining data/pbbam-1.6.0+dfsg/src/MemoryUtils.cpp
Examining data/pbbam-1.6.0+dfsg/src/MemoryUtils.h
Examining data/pbbam-1.6.0+dfsg/src/PbbamInternalConfig.h
Examining data/pbbam-1.6.0+dfsg/src/PbiBuilder.cpp
Examining data/pbbam-1.6.0+dfsg/src/PbiFile.cpp
Examining data/pbbam-1.6.0+dfsg/src/PbiFilter.cpp
Examining data/pbbam-1.6.0+dfsg/src/PbiFilterQuery.cpp
Examining data/pbbam-1.6.0+dfsg/src/PbiFilterTypes.cpp
Examining data/pbbam-1.6.0+dfsg/src/PbiIndexIO.cpp
Examining data/pbbam-1.6.0+dfsg/src/PbiIndexIO.h
Examining data/pbbam-1.6.0+dfsg/src/PbiIndexedBamReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/PbiRawData.cpp
Examining data/pbbam-1.6.0+dfsg/src/ProgramInfo.cpp
Examining data/pbbam-1.6.0+dfsg/src/Pulse2BaseCache.h
Examining data/pbbam-1.6.0+dfsg/src/ReadGroupInfo.cpp
Examining data/pbbam-1.6.0+dfsg/src/RecordType.cpp
Examining data/pbbam-1.6.0+dfsg/src/RunMetadata.cpp
Examining data/pbbam-1.6.0+dfsg/src/RunMetadataParser.cpp
Examining data/pbbam-1.6.0+dfsg/src/RunMetadataParser.h
Examining data/pbbam-1.6.0+dfsg/src/SamReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/SamTagCodec.cpp
Examining data/pbbam-1.6.0+dfsg/src/SamWriter.cpp
Examining data/pbbam-1.6.0+dfsg/src/SequenceInfo.cpp
Examining data/pbbam-1.6.0+dfsg/src/SequenceUtils.h
Examining data/pbbam-1.6.0+dfsg/src/StringUtilities.cpp
Examining data/pbbam-1.6.0+dfsg/src/Tag.cpp
Examining data/pbbam-1.6.0+dfsg/src/TagCollection.cpp
Examining data/pbbam-1.6.0+dfsg/src/TextFileReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/TextFileWriter.cpp
Examining data/pbbam-1.6.0+dfsg/src/TimeUtils.h
Examining data/pbbam-1.6.0+dfsg/src/ValidationErrors.cpp
Examining data/pbbam-1.6.0+dfsg/src/ValidationErrors.h
Examining data/pbbam-1.6.0+dfsg/src/ValidationException.cpp
Examining data/pbbam-1.6.0+dfsg/src/Validator.cpp
Examining data/pbbam-1.6.0+dfsg/src/Version.cpp
Examining data/pbbam-1.6.0+dfsg/src/Version.h
Examining data/pbbam-1.6.0+dfsg/src/VirtualRegion.cpp
Examining data/pbbam-1.6.0+dfsg/src/VirtualRegionTypeMap.cpp
Examining data/pbbam-1.6.0+dfsg/src/VirtualStitching.h
Examining data/pbbam-1.6.0+dfsg/src/VirtualZmwBamRecord.cpp
Examining data/pbbam-1.6.0+dfsg/src/VirtualZmwCompositeReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/VirtualZmwCompositeReader.h
Examining data/pbbam-1.6.0+dfsg/src/VirtualZmwReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/VirtualZmwReader.h
Examining data/pbbam-1.6.0+dfsg/src/WhitelistedZmwReadStitcher.cpp
Examining data/pbbam-1.6.0+dfsg/src/XmlReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/XmlReader.h
Examining data/pbbam-1.6.0+dfsg/src/XmlWriter.cpp
Examining data/pbbam-1.6.0+dfsg/src/XmlWriter.h
Examining data/pbbam-1.6.0+dfsg/src/ZmwChunkedFastaReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/ZmwChunkedFastqReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/ZmwChunkedFastxBgzfReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/ZmwChunkedFastxBgzfReader.h
Examining data/pbbam-1.6.0+dfsg/src/ZmwChunkedFastxReaderImpl.cpp
Examining data/pbbam-1.6.0+dfsg/src/ZmwChunkedFastxReaderImpl.h
Examining data/pbbam-1.6.0+dfsg/src/ZmwChunkedFastxTextReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/ZmwChunkedFastxTextReader.h
Examining data/pbbam-1.6.0+dfsg/src/ZmwGroupQuery.cpp
Examining data/pbbam-1.6.0+dfsg/src/ZmwQuery.cpp
Examining data/pbbam-1.6.0+dfsg/src/ZmwReadStitcher.cpp
Examining data/pbbam-1.6.0+dfsg/src/ZmwTypeMap.cpp
Examining data/pbbam-1.6.0+dfsg/src/bed/BedReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/bed/BedWriter.cpp
Examining data/pbbam-1.6.0+dfsg/src/ccs/CCSPbiBuilder.cpp
Examining data/pbbam-1.6.0+dfsg/src/ccs/CCSRecord.cpp
Examining data/pbbam-1.6.0+dfsg/src/ccs/CCSRecordFormat.cpp
Examining data/pbbam-1.6.0+dfsg/src/ccs/CCSRecordReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/ccs/CCSRecordWriter.cpp
Examining data/pbbam-1.6.0+dfsg/src/pugixml/pugiconfig.hpp
Examining data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp
Examining data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.hpp
Examining data/pbbam-1.6.0+dfsg/src/vcf/VcfFile.cpp
Examining data/pbbam-1.6.0+dfsg/src/vcf/VcfFormat.cpp
Examining data/pbbam-1.6.0+dfsg/src/vcf/VcfFormatException.h
Examining data/pbbam-1.6.0+dfsg/src/vcf/VcfHeader.cpp
Examining data/pbbam-1.6.0+dfsg/src/vcf/VcfHeaderTypes.cpp
Examining data/pbbam-1.6.0+dfsg/src/vcf/VcfQuery.cpp
Examining data/pbbam-1.6.0+dfsg/src/vcf/VcfReader.cpp
Examining data/pbbam-1.6.0+dfsg/src/vcf/VcfSort.cpp
Examining data/pbbam-1.6.0+dfsg/src/vcf/VcfVariant.cpp
Examining data/pbbam-1.6.0+dfsg/src/vcf/VcfWriter.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/FastxTests.h
Examining data/pbbam-1.6.0+dfsg/tests/src/test_AlignmentPrinter.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_BamFile.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_BamHeader.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_BamReader.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_BamRecord.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_BamRecordClipping.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_BamRecordImplCore.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_BamRecordImplTags.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_BamRecordImplVariableData.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_BamRecordMapping.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_BamWriter.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_BedReader.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_BedWriter.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_BgzipFastaWriter.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_BgzipFastqWriter.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_BgzipWriter.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_CCSPbiBuilder.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_CCSRecord.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_CCSRecordIO.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_CollectionMetadata.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_Compare.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_CompositeBamReaders.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_DataSetCore.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_DataSetGenomicIntervals.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_DataSetIO.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_DataSetQuery.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_DataSetXsd.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_EndToEnd.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_EntireFileQuery.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_FaiIndex.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_FaiZmwChunker.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_FastaCache.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_FastaReader.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_FastaSequence.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_FastaSequenceQuery.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_FastaWriter.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_FastqReader.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_FastqSequence.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_FastqWriter.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_FileUtils.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_GenomicIntervalQuery.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_IndexedBamWriter.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_IndexedFastaReader.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_IndexedFastqReader.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_LongCigar.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_PacBioIndex.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_PbiFilter.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_PbiFilterQuery.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_Pulse2BaseCache.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_QualityValues.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_RunMetadata.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_SamIO.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_SequenceUtils.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_StringUtils.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_Tags.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_TextFileReader.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_TextFileWriter.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_TimeUtils.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_Validator.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_VcfFile.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_VcfFormat.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_VcfHeader.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_VcfQuery.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_VcfReader.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_VcfSort.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_VcfVariant.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_VcfWriter.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_Version.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_WhitelistedZmwReadStitcher.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_ZmwChunkedFastxReader.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_ZmwQuery.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_ZmwReadStitcher.cpp
Examining data/pbbam-1.6.0+dfsg/tests/src/test_ReadGroupInfo.cpp
Examining data/pbbam-1.6.0+dfsg/tests/zero_byte_check/main.cpp
Examining data/pbbam-1.6.0+dfsg/tools/bam2sam/src/Bam2SamSettings.cpp
Examining data/pbbam-1.6.0+dfsg/tools/bam2sam/src/Bam2SamSettings.h
Examining data/pbbam-1.6.0+dfsg/tools/bam2sam/src/Bam2SamWorkflow.cpp
Examining data/pbbam-1.6.0+dfsg/tools/bam2sam/src/Bam2SamWorkflow.h
Examining data/pbbam-1.6.0+dfsg/tools/bam2sam/src/main.cpp
Examining data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifySettings.cpp
Examining data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifySettings.h
Examining data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp
Examining data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.h
Examining data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/main.cpp
Examining data/pbbam-1.6.0+dfsg/tools/pbbamify/src/PbBamifySettings.cpp
Examining data/pbbam-1.6.0+dfsg/tools/pbbamify/src/PbBamifySettings.h
Examining data/pbbam-1.6.0+dfsg/tools/pbbamify/src/PbBamifyWorkflow.cpp
Examining data/pbbam-1.6.0+dfsg/tools/pbbamify/src/PbBamifyWorkflow.h
Examining data/pbbam-1.6.0+dfsg/tools/pbbamify/src/QueryLookup.cpp
Examining data/pbbam-1.6.0+dfsg/tools/pbbamify/src/QueryLookup.h
Examining data/pbbam-1.6.0+dfsg/tools/pbbamify/src/main.cpp
Examining data/pbbam-1.6.0+dfsg/tools/pbindex/src/PbIndexSettings.cpp
Examining data/pbbam-1.6.0+dfsg/tools/pbindex/src/PbIndexSettings.h
Examining data/pbbam-1.6.0+dfsg/tools/pbindex/src/PbIndexWorkflow.cpp
Examining data/pbbam-1.6.0+dfsg/tools/pbindex/src/PbIndexWorkflow.h
Examining data/pbbam-1.6.0+dfsg/tools/pbindex/src/main.cpp
Examining data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/CppFormatter.cpp
Examining data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/CppFormatter.h
Examining data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp
Examining data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.h
Examining data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/PbIndexDumpSettings.cpp
Examining data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/PbIndexDumpSettings.h
Examining data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/PbIndexDumpWorkflow.cpp
Examining data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/PbIndexDumpWorkflow.h
Examining data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/main.cpp
Examining data/pbbam-1.6.0+dfsg/tools/pbmerge/src/PbMergeSettings.cpp
Examining data/pbbam-1.6.0+dfsg/tools/pbmerge/src/PbMergeSettings.h
Examining data/pbbam-1.6.0+dfsg/tools/pbmerge/src/PbMergeWorkflow.cpp
Examining data/pbbam-1.6.0+dfsg/tools/pbmerge/src/PbMergeWorkflow.h
Examining data/pbbam-1.6.0+dfsg/tools/pbmerge/src/main.cpp
FINAL RESULTS:
data/pbbam-1.6.0+dfsg/tests/src/test_EndToEnd.cpp:70:12: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return system(s.str().c_str());
data/pbbam-1.6.0+dfsg/tests/src/test_EndToEnd.cpp:77:12: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return system(s.str().c_str());
data/pbbam-1.6.0+dfsg/tests/src/test_FileUtils.cpp:31:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
ASSERT_EQ(0, system(cmd.c_str()));
data/pbbam-1.6.0+dfsg/tests/src/test_FileUtils.cpp:48:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const auto ret = system(rmCmd.c_str());
data/pbbam-1.6.0+dfsg/tests/src/test_FileUtils.cpp:50:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
ASSERT_EQ(0, system(touchCmd.c_str()));
data/pbbam-1.6.0+dfsg/tests/src/test_FileUtils.cpp:118:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
ASSERT_EQ(0, system(cmd.c_str()));
data/pbbam-1.6.0+dfsg/tests/src/test_PacBioIndex.cpp:152:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const auto cmdResult = system(cmd.c_str());
data/pbbam-1.6.0+dfsg/tests/src/test_PacBioIndex.cpp:271:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
const auto cmdResult = system(cmd.c_str());
data/pbbam-1.6.0+dfsg/src/ChemistryTable.cpp:144:23: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
const char* pth = getenv("SMRT_CHEMISTRY_BUNDLE_DIR");
data/pbbam-1.6.0+dfsg/src/BamRecordImpl.cpp:65:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&numElements, &CG[2], sizeof(uint32_t));
data/pbbam-1.6.0+dfsg/src/BamRecordImpl.cpp:415:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(d_->data, name.c_str(), numChars);
data/pbbam-1.6.0+dfsg/src/BamRecordImpl.cpp:641:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(pEncodedSequence, sequence, encodedSequenceLength);
data/pbbam-1.6.0+dfsg/src/BamRecordImpl.cpp:700:14: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
std::memcpy(static_cast<void*>(tagStart), data, numBytes);
data/pbbam-1.6.0+dfsg/src/BamRecordImpl.cpp:814:17: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&numElements, &tagStart[i], sizeof(uint32_t));
data/pbbam-1.6.0+dfsg/src/BamTagCodec.cpp:48:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&numElements, &src[offset], sizeof(uint32_t));
data/pbbam-1.6.0+dfsg/src/BamTagCodec.cpp:296:14: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
std::memcpy(reinterpret_cast<char*>(result.data()), str.s, str.l);
data/pbbam-1.6.0+dfsg/src/BamTagCodec.cpp:470:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(reinterpret_cast<char*>(&result[0]), str.s, str.l);
data/pbbam-1.6.0+dfsg/src/FastaWriter.cpp:26:11: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file_.open(fn);
data/pbbam-1.6.0+dfsg/src/FastqWriter.cpp:27:11: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file_.open(fn);
data/pbbam-1.6.0+dfsg/src/FileUtils.cpp:146:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[chunkSize];
data/pbbam-1.6.0+dfsg/src/IndexedBamWriter.cpp:257:26: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
tempFile_{std::fopen(tempFilename_.c_str(), "w+b")},
data/pbbam-1.6.0+dfsg/src/IndexedBamWriter.cpp:583:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char reserved[18];
data/pbbam-1.6.0+dfsg/src/IndexedBamWriter.cpp:597:61: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
std::unique_ptr<FILE, Utility::FileDeleter> gziFile{fopen(gziFn.c_str(), "rb")};
data/pbbam-1.6.0+dfsg/src/IndexedFastqTextReader.cpp:21:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
, file_{fopen(fastqFilename_.c_str(), "r")}
data/pbbam-1.6.0+dfsg/src/MD5.cpp:27:18: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char digest[16];
data/pbbam-1.6.0+dfsg/src/MD5.cpp:30:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char hexdigest[33]; // leave space for null-term
data/pbbam-1.6.0+dfsg/src/MemoryUtils.cpp:35:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(rawData->text, text.c_str(), rawData->l_text);
data/pbbam-1.6.0+dfsg/src/PbiBuilder.cpp:265:26: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
, tempFile_{std::fopen(tempFilename_.c_str(), "w+b")}
data/pbbam-1.6.0+dfsg/src/PbiBuilder.cpp:606:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char reserved[18];
data/pbbam-1.6.0+dfsg/src/PbiIndexIO.cpp:211:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char magic[4];
data/pbbam-1.6.0+dfsg/src/PbiIndexIO.cpp:237:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char reserved[18];
data/pbbam-1.6.0+dfsg/src/PbiIndexIO.cpp:354:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char reserved[18];
data/pbbam-1.6.0+dfsg/src/SequenceInfo.cpp:119:20: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
const long l = atol(length_.c_str());
data/pbbam-1.6.0+dfsg/src/TextFileWriter.cpp:46:18: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
out_.open(TempFilename());
data/pbbam-1.6.0+dfsg/src/TimeUtils.h:32:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char date_time_str[50];
data/pbbam-1.6.0+dfsg/src/TimeUtils.h:56:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char date_time_str[50];
data/pbbam-1.6.0+dfsg/src/ZmwChunkedFastxTextReader.cpp:21:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
, file_{fopen(fastxFilename_.c_str(), "r")}
data/pbbam-1.6.0+dfsg/src/ccs/CCSPbiBuilder.cpp:120:26: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
, tempFile_{std::fopen(tempFilename_.c_str(), "w+b")}
data/pbbam-1.6.0+dfsg/src/ccs/CCSPbiBuilder.cpp:244:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char reserved[18];
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:111:50: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
#define PUGI__STATIC_ASSERT(cond) { static const char condition_failed[(cond) ? 1 : -1] = {0}; (void)condition_failed[0]; }
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:122:12: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
using std::memcpy;
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:1231:24: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static const unsigned char chartype_table[256] =
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:1261:24: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static const unsigned char chartypex_table[256] =
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:1373:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buffer, contents, length * sizeof(char_t));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:1645:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buffer, data, prefix_length);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:1790:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dest, source, (source_length + 1) * sizeof(char_t));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:1803:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buf, source, (source_length + 1) * sizeof(char_t));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:3198:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buffer + bufsize, data, length * sizeof(char_t));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:3208:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buffer + offset, data, length * sizeof(char_t));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:3966:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[128];
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:3967:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf, "%d", value);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:3974:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[128];
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:3975:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf, "%u", value);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:3982:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[128];
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:3983:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf, "%.9g", value);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:3990:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[128];
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:3991:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf, "%.17g", value);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:4004:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[128];
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:4005:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf, "%lld", value);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:4012:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[128];
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:4013:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf, "%llu", value);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:4199:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(write, chunk->data, chunk->size);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:4305:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char mode_ascii[4] = {0};
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:4309:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* result = fopen(path_utf8, mode_ascii);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:6108:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* file = fopen(path_, "rb");
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:6187:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* file = fopen(path_, (flags & format_save_file_text) ? "w" : "wb");
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:6528:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char data[
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:6627:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(result, ptr, old_size);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:6750:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(result, string, length * sizeof(char_t));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:6808:22: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if (!_uses_heap) memcpy(result, _buffer, target_length * sizeof(char_t));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:6811:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(result + target_length, o._buffer, source_length * sizeof(char_t));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:7212:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buffer, "%.*e", DBL_DIG, value);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:7220:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int exponent = atoi(exponent_string + 1);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:7247:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char mantissa_buffer[32];
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:7363:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(scratch, begin, length * sizeof(char_t));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:7514:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char table[128] = {0};
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:7540:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(result, table, sizeof(table));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:7652:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(result->name, name, (length + 1) * sizeof(char_t));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:7722:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(scratch, begin, length * sizeof(char_t));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:7864:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(_end, begin_, count * sizeof(xpath_node));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:10050:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(c, value.begin, length * sizeof(char_t));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:11003:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(storage, begin_, size_ * sizeof(xpath_node));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:11178:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(copy, value, size);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:11380:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buffer, r.c_str(), (size - 1) * sizeof(char_t));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.hpp:938:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char _memory[192];
data/pbbam-1.6.0+dfsg/tests/src/test_BamHeader.cpp:221:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(rawData->text, text.c_str(), rawData->l_text);
data/pbbam-1.6.0+dfsg/tests/src/test_BamHeader.cpp:274:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(rawData->text, text.c_str(), rawData->l_text);
data/pbbam-1.6.0+dfsg/tests/src/test_Tags.cpp:947:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char valueBytes[sizeof x];
data/pbbam-1.6.0+dfsg/tests/src/test_Tags.cpp:960:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char numCharsValueBytes[sizeof numChars];
data/pbbam-1.6.0+dfsg/tests/src/test_Tags.cpp:1002:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char numCharsValueBytes[sizeof numChars];
data/pbbam-1.6.0+dfsg/tests/src/test_Tags.cpp:1031:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char valueBytes[sizeof x];
data/pbbam-1.6.0+dfsg/src/BamRecordImpl.cpp:651:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((qualities == nullptr) || (strlen(qualities) == 0))
data/pbbam-1.6.0+dfsg/src/BamRecordImpl.cpp:784:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
i += strlen(reinterpret_cast<const char*>(&tagStart[i])) + 1;
data/pbbam-1.6.0+dfsg/src/BamTagCodec.cpp:111:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const size_t dataLength = strlen(reinterpret_cast<const char*>(&pData[i]));
data/pbbam-1.6.0+dfsg/src/BamTagCodec.cpp:331:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const size_t dataLength = strlen(reinterpret_cast<const char*>(&rawData[0]));
data/pbbam-1.6.0+dfsg/src/IndexedBamWriter.cpp:797:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
refHeader += (8 + (strlen(n) + 1));
data/pbbam-1.6.0+dfsg/src/IndexedBamWriter.cpp:965:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
refHeader += (8 + (strlen(n) + 1));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:199:10: [1] (buffer) wcslen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return wcslen(s);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:201:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return strlen(s);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:233:10: [1] (buffer) wcslen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return wcslen(s);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:4177:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
stream.read(chunk->data, static_cast<std::streamsize>(sizeof(chunk->data) / sizeof(T)));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:4233:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
stream.read(static_cast<T*>(buffer.data), static_cast<std::streamsize>(read_length));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:6225:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return impl::as_wide_impl(str, strlen(str));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:7202:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
truncate_zeros(buffer, buffer + strlen(buffer));
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:7213:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
assert(strlen(buffer) < buffer_size);
data/pbbam-1.6.0+dfsg/src/pugixml/pugixml.cpp:7254:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t result_size = strlen(mantissa_buffer) + (exponent > 0 ? exponent : -exponent) + 4;
data/pbbam-1.6.0+dfsg/tests/src/test_BedWriter.cpp:41:22: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
EXPECT_TRUE(std::equal(BedWriterTests::Intervals.cbegin(), BedWriterTests::Intervals.cend(),
data/pbbam-1.6.0+dfsg/tests/src/test_BgzipFastaWriter.cpp:36:22: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
EXPECT_TRUE(std::equal(sequences.cbegin(), sequences.cend(), observed.cbegin()));
data/pbbam-1.6.0+dfsg/tests/src/test_BgzipFastqWriter.cpp:35:22: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
EXPECT_TRUE(std::equal(sequences.cbegin(), sequences.cend(), observed.cbegin()));
data/pbbam-1.6.0+dfsg/tests/src/test_CCSRecord.cpp:28:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
EXPECT_EQ(holeNumber, read.Id.HoleNumber);
data/pbbam-1.6.0+dfsg/tests/src/test_CCSRecord.cpp:29:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
EXPECT_EQ(qStart, read.QueryStart);
data/pbbam-1.6.0+dfsg/tests/src/test_CCSRecord.cpp:30:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
EXPECT_EQ(qEnd, read.QueryEnd);
data/pbbam-1.6.0+dfsg/tests/src/test_CCSRecord.cpp:31:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
EXPECT_EQ(ctxtFlags, read.Flags);
data/pbbam-1.6.0+dfsg/tests/src/test_CCSRecord.cpp:32:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
EXPECT_EQ(acc, read.ReadAccuracy);
data/pbbam-1.6.0+dfsg/tests/src/test_CCSRecord.cpp:33:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
EXPECT_EQ(snr, read.SignalToNoise);
data/pbbam-1.6.0+dfsg/tests/src/test_CCSRecord.cpp:34:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
EXPECT_EQ(seq, read.Seq);
data/pbbam-1.6.0+dfsg/tests/src/test_CCSRecord.cpp:35:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
EXPECT_EQ(pw, read.PulseWidth);
data/pbbam-1.6.0+dfsg/tests/src/test_CCSRecordIO.cpp:86:22: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
EXPECT_TRUE(std::equal(expected.PulseWidths.cbegin(), expected.PulseWidths.cend(),
data/pbbam-1.6.0+dfsg/tests/src/test_CCSRecordIO.cpp:160:22: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
EXPECT_TRUE(std::equal(lines.cbegin(), lines.cend(), expected.cbegin()));
data/pbbam-1.6.0+dfsg/tests/src/test_FaiIndex.cpp:35:22: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
EXPECT_TRUE(std::equal(expectedNames.cbegin(), expectedNames.cend(), names.cbegin()));
data/pbbam-1.6.0+dfsg/tests/src/test_FaiIndex.cpp:48:22: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
EXPECT_TRUE(std::equal(expectedNames.cbegin(), expectedNames.cend(), names.cbegin()));
data/pbbam-1.6.0+dfsg/tests/src/test_PbiFilterQuery.cpp:121:26: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
EXPECT_TRUE(std::equal(chems.begin(), chems.end(), expected.begin()));
data/pbbam-1.6.0+dfsg/tests/src/test_TextFileWriter.cpp:35:22: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
EXPECT_TRUE(std::equal(TextFileWriterTests::Lines.cbegin(), TextFileWriterTests::Lines.cend(),
data/pbbam-1.6.0+dfsg/tests/src/test_ZmwQuery.cpp:97:22: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
EXPECT_TRUE(std::equal(numRecordsPerZmw.cbegin(), numRecordsPerZmw.cend(),
data/pbbam-1.6.0+dfsg/tests/src/test_ZmwQuery.cpp:126:14: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
std::equal(holeNumbers.cbegin(), holeNumbers.cbegin() + 6, expectedHoleNumbers.cbegin()));
data/pbbam-1.6.0+dfsg/tests/src/test_ZmwQuery.cpp:148:14: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
std::equal(holeNumbers.cbegin(), holeNumbers.cbegin() + 5, expectedHoleNumbers.cbegin()));
data/pbbam-1.6.0+dfsg/tests/src/test_ZmwQuery.cpp:172:22: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
EXPECT_TRUE(std::equal(holeNumbers.cbegin(), holeNumbers.cend(), expectedHoleNumbers.cbegin()));
data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifySettings.cpp:18:41: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
"for creating a strand-specific read."
data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:46:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : inputBamReader) {
data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:47:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const std::string readName = read.FullName();
data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:50:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.Type() != BAM::RecordType::CCS)
data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:51:87: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
throw std::runtime_error{"Read '" + readName + "' is of " + BAM::ToString(read.Type()) +
data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:53:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.IsMapped())
data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:56:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.HasPulseWidth())
data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:60:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.HasIPD())
data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:65:46: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BAM::BamRecordImpl& readImpl = read.Impl();
data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:83:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const int32_t holeNumber = read.HoleNumber();
data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:84:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto snr = read.SignalToNoise();
data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:85:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto rq = read.ReadAccuracy();
data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:87:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::string seq = read.Sequence();
data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:88:37: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Data::QualityValues quals = read.Qualities();
data/pbbam-1.6.0+dfsg/tools/ccs-kinetics-bystrandify/src/CcsKineticsBystrandifyWorkflow.cpp:91:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BAM::ReadGroupInfo rg = read.ReadGroup();
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:93:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
JSON::Json read;
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:97:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["rgId"] = basicData.rgId_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:98:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["qStart"] = basicData.qStart_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:99:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["qEnd"] = basicData.qEnd_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:100:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["holeNumber"] = basicData.holeNumber_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:101:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["readQuality"] = basicData.readQual_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:102:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["contextFlag"] = basicData.ctxtFlag_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:103:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["fileOffset"] = basicData.fileOffset_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:108:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["bcForward"] = barcodeData.bcForward_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:109:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["bcReverse"] = barcodeData.bcReverse_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:110:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["bcQuality"] = barcodeData.bcQual_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:118:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["tId"] = static_cast<int32_t>(mappedData.tId_[i]);
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:119:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["tStart"] = static_cast<int32_t>(mappedData.tStart_[i]);
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:120:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["tEnd"] = static_cast<int32_t>(mappedData.tEnd_[i]);
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:122:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["aStart"] = mappedData.aStart_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:123:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["aEnd"] = mappedData.aEnd_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:124:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["nM"] = mappedData.nM_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:125:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["nMM"] = mappedData.nMM_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:126:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["mapQuality"] = mappedData.mapQV_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:127:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read["reverseStrand"] = mappedData.revStrand_[i];
data/pbbam-1.6.0+dfsg/tools/pbindexdump/src/JsonFormatter.cpp:130:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
reads.push_back(std::move(read));
ANALYSIS SUMMARY:
Hits = 163
Lines analyzed = 83335 in approximately 1.94 seconds (42927 lines/second)
Physical Source Lines of Code (SLOC) = 57543
Hits@level = [0] 9 [1] 72 [2] 82 [3] 1 [4] 8 [5] 0
Hits@level+ = [0+] 172 [1+] 163 [2+] 91 [3+] 9 [4+] 8 [5+] 0
Hits/KSLOC@level+ = [0+] 2.98907 [1+] 2.83266 [2+] 1.58143 [3+] 0.156405 [4+] 0.139026 [5+] 0
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.