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/plast-2.3.2+dfsg/src/database/impl/ReadingFrameSequenceIterator.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/ReadingFrameSequenceDatabase.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/BufferedCachedSequenceDatabase.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/CompositeSequenceDatabase.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/BufferedSequenceDatabase.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/BasicSequenceBuilder.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/CompositeSequenceDatabase.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/SequenceTokenizer.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/FastaSequenceIterator.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/BlastdbAsn1HeaderDecoder.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/BlastdbSequenceIterator.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/BlastdbDatabaseQuickReader.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/AminoAcidDatabaseQuickReader.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/BlastdbFileIndexReader.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/AbstractSequenceIterator.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/FastaSequenceOutput.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/BlastdbSequenceIterator.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/ReadingFrameSequenceIterator.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/FastaSequenceOutput.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/BlastdbDatabaseQuickReader.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/Sequence.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/BufferedSequenceDatabase.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/DefaultAlphabet.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/TruncatedSequenceIterator.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/ReverseStrandSequenceIterator.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/StringSequenceIterator.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/BasicSequenceBuilder.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/FastaSequenceIterator.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/ReadingFrameSequenceDatabase.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/DatabaseVisitorComment.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/AbstractSequenceIterator.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/BlastdbFileIndexReader.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/ReverseStrandSequenceIterator.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/BlastdbAsn1HeaderDecoder.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/SequenceTokenizer.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/BufferedCachedSequenceDatabase.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/DatabaseUtility.hpp
Examining data/plast-2.3.2+dfsg/src/database/impl/StringSequenceIterator.cpp
Examining data/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp
Examining data/plast-2.3.2+dfsg/src/database/api/ISequenceDatabase.hpp
Examining data/plast-2.3.2+dfsg/src/database/api/ISequenceCache.hpp
Examining data/plast-2.3.2+dfsg/src/database/api/ISequenceIterator.hpp
Examining data/plast-2.3.2+dfsg/src/database/api/ISequenceBuilder.hpp
Examining data/plast-2.3.2+dfsg/src/database/api/IDatabaseQuickReader.hpp
Examining data/plast-2.3.2+dfsg/src/database/api/IAlphabet.hpp
Examining data/plast-2.3.2+dfsg/src/database/api/ISequence.hpp
Examining data/plast-2.3.2+dfsg/src/database/api/IWord.hpp
Examining data/plast-2.3.2+dfsg/src/index/impl/AbstractDatabaseIndex.hpp
Examining data/plast-2.3.2+dfsg/src/index/impl/DatabaseIndexHash.cpp
Examining data/plast-2.3.2+dfsg/src/index/impl/DatabaseNucleotidIndex.cpp
Examining data/plast-2.3.2+dfsg/src/index/impl/retrievall.c
Examining data/plast-2.3.2+dfsg/src/index/impl/DatabaseNucleotidIndexOptim.hpp
Examining data/plast-2.3.2+dfsg/src/index/impl/DatabaseIndex.hpp
Examining data/plast-2.3.2+dfsg/src/index/impl/DatabaseNucleotidIndexOptim.cpp
Examining data/plast-2.3.2+dfsg/src/index/impl/retrievall.h
Examining data/plast-2.3.2+dfsg/src/index/impl/DatabaseIndexHash.hpp
Examining data/plast-2.3.2+dfsg/src/index/impl/DatabaseIndex.cpp
Examining data/plast-2.3.2+dfsg/src/index/impl/AbstractDatabaseIndex.cpp
Examining data/plast-2.3.2+dfsg/src/index/impl/DatabaseNucleotidIndex.hpp
Examining data/plast-2.3.2+dfsg/src/index/api/IDatabaseIndex.hpp
Examining data/plast-2.3.2+dfsg/src/index/api/IOccurrenceIterator.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/impl/BasicAlignmentContainer.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/impl/UngapAlignmentContainer.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/impl/HspContainer.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/impl/UngapAlignmentContainer.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/impl/NullAlignmentContainer.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/impl/BasicAlignmentContainer.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/impl/ReaderAlignmentContainer.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/impl/AbstractAlignmentContainer.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/impl/HspContainer.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/impl/AbstractAlignmentContainer.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/impl/ReaderAlignmentContainer.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/impl/Alignment.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/api/IAlignmentContainerModel.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/api/IHspContainer.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/api/IAlignmentContainerVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/api/IAlignmentContainerFactory.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/api/Alignment.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/core/api/IAlignmentContainer.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/tools/impl/SemiGappedAlign.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentSplitterBanded.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentOverlapCmd.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentSplitter.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentSplitter.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentContainerShrinkCmd.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentSplitterBanded.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentOverlapCmd.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/tools/impl/SemiGappedAlign.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentContainerShrinkCmd.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/tools/impl/SemiGappedAlignTraceback.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/tools/impl/SemiGappedAlignTraceback.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/tools/api/IAlignmentSplitter.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/tools/api/ISemiGappedAlign.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/filter/impl/AlignmentFilterXML.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/filter/impl/AlignmentFilterOperator.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/filter/impl/AbstractAlignmentFilterFactory.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/filter/impl/AlignmentFilterFactory.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/filter/impl/AlignmentFilterXML.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/filter/impl/AbstractAlignmentFilterFactory.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/filter/impl/AlignmentFilterFactory.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/filter/impl/AlignmentFilterOperator.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/filter/api/IAlignmentFilter.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/ModelBuilderVisitor.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/QueryReorderVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/ProxyVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/ModelBuilderVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/ShrinkContainerVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/CompareResultVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/ModifierContainerVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/NucleotidConversionVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/MaxHitsPerQueryVisitor.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/HierarchyAlignmentVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/NucleotidConversionVisitor.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/AdapterAlignmentVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/CompareContainerVisitor.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/TabulatedOutputVisitor.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/QueryReorderVisitor.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/MaxHitsPerQueryVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/SortContainerVisitor.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/ReverseStrandVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/CompareContainerVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/ShrinkContainerVisitor.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/OstreamVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/FilterContainerVisitor.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/ReverseStrandVisitor.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/SortContainerVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/CompareResultQryVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/CompareResultVisitor.cpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/XmlOutputVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/TabulatedOutputVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/RawOutputVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/FilterContainerVisitor.hpp
Examining data/plast-2.3.2+dfsg/src/alignment/visitors/impl/XmlOutputVisitor.cpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/Observer.cpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/TokenizerIterator.cpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/Property.cpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/FileLineIterator.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/DirectoryIterator.cpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/ListIterator.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/ConfigFileProperties.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/IteratorGet.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/CommandDispatcher.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/Vectorterator.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/WrapperIterator.cpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/CommandDispatcher.cpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/DirectoryIterator.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/Property.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/EventCatch.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/XmlReader.cpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/WrapperIterator.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/ConfigFileProperties.cpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/FileLineIterator.cpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/TokenizerIterator.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/Observer.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/ProductIterator.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/RangeIterator.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/impl/XmlReader.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/api/IProperty.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/api/IObserver.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/api/ICommand.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/api/SmartPointer.hpp
Examining data/plast-2.3.2+dfsg/src/designpattern/api/Iterator.hpp
Examining data/plast-2.3.2+dfsg/src/tools/PlastCmd.cpp
Examining data/plast-2.3.2+dfsg/src/seg/impl/DustMasker.hpp
Examining data/plast-2.3.2+dfsg/src/seg/impl/genwin.c
Examining data/plast-2.3.2+dfsg/src/seg/impl/dust.c
Examining data/plast-2.3.2+dfsg/src/seg/impl/seg.c
Examining data/plast-2.3.2+dfsg/src/seg/impl/DustMasker.cpp
Examining data/plast-2.3.2+dfsg/src/seg/api/seg.h
Examining data/plast-2.3.2+dfsg/src/seg/api/genwin.h
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/AlgorithmPlastn.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/AbstractAlgorithm.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/DatabasesProvider.cpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/PlastnAlgoConfig.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/AlgoIndexatorNucleotide.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/ScoreMatrix.cpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/AbstractAlgorithm.cpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoConfig.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/PlastnAlgoConfig.cpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/AlgoIndexatorNucleotide.cpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoConfig.cpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/BasicAlgoIndexator.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/BasicAlgoIndexator.cpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/DatabasesProvider.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/AlgorithmPlastn.cpp
Examining data/plast-2.3.2+dfsg/src/algo/core/impl/ScoreMatrix.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/api/IDatabasesProvider.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/api/IAlgoIndexator.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/api/IScoreMatrix.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/api/IAlgorithm.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/api/IAlgoParameters.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/api/IAlgoEnvironment.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/api/IAlgoEvents.hpp
Examining data/plast-2.3.2+dfsg/src/algo/core/api/IAlgoConfig.hpp
Examining data/plast-2.3.2+dfsg/src/algo/stats/impl/StatisticsPlastn.cpp
Examining data/plast-2.3.2+dfsg/src/algo/stats/impl/Statistics.hpp
Examining data/plast-2.3.2+dfsg/src/algo/stats/impl/StatisticsSpouge.cpp
Examining data/plast-2.3.2+dfsg/src/algo/stats/impl/StatisticsSpouge.hpp
Examining data/plast-2.3.2+dfsg/src/algo/stats/impl/StatisticsPlastn.hpp
Examining data/plast-2.3.2+dfsg/src/algo/stats/impl/Statistics.cpp
Examining data/plast-2.3.2+dfsg/src/algo/stats/api/IStatistics.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/ungap/UngapHitIterator.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/ungap/UngapHitIteratorNull.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/ungap/UngapHitIteratorSSE8.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/ungap/UngapHitIteratorNull.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/ungap/UngapHitIteratorSSE16.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/ungap/UngapExtendHitIterator.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/ungap/UngapHitIteratorSSE16.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/ungap/UngapExtendHitIterator.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/ungap/UngapHitIterator.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/ungap/UngapHitIteratorSSE8.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/common/AbstractHitIterator.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/common/AbstractPipeHitIterator.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/common/AbstractPipeHitIterator.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/common/AbstractHitIterator.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/api/IHitIterator.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/gap/FullGapHitIterator.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/gap/SmallGapHitIterator.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/gap/SmallGapHitIteratorNull.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/gap/SmallGapHitIteratorNull.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/gap/CompositionHitIterator.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/gap/SmallGapHitIterator.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/gap/FullGapHitIterator.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/gap/SmallGapHitIteratorSSE8.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/gap/CompositionHitIterator.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/hsp/HspGeneratorCmd.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/hsp/AlignmentGeneratorCmd.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/hsp/HspExtensionCmd.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/hsp/HspExtensionCmd.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/hsp/AlignmentGeneratorCmd.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/hsp/HspGeneratorCmd.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/seed/SeedHitIteratorCached.cpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/seed/SeedHitIterator.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/seed/SeedHitIteratorCached.hpp
Examining data/plast-2.3.2+dfsg/src/algo/hits/seed/SeedHitIterator.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/core/PlastOptionsParser.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/core/PlastCmd.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/core/PlastOptionsParser.hpp
Examining data/plast-2.3.2+dfsg/src/launcher/core/PlastCmd.hpp
Examining data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Hit.h
Examining data/plast-2.3.2+dfsg/src/launcher/jni/Wrapper.hpp
Examining data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.h
Examining data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/jni/Helper.hpp
Examining data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_QueryResult.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.h
Examining data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestController.h
Examining data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Hit.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_QueryResult.h
Examining data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Request.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_Request.h
Examining data/plast-2.3.2+dfsg/src/launcher/jni/Helper.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/jni/JniObsfucation.h
Examining data/plast-2.3.2+dfsg/src/launcher/jni/Wrapper.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/observers/AlgoHitsResultObserver.hpp
Examining data/plast-2.3.2+dfsg/src/launcher/observers/BargraphObserver.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/observers/FileProgressionObserver.hpp
Examining data/plast-2.3.2+dfsg/src/launcher/observers/AlgoExecutionObserver.hpp
Examining data/plast-2.3.2+dfsg/src/launcher/observers/AbstractProgressionObserver.hpp
Examining data/plast-2.3.2+dfsg/src/launcher/observers/AlgoResultObserver.hpp
Examining data/plast-2.3.2+dfsg/src/launcher/observers/FileProgressionObserver.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/observers/AlgoExecutionObserver.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/observers/BargraphObserver.hpp
Examining data/plast-2.3.2+dfsg/src/launcher/observers/AbstractObserver.hpp
Examining data/plast-2.3.2+dfsg/src/launcher/observers/AbstractProgressionObserver.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/observers/AlgoHitsResultObserver.cpp
Examining data/plast-2.3.2+dfsg/src/launcher/observers/AlgoResultObserver.cpp
Examining data/plast-2.3.2+dfsg/src/misc/impl/ObsfucatedString.cpp
Examining data/plast-2.3.2+dfsg/src/misc/impl/ObsfucatedString.hpp
Examining data/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.cpp
Examining data/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.hpp
Examining data/plast-2.3.2+dfsg/src/misc/impl/RangeTree.cpp
Examining data/plast-2.3.2+dfsg/src/misc/impl/Option.hpp
Examining data/plast-2.3.2+dfsg/src/misc/api/CompleteSubjectDatabaseStats.hpp
Examining data/plast-2.3.2+dfsg/src/misc/api/PlastStringsRepository.hpp
Examining data/plast-2.3.2+dfsg/src/misc/api/CompleteSubjectDatabaseStats.cpp
Examining data/plast-2.3.2+dfsg/src/misc/api/macros.hpp
Examining data/plast-2.3.2+dfsg/src/misc/api/PlastStrings.hpp
Examining data/plast-2.3.2+dfsg/src/misc/api/RangeTree.hpp
Examining data/plast-2.3.2+dfsg/src/misc/api/version.hpp
Examining data/plast-2.3.2+dfsg/src/misc/api/obsfucation.h
Examining data/plast-2.3.2+dfsg/src/misc/api/types.hpp
Examining data/plast-2.3.2+dfsg/src/misc/api/Vector.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/MacOsMemoryFile.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/DefaultOsFactory.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/WindowsMemoryFile.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/LinuxFile.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/WindowsFile.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/LinuxMemoryFile.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/MacOsFile.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/MacOsMemoryFile.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/LinuxMemoryFile.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/WindowsFile.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/WindowsTime.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/ZlibFile.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/WindowsThread.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/LinuxThread.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/MacOsMemory.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/MacOsFile.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/TimeTools.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/MacOsTime.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/MacOsThread.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/WindowsTime.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/LinuxThread.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/MacOsThread.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/LinuxTime.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/MacOsTime.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/MacOsMemory.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/ZlibFile.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/LinuxTime.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/WindowsThread.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/WindowsMemoryFile.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/WindowsMemory.cpp
Examining data/plast-2.3.2+dfsg/src/os/impl/CommonOsImpl.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/DefaultOsFactory.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/WindowsMemory.hpp
Examining data/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.cpp
Examining data/plast-2.3.2+dfsg/src/os/api/ITime.hpp
Examining data/plast-2.3.2+dfsg/src/os/api/IOsFactory.hpp
Examining data/plast-2.3.2+dfsg/src/os/api/IMemoryFile.hpp
Examining data/plast-2.3.2+dfsg/src/os/api/IFile.hpp
Examining data/plast-2.3.2+dfsg/src/os/api/IThread.hpp
Examining data/plast-2.3.2+dfsg/src/os/api/IResource.hpp
Examining data/plast-2.3.2+dfsg/src/os/api/IMemory.hpp
Examining data/plast-2.3.2+dfsg/src/seed/impl/AbstractSeedModel.cpp
Examining data/plast-2.3.2+dfsg/src/seed/impl/AbstractSeedModel.hpp
Examining data/plast-2.3.2+dfsg/src/seed/impl/AbstractSeedIterator.hpp
Examining data/plast-2.3.2+dfsg/src/seed/impl/SubSeedModel.cpp
Examining data/plast-2.3.2+dfsg/src/seed/impl/SubSeedModel.hpp
Examining data/plast-2.3.2+dfsg/src/seed/impl/BasicSeedModel.hpp
Examining data/plast-2.3.2+dfsg/src/seed/impl/BasicSeedModel.cpp
Examining data/plast-2.3.2+dfsg/src/seed/impl/AbstractSeedIterator.cpp
Examining data/plast-2.3.2+dfsg/src/seed/api/ISeed.hpp
Examining data/plast-2.3.2+dfsg/src/seed/api/ISeedModel.hpp
Examining data/plast-2.3.2+dfsg/src/seed/api/ISeedIterator.hpp
FINAL RESULTS:
data/plast-2.3.2+dfsg/src/designpattern/impl/FileLineIterator.hpp:109:46: [5] (buffer) gets:
Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
_readCurrentSize = _currentFile->gets (_line, _lineMaxSize);
data/plast-2.3.2+dfsg/src/os/api/IFile.hpp:70:17: [5] (buffer) gets:
Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
virtual int gets (char* s, int size) = 0;
data/plast-2.3.2+dfsg/src/os/impl/CommonOsImpl.hpp:66:9: [5] (buffer) gets:
Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
int gets (char *s, int size)
data/plast-2.3.2+dfsg/src/os/impl/ZlibFile.cpp:64:9: [5] (buffer) gets:
Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
int gets (char* s, int size)
data/plast-2.3.2+dfsg/src/algo/hits/hsp/HspGeneratorCmd.cpp:53:21: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define INFO(a) printf a
data/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentSplitter.cpp:29:19: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define INFO(a) printf a
data/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentSplitterBanded.cpp:29:19: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define INFO(a) printf a
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/QueryReorderVisitor.cpp:282:22: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
int result = sscanf (line, "%c %d %s", &c, &seq.length, commentBuffer);
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/XmlOutputVisitor.cpp:267:5: [4] (format) vsprintf:
Potential format string problem (CWE-134). Make format string constant.
vsprintf (buffer, format, va);
data/plast-2.3.2+dfsg/src/database/impl/BasicSequenceBuilder.cpp:25:19: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define INFO(a) printf a
data/plast-2.3.2+dfsg/src/database/impl/FastaSequenceIterator.cpp:29:19: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define INFO(a) printf a
data/plast-2.3.2+dfsg/src/database/impl/FastaSequenceOutput.cpp:25:19: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define INFO(a) printf a
data/plast-2.3.2+dfsg/src/database/impl/FastaSequenceOutput.cpp:125:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (buffer, ">%s", (*_itComments).c_str());
data/plast-2.3.2+dfsg/src/database/impl/FastaSequenceOutput.cpp:130:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (buffer, ">%s",seq->comment);
data/plast-2.3.2+dfsg/src/database/impl/StringSequenceIterator.cpp:121:9: [4] (format) snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
snprintf (comment, sizeof(comment), commentFormat, _currentIdx+1);
data/plast-2.3.2+dfsg/src/designpattern/api/Iterator.hpp:241:9: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf (_buffer, sizeof(_buffer), message, ap);
data/plast-2.3.2+dfsg/src/designpattern/impl/Property.cpp:155:9: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf (buffer, sizeof(buffer), format, ap);
data/plast-2.3.2+dfsg/src/designpattern/impl/Property.cpp:696:9: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf (buffer, sizeof(buffer), format, ap);
data/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp:46:5: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf (_buffer, sizeof(_buffer), format, ap);
data/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp:63:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (_buffer, request.c_str());
data/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp:85:5: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf (tmp, sizeof(tmp), format, ap);
data/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp:119:9: [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.
system (tmp);
data/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp:138:15: [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.
_status = system (_buffer);
data/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.cpp:135:21: [4] (format) snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
snprintf (buffer, sizeof(buffer), MSG_OPTIONS_MSG1, optionMatch->getLabel().c_str());
data/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.cpp:141:21: [4] (format) snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
snprintf (buffer, sizeof(buffer), MSG_OPTIONS_MSG2,
data/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.cpp:314:9: [4] (format) snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
snprintf (buffer, sizeof(buffer), MSG_OPTIONS_MSG3, option->getLabel().c_str());
data/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.cpp:331:9: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf (fp, MSG_OPTIONS_MSG4, it->c_str());
data/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.cpp:347:9: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf (fp, MSG_OPTIONS_MSG5, it->c_str());
data/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.cpp:492:17: [4] (format) snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
snprintf (buffer, sizeof(buffer),
data/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.cpp:526:13: [4] (format) snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
snprintf (buffer, sizeof(buffer), MSG_OPTIONS_MSG7, (*it)->getLabel().c_str());
data/plast-2.3.2+dfsg/src/os/impl/CommonOsImpl.hpp:100:9: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf (_handle, format, args);
data/plast-2.3.2+dfsg/src/os/impl/LinuxFile.cpp:42:13: [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.
system (ss.str().c_str());
data/plast-2.3.2+dfsg/src/tools/PlastCmd.cpp:155:9: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf (stderr, MSG_MAIN_MSG2, e.getMessage());
data/plast-2.3.2+dfsg/src/tools/PlastCmd.cpp:160:9: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf (stderr, MSG_MAIN_MSG3, e);
data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp:251:22: [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.
string plastrc = getenv ("HOME") ? string (getenv("HOME")) + string("/.plastrc") : "";
data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp:251:48: [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.
string plastrc = getenv ("HOME") ? string (getenv("HOME")) + string("/.plastrc") : "";
data/plast-2.3.2+dfsg/src/misc/impl/ObsfucatedString.cpp:50:5: [3] (random) srand:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
srand (seed);
data/plast-2.3.2+dfsg/src/misc/impl/ObsfucatedString.cpp:124:5: [3] (random) srand:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
srand (seed);
data/plast-2.3.2+dfsg/src/misc/impl/ObsfucatedString.hpp:80:17: [3] (random) srand:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
static void srand (LONG s) { seed = s; }
data/plast-2.3.2+dfsg/src/tools/PlastCmd.cpp:135:30: [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.
string plastrc = getenv (MSG_MAIN_HOME) ? string (getenv(MSG_MAIN_HOME)) + string(MSG_MAIN_RC_FILE) : "";
data/plast-2.3.2+dfsg/src/tools/PlastCmd.cpp:135:63: [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.
string plastrc = getenv (MSG_MAIN_HOME) ? string (getenv(MSG_MAIN_HOME)) + string(MSG_MAIN_RC_FILE) : "";
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:569:79: [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).
else { params->filterQuery = misc::atoi(prop->value.c_str()); }
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:572:133: [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).
if ( (prop = properties->getProperty (STR_OPTION_UNGAP_NEIGHBOUR_LENGTH)) != 0) { params->ungapNeighbourLength = misc::atoi (prop->value.c_str()); }
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:573:133: [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).
if ( (prop = properties->getProperty (STR_OPTION_UNGAP_SCORE_THRESHOLD)) != 0) { params->ungapScoreThreshold = misc::atoi (prop->value.c_str()); }
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:574:133: [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).
if ( (prop = properties->getProperty (STR_OPTION_SMALLGAP_BAND_WITH)) != 0) { params->smallGapBandWidth = misc::atoi (prop->value.c_str()); }
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:575:133: [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).
if ( (prop = properties->getProperty (STR_OPTION_SMALLGAP_THRESHOLD)) != 0) { params->smallGapThreshold = misc::atoi (prop->value.c_str()); }
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:576:133: [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).
if ( (prop = properties->getProperty (STR_OPTION_OPEN_GAP_COST)) != 0) { params->openGapCost = misc::atoi (prop->value.c_str()); }
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:577:133: [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).
if ( (prop = properties->getProperty (STR_OPTION_EXTEND_GAP_COST)) != 0) { params->extendGapCost = misc::atoi (prop->value.c_str()); }
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:579:133: [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).
if ( (prop = properties->getProperty (STR_OPTION_X_DROPOFF_UNGAPPED)) != 0) { params->XdroppofUnGap = misc::atoi (prop->value.c_str()); }
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:580:133: [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).
if ( (prop = properties->getProperty (STR_OPTION_X_DROPOFF_GAPPED)) != 0) { params->XdroppofGap = misc::atoi (prop->value.c_str()); }
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:581:133: [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).
if ( (prop = properties->getProperty (STR_OPTION_X_DROPOFF_FINAL)) != 0) { params->finalXdroppofGap = misc::atoi (prop->value.c_str()); }
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:582:149: [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).
if ( (prop = properties->getProperty (STR_OPTION_INDEX_NEIGHBOUR_THRESHOLD)) != 0) { params->index_neighbor_threshold = misc::atoi (prop->value.c_str()); }
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:584:120: [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).
if ( (prop = properties->getProperty (STR_OPTION_REWARD)) != 0) { params->reward = misc::atoi (prop->value.c_str()); }
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:585:120: [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).
if ( (prop = properties->getProperty (STR_OPTION_PENALTY)) != 0) { params->penalty = misc::atoi (prop->value.c_str()); }
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:587:121: [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).
if ( (prop = properties->getProperty (STR_OPTION_WORD_SIZE)) != 0) { params->seedSpan = misc::atoi (prop->value.c_str()); }
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:610:66: [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).
ReadingFrame_e val = (ReadingFrame_e) (misc::atoi(it.currentItem()) - 1);
data/plast-2.3.2+dfsg/src/algo/hits/gap/SmallGapHitIterator.cpp:256:5: [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 (bufOut, bufIn, MIN (neighbourLength, occur->sequence.data.letters.size - occur->offsetInSequence));
data/plast-2.3.2+dfsg/src/algo/hits/gap/SmallGapHitIteratorSSE8.cpp:267:5: [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 (right, bufIn, MIN (neighbourLength, occur->sequence.data.letters.size - occur->offsetInSequence));
data/plast-2.3.2+dfsg/src/alignment/core/impl/Alignment.cpp:68:56: [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).
else if (idx==3) { this->setLength (misc::atoi (token)); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/Alignment.cpp:69:56: [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).
else if (idx==4) { this->setNbMisses (misc::atoi (token)); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/Alignment.cpp:70:46: [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).
else if (idx==5) { nbGaps = misc::atoi (token); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/Alignment.cpp:71:54: [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).
else if (idx==6) { qryRange.begin = misc::atoi (token); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/Alignment.cpp:72:54: [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).
else if (idx==7) { qryRange.end = misc::atoi (token); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/Alignment.cpp:73:54: [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).
else if (idx==8) { sbjRange.begin = misc::atoi (token); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/Alignment.cpp:74:54: [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).
else if (idx==9) { sbjRange.end = misc::atoi (token); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.cpp:156:60: [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).
else if (idx==3) { align.setLength (misc::atoi (token)); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.cpp:157:60: [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).
else if (idx==4) { align.setNbMisses (misc::atoi (token)); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.cpp:158:50: [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).
else if (idx==5) { nbGaps = misc::atoi (token); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.cpp:159:58: [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).
else if (idx==6) { qryRange.begin = misc::atoi (token); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.cpp:160:58: [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).
else if (idx==7) { qryRange.end = misc::atoi (token); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.cpp:161:58: [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).
else if (idx==8) { sbjRange.begin = misc::atoi (token); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.cpp:162:58: [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).
else if (idx==9) { sbjRange.end = misc::atoi (token); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.cpp:166:62: [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).
else if (idx==12) { qrySequence.length = misc::atol (token); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.cpp:167:76: [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).
else if (idx==13) { align.setNbGaps (Alignment::QUERY, misc::atol (token)); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.cpp:168:76: [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).
else if (idx==14) { align.setFrame (Alignment::QUERY, misc::atoi (token)); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.cpp:170:62: [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).
else if (idx==12) { sbjSequence.length = misc::atol (token); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.cpp:171:78: [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).
else if (idx==13) { align.setNbGaps (Alignment::SUBJECT, misc::atol (token)); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.cpp:172:78: [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).
else if (idx==14) { align.setFrame (Alignment::SUBJECT, misc::atoi (token)); }
data/plast-2.3.2+dfsg/src/alignment/core/impl/AlignmentContainerFactory.cpp:174:63: [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).
else if (idx==15) { align.setNbPositives (misc::atol (token)); }
data/plast-2.3.2+dfsg/src/alignment/filter/impl/AlignmentFilterXML.cpp:75:8: [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).
is.open (xmlFileUri.c_str(), ios::binary);
data/plast-2.3.2+dfsg/src/alignment/filter/impl/AlignmentFilterXML.cpp:212:9: [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).
if (open)
data/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentSplitter.cpp:215:5: [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 qryLocal [10000];
data/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentSplitter.cpp:216:5: [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 subLocal [10000];
data/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentSplitter.cpp:326:38: [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 (output.subjectAlign != 0) { memcpy (output.subjectAlign, subLocal, output.alignSize); }
data/plast-2.3.2+dfsg/src/alignment/tools/impl/AlignmentSplitter.cpp:327:38: [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 (output.queryAlign != 0) { memcpy (output.queryAlign, qryLocal, output.alignSize); }
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/OstreamVisitor.hpp:63:16: [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 (uri.c_str());
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/QueryReorderVisitor.cpp:279:9: [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 commentBuffer[4*1024];
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/QueryReorderVisitor.cpp:286:28: [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).
seq.length = misc::atoi (line); while (*(line++) != ' ') ;
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/QueryReorderVisitor.cpp:408:18: [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).
_indexesFile.open (getIndexesFileUri().c_str(), ios::out | ios::in | ios::trunc);
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/QueryReorderVisitor.cpp:574:13: [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 id[1024];
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/QueryReorderVisitor.hpp:104:5: [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 _queryId[1024];
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/TabulatedOutputVisitor.cpp:43:13: [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 (uri.c_str(), "w");
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/TabulatedOutputVisitor.cpp:92:5: [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 queryName[128];
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/TabulatedOutputVisitor.cpp:96:5: [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 subjectName[128] = "";
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/TabulatedOutputVisitor.cpp:103:5: [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 evalueStr[32];
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/TabulatedOutputVisitor.cpp:106:33: [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.
if (ev < 1.0e-99) { sprintf (evalueStr, "%2.0le", ev); }
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/TabulatedOutputVisitor.cpp:107:33: [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.
else if (ev < 0.0009) { sprintf (evalueStr, "%3.0le", ev); }
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/TabulatedOutputVisitor.cpp:108:33: [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.
else if (ev < 0.1) { sprintf (evalueStr, "%4.3lf", ev); }
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/TabulatedOutputVisitor.cpp:109:33: [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.
else if (ev < 1.0) { sprintf (evalueStr, "%2.1lf", ev); }
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/TabulatedOutputVisitor.cpp:110:33: [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.
else if (ev < 10.0) { sprintf (evalueStr, "%2.1lf", ev); }
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/TabulatedOutputVisitor.cpp:111:33: [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.
else { sprintf (evalueStr, "%5.0lf", ev); }
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/XmlOutputVisitor.cpp:263:5: [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[BUFFER_SIZE];
data/plast-2.3.2+dfsg/src/database/api/ISequence.hpp:103:9: [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 buffer[128];
data/plast-2.3.2+dfsg/src/database/api/ISequence.hpp:118:9: [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 buffer[256];
data/plast-2.3.2+dfsg/src/database/impl/BasicSequenceBuilder.cpp:91:2: [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 bufferNumber[50];
data/plast-2.3.2+dfsg/src/database/impl/BasicSequenceBuilder.cpp:94:5: [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(bufferNumber,",%d,%d",offsetHeader,size);
data/plast-2.3.2+dfsg/src/database/impl/BlastdbAsn1HeaderDecoder.cpp:228:2: [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 tempValue[10];
data/plast-2.3.2+dfsg/src/database/impl/BlastdbAsn1HeaderDecoder.cpp:252:3: [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(tempValue,"%d", value);
data/plast-2.3.2+dfsg/src/database/impl/BlastdbAsn1HeaderDecoder.cpp:268:11: [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 hdr[2];
data/plast-2.3.2+dfsg/src/database/impl/BlastdbAsn1HeaderDecoder.cpp:319:11: [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 hdr[2];
data/plast-2.3.2+dfsg/src/database/impl/BlastdbSequenceIterator.cpp:373:2: [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 fileNamePath[2048] = "";
data/plast-2.3.2+dfsg/src/database/impl/BlastdbSequenceIterator.cpp:404:22: [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).
startOffset = misc::atoi(filename+1);
data/plast-2.3.2+dfsg/src/database/impl/BlastdbSequenceIterator.cpp:406:22: [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).
sizeComment = misc::atoi(startOff+1);
data/plast-2.3.2+dfsg/src/database/impl/BufferedSequenceDatabase.cpp:622:2: [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 bufferNumber[30];
data/plast-2.3.2+dfsg/src/database/impl/BufferedSequenceDatabase.cpp:634:5: [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(bufferNumber,",%d,%d",offsetHeader,size);
data/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:195:18: [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* file = fopen (uri.c_str(), "rb");
data/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:280:18: [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* file = fopen (uri.c_str(), "wb");
data/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:370:18: [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* file = fopen (filename.c_str(), "rb");
data/plast-2.3.2+dfsg/src/database/impl/FastaSequenceOutput.cpp:121:9: [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 buffer[256];
data/plast-2.3.2+dfsg/src/database/impl/ReadingFrameSequenceIterator.cpp:155:13: [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 message[256];
data/plast-2.3.2+dfsg/src/database/impl/StringSequenceIterator.cpp:120:9: [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 comment[64];
data/plast-2.3.2+dfsg/src/designpattern/api/IProperty.hpp:87:54: [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).
long getInt () { return misc::atol (value.c_str()); }
data/plast-2.3.2+dfsg/src/designpattern/api/Iterator.hpp:265:5: [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[256];
data/plast-2.3.2+dfsg/src/designpattern/impl/Property.cpp:152:9: [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 buffer[256];
data/plast-2.3.2+dfsg/src/designpattern/impl/Property.cpp:692:9: [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 buffer[4*1024];
data/plast-2.3.2+dfsg/src/designpattern/impl/Property.cpp:715:13: [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 (filename.c_str(), "w");
data/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp:82:5: [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 tmp[1024];
data/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.cpp:118:9: [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 tmp[256]; snprintf (tmp, sizeof(tmp), "/bin/rm %s", _tmpFilename);
data/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.hpp:99:5: [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 _tmpFilename[128];
data/plast-2.3.2+dfsg/src/designpattern/impl/SystemCommand.hpp:101:5: [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[4*1024];
data/plast-2.3.2+dfsg/src/index/impl/DatabaseIndex.cpp:449:9: [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 (bufOut, bufIn, imin1);
data/plast-2.3.2+dfsg/src/index/impl/DatabaseIndex.cpp:463:9: [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 (bufOut, bufIn - imin2, imin2);
data/plast-2.3.2+dfsg/src/index/impl/DatabaseIndex.cpp:628:13: [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 (bufOut, bufIn, imin1);
data/plast-2.3.2+dfsg/src/index/impl/DatabaseNucleotidIndex.cpp:104:9: [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 (_maskIn, otherIndex->getMask(), sizeof(word_t)*maskSize);
data/plast-2.3.2+dfsg/src/index/impl/DatabaseNucleotidIndexOptim.cpp:325:55: [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 (otherIndex != 0 && otherIndex->getMask()) { memcpy (_maskIn, otherIndex->getMask(), sizeof(word_t)*maskSize); }
data/plast-2.3.2+dfsg/src/index/impl/retrievall.c:596:10: [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 retr_count_table[256] ={
data/plast-2.3.2+dfsg/src/index/impl/retrievall.c:614:10: [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 retr_pack3_table[15]={0,1,2,0,3,6,0,9,18,0,27,54,0,81,162};
data/plast-2.3.2+dfsg/src/index/impl/retrievall.c:615:10: [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 retr_decode3_table[256*5] ={
data/plast-2.3.2+dfsg/src/index/impl/retrievall.c:696:10: [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 retr_pack5_table[15]={0,1,2,3,4,0,5,10,15,20,0,25,50,75,100};
data/plast-2.3.2+dfsg/src/index/impl/retrievall.c:697:10: [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 retr_decode5_table[128*3]={
data/plast-2.3.2+dfsg/src/index/impl/retrievall.c:722:10: [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 retr_mod3_table[9]={0,1,2,0,1,2,0,1,2};
data/plast-2.3.2+dfsg/src/index/impl/retrievall.c:723:10: [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 retr_mod5_table[15]={0,1,2,3,4,0,1,2,3,4,0,1,2,3,4};
data/plast-2.3.2+dfsg/src/index/impl/retrievall.c:724:10: [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 retr_mod6_table[18]={0,1,2,3,4,5,0,1,2,3,4,5,0,1,2,3,4,5};
data/plast-2.3.2+dfsg/src/index/impl/retrievall.c:725:10: [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 retr_fls_table[256]={
data/plast-2.3.2+dfsg/src/launcher/core/PlastCmd.cpp:149:45: [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).
if (p != 0) { bargraphSize = misc::atoi (p->value.c_str()); }
data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_QueryResult.cpp:85:9: [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 bufId[256]; size_t lenId = sizeof(bufId);
data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_QueryResult.cpp:86:9: [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 bufDef[1024]; size_t lenDef = sizeof(bufDef);
data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.cpp:85:9: [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 bufId[256]; size_t lenId = sizeof(bufId);
data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestResult.cpp:86:9: [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 bufDef[1024]; size_t lenDef = sizeof(bufDef);
data/plast-2.3.2+dfsg/src/launcher/observers/AbstractProgressionObserver.cpp:193:5: [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[256];
data/plast-2.3.2+dfsg/src/launcher/observers/BargraphObserver.cpp:109:9: [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 ellapsed[32]; fillTimeBuffer (_ellapsedTime/1000, ellapsed);
data/plast-2.3.2+dfsg/src/launcher/observers/BargraphObserver.cpp:110:9: [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 remaining[32]; fillTimeBuffer (_remainingTime/1000, remaining);
data/plast-2.3.2+dfsg/src/launcher/observers/BargraphObserver.cpp:111:9: [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 fulltime[32]; fillTimeBuffer ((_ellapsedTime+_remainingTime)/1000, fulltime);
data/plast-2.3.2+dfsg/src/launcher/observers/BargraphObserver.cpp:113:9: [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 buf[512];
data/plast-2.3.2+dfsg/src/launcher/observers/BargraphObserver.cpp:151:5: [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, "%02ld:%02ld:%02ld", h, m, s);
data/plast-2.3.2+dfsg/src/launcher/observers/FileProgressionObserver.cpp:124:13: [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 (filename.c_str(), "w");
data/plast-2.3.2+dfsg/src/launcher/observers/FileProgressionObserver.cpp:222:13: [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 (filename.c_str(), "w");
data/plast-2.3.2+dfsg/src/misc/api/CompleteSubjectDatabaseStats.cpp:34:18: [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).
size = misc::atoi(prop->value.c_str());
data/plast-2.3.2+dfsg/src/misc/api/CompleteSubjectDatabaseStats.cpp:46:31: [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).
numberOfSequences = misc::atoi(prop->value.c_str());
data/plast-2.3.2+dfsg/src/misc/api/Vector.hpp:74:13: [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 (data, v.data, size);
data/plast-2.3.2+dfsg/src/misc/api/Vector.hpp:125:17: [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 (data, v.data, size);
data/plast-2.3.2+dfsg/src/misc/api/types.hpp:222:13: [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).
inline int atoi (const char* str) { return ::atoi (str); }
data/plast-2.3.2+dfsg/src/misc/api/types.hpp:222:48: [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).
inline int atoi (const char* str) { return ::atoi (str); }
data/plast-2.3.2+dfsg/src/misc/api/types.hpp:223:13: [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).
inline long atol (const char* str) { return ::atol (str); }
data/plast-2.3.2+dfsg/src/misc/api/types.hpp:223:48: [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).
inline long atol (const char* str) { return ::atol (str); }
data/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.cpp:134:21: [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[128];
data/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.cpp:140:21: [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[128];
data/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.cpp:313:9: [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 buffer [128];
data/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.cpp:491:17: [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[128];
data/plast-2.3.2+dfsg/src/misc/impl/OptionsParser.cpp:525:13: [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[128];
data/plast-2.3.2+dfsg/src/os/impl/CommonOsImpl.hpp:56:42: [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).
_handle = _isStdout ? stdout : fopen (path, mode);
data/plast-2.3.2+dfsg/src/os/impl/CommonOsImpl.hpp:149:22: [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 (filename.c_str(), "rb");
data/plast-2.3.2+dfsg/src/os/impl/CommonOsImpl.hpp:217:34: [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 (ptr != 0) { memcpy (result, ptr, size); }
data/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.cpp:42:18: [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* file = fopen ("/proc/self/statm", "r");
data/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.cpp:45:9: [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 buffer[128];
data/plast-2.3.2+dfsg/src/os/impl/LinuxMemory.cpp:48:37: [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).
if (locate) { val = misc::atol(locate); }
data/plast-2.3.2+dfsg/src/os/impl/LinuxMemoryFile.cpp:45:23: [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_handle = ::open(path, O_RDONLY);
data/plast-2.3.2+dfsg/src/os/impl/LinuxThread.cpp:112:18: [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* file = fopen ("/proc/cpuinfo", "r");
data/plast-2.3.2+dfsg/src/os/impl/LinuxThread.cpp:115:9: [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 buffer[256];
data/plast-2.3.2+dfsg/src/os/impl/LinuxThread.cpp:142:5: [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 hostname[1024];
data/plast-2.3.2+dfsg/src/os/impl/MacOsMemoryFile.cpp:45:23: [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_handle = ::open(path, O_RDONLY);
data/plast-2.3.2+dfsg/src/os/impl/MacOsThread.cpp:148:5: [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 hostname[1024];
data/plast-2.3.2+dfsg/src/os/impl/WindowsThread.cpp:166:5: [2] (buffer) TCHAR:
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.
TCHAR infoBuf[1024];
data/plast-2.3.2+dfsg/src/seed/impl/SubSeedModel.cpp:68:19: [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).
_span = misc::atoi (it.currentItem());
data/plast-2.3.2+dfsg/src/seed/impl/SubSeedModel.cpp:634:5: [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 (_currentItem.kmer.letters.data, &(_allSeedsTable[_span*actualIdx]), _span);
data/plast-2.3.2+dfsg/src/seg/impl/genwin.c:25:17: [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 unsigned char aaflag[128];
data/plast-2.3.2+dfsg/src/seg/impl/genwin.c:26:8: [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 char aachar[20];
data/plast-2.3.2+dfsg/src/seg/impl/genwin.c:106:5: [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(win->seq, (parent->seq)+start, length);
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:161:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
_quickQueryDbReader->read (maxblocksize);
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:665:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
_quickSubjectDbReader->read (maxblocksize);
data/plast-2.3.2+dfsg/src/algo/core/impl/DefaultAlgoEnvironment.cpp:674:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
_quickSubjectDbReader->read (maxblocksize);
data/plast-2.3.2+dfsg/src/algo/hits/hsp/HspGeneratorCmd.cpp:115:13: [1] (buffer) mismatch:
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.
int32_t mismatch,
data/plast-2.3.2+dfsg/src/algo/hits/hsp/HspGeneratorCmd.cpp:121:55: [1] (buffer) mismatch:
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.
_threshold(threshold), _match(match), _mismatch(mismatch), _xdrop(xdrop), _alpha_threshold(alpha_threshold)
data/plast-2.3.2+dfsg/src/algo/hits/hsp/HspGeneratorCmd.cpp:124:21: [1] (buffer) mismatch:
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.
threshold, match, mismatch, xdrop, alpha_threshold
data/plast-2.3.2+dfsg/src/algo/hits/hsp/HspGeneratorCmd.hpp:58:17: [1] (buffer) mismatch:
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.
int32_t mismatch,
data/plast-2.3.2+dfsg/src/alignment/filter/impl/AlignmentFilterXML.cpp:84:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
reader.read();
data/plast-2.3.2+dfsg/src/alignment/visitors/impl/QueryReorderVisitor.cpp:288:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (commentBuffer, line, sizeof(commentBuffer));
data/plast-2.3.2+dfsg/src/database/api/IDatabaseQuickReader.hpp:79:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual void read (u_int64_t maxblocksize = 0) = 0;
data/plast-2.3.2+dfsg/src/database/api/ISequence.hpp:149:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (bufId, comment, lenId);
data/plast-2.3.2+dfsg/src/database/api/ISequence.hpp:152:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (bufDef, lookup+1, lenDef);
data/plast-2.3.2+dfsg/src/database/api/ISequence.hpp:158:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (bufId, comment, lenId);
data/plast-2.3.2+dfsg/src/database/api/ISequence.hpp:184:68: [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 l = (lookup != 0 ? (size_t) (lookup-comment) : strlen(comment));
data/plast-2.3.2+dfsg/src/database/api/ISequence.hpp:187:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (bufId, comment, lenId);
data/plast-2.3.2+dfsg/src/database/api/ISequence.hpp:208:32: [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 (lookup != 0 && strlen(lookup)>1)
data/plast-2.3.2+dfsg/src/database/api/ISequence.hpp:210:37: [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 l = (size_t) strlen(lookup)-1;
data/plast-2.3.2+dfsg/src/database/api/ISequence.hpp:213:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (bufDef, lookup+1, lenDef);
data/plast-2.3.2+dfsg/src/database/impl/AminoAcidDatabaseQuickReader.hpp:59:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void read (u_int64_t maxblocksize) { _ref->read (maxblocksize); }
data/plast-2.3.2+dfsg/src/database/impl/AminoAcidDatabaseQuickReader.hpp:59:50: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void read (u_int64_t maxblocksize) { _ref->read (maxblocksize); }
data/plast-2.3.2+dfsg/src/database/impl/BasicSequenceBuilder.cpp:93:29: [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).
_comment.assign (filename, strlen(filename));
data/plast-2.3.2+dfsg/src/database/impl/BasicSequenceBuilder.cpp:95:36: [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).
_comment.append (bufferNumber, strlen(bufferNumber));
data/plast-2.3.2+dfsg/src/database/impl/BlastdbDatabaseQuickReader.cpp:83:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void BlastdbDatabaseQuickReader::read (u_int64_t maxblocksize)
data/plast-2.3.2+dfsg/src/database/impl/BlastdbDatabaseQuickReader.cpp:117:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(*filesIterator)->read();
data/plast-2.3.2+dfsg/src/database/impl/BlastdbDatabaseQuickReader.hpp:95:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void read (u_int64_t maxblocksize=0);
data/plast-2.3.2+dfsg/src/database/impl/BlastdbFileIndexReader.cpp:90:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void BlastdbFileIndexReader::read ()
data/plast-2.3.2+dfsg/src/database/impl/BlastdbFileIndexReader.hpp:60:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void read ();
data/plast-2.3.2+dfsg/src/database/impl/BlastdbSequenceIterator.cpp:355:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
_currentIndexFile->read();
data/plast-2.3.2+dfsg/src/database/impl/BlastdbSequenceIterator.cpp:393:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(fileNamePath,comment,(filename-comment));
data/plast-2.3.2+dfsg/src/database/impl/BufferedSequenceDatabase.cpp:633:62: [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).
_cache->comments [_cache->nbSequences].assign (filename, strlen(filename));
data/plast-2.3.2+dfsg/src/database/impl/BufferedSequenceDatabase.cpp:635:66: [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).
_cache->comments [_cache->nbSequences].append (bufferNumber, strlen(bufferNumber));
data/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.cpp:90:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void FastaDatabaseQuickReader::read (u_int64_t maxblocksize)
data/plast-2.3.2+dfsg/src/database/impl/FastaDatabaseQuickReader.hpp:98:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void read (u_int64_t maxblocksize=0);
data/plast-2.3.2+dfsg/src/database/impl/FastaSequenceIterator.cpp:130:26: [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 len = strlen (buffer);
data/plast-2.3.2+dfsg/src/database/impl/FastaSequenceIterator.cpp:149:65: [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 (builder) { builder->addData ((LETTER*)buffer, strlen(buffer), ASCII); }
data/plast-2.3.2+dfsg/src/database/impl/ReadingFrameSequenceIterator.cpp:232:49: [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).
builder->setComment (_sequence.comment, strlen(_sequence.comment));
data/plast-2.3.2+dfsg/src/database/impl/ReverseStrandSequenceIterator.cpp:154:49: [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).
builder->setComment (_sequence.comment, strlen(_sequence.comment));
data/plast-2.3.2+dfsg/src/database/impl/StringSequenceIterator.cpp:124:44: [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).
getBuilder()->setComment (comment, strlen(comment));
data/plast-2.3.2+dfsg/src/designpattern/impl/Property.cpp:269:37: [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).
char* value = key + strlen (key) + 1;
data/plast-2.3.2+dfsg/src/designpattern/impl/Property.cpp:347:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
reader.read ();
data/plast-2.3.2+dfsg/src/designpattern/impl/XmlReader.cpp:66:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void XmlReader::read ()
data/plast-2.3.2+dfsg/src/designpattern/impl/XmlReader.hpp:179:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void read ();
data/plast-2.3.2+dfsg/src/index/impl/retrievall.c:752:11: [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).
key_len=strlen(key);
data/plast-2.3.2+dfsg/src/index/impl/retrievall.c:792:12: [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).
key_len=strlen(key);
data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp:63:25: [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 len = strlen (dup);
data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp:64:25: [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 lenVersion = strlen (PLAST_VERSION);
data/plast-2.3.2+dfsg/src/launcher/jni/org_inria_genscale_dbscan_impl_plast_RequestManager.cpp:102:18: [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 len = strlen (dup);
data/plast-2.3.2+dfsg/src/misc/api/obsfucation.h:526:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
#define read x503
data/plast-2.3.2+dfsg/src/os/api/IFile.hpp:97:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual size_t read (void* buffer, size_t size, size_t count) = 0;
data/plast-2.3.2+dfsg/src/os/impl/CommonOsImpl.hpp:77:22: [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).
result = strlen (tmp);
data/plast-2.3.2+dfsg/src/os/impl/CommonOsImpl.hpp:80:89: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (result > 0) { for (char c = tmp[result-1]; c !='\n' && c!=EOF; c = fgetc (_handle)) {} }
data/plast-2.3.2+dfsg/src/os/impl/CommonOsImpl.hpp:109:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
size_t read (void * buffer, size_t size, size_t count)
data/plast-2.3.2+dfsg/src/os/impl/LinuxThread.cpp:146:30: [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).
result.assign (hostname, strlen(hostname));
data/plast-2.3.2+dfsg/src/os/impl/MacOsThread.cpp:152:30: [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).
result.assign (hostname, strlen(hostname));
data/plast-2.3.2+dfsg/src/os/impl/WindowsThread.cpp:171:33: [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).
result.assign (infoBuf, strlen(infoBuf));
data/plast-2.3.2+dfsg/src/os/impl/ZlibFile.cpp:75:22: [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).
result = strlen (tmp);
ANALYSIS SUMMARY:
Hits = 244
Lines analyzed = 66957 in approximately 2.07 seconds (32384 lines/second)
Physical Source Lines of Code (SLOC) = 31166
Hits@level = [0] 98 [1] 56 [2] 147 [3] 7 [4] 30 [5] 4
Hits@level+ = [0+] 342 [1+] 244 [2+] 188 [3+] 41 [4+] 34 [5+] 4
Hits/KSLOC@level+ = [0+] 10.9735 [1+] 7.82904 [2+] 6.03221 [3+] 1.31554 [4+] 1.09093 [5+] 0.128345
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.