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/ray-2.3.1/code/application_core/ray_main.cpp
Examining data/ray-2.3.1/code/application_core/Machine.h
Examining data/ray-2.3.1/code/application_core/Machine.cpp
Examining data/ray-2.3.1/code/Partitioner/Partitioner.h
Examining data/ray-2.3.1/code/Partitioner/Partitioner.cpp
Examining data/ray-2.3.1/code/Searcher/DistributionWriter.cpp
Examining data/ray-2.3.1/code/Searcher/Searcher.cpp
Examining data/ray-2.3.1/code/Searcher/VirtualKmerColor.h
Examining data/ray-2.3.1/code/Searcher/ContigHit.cpp
Examining data/ray-2.3.1/code/Searcher/Searcher.h
Examining data/ray-2.3.1/code/Searcher/ContigSearchEntry.cpp
Examining data/ray-2.3.1/code/Searcher/QualityCaller.h
Examining data/ray-2.3.1/code/Searcher/SearchDirectory.h
Examining data/ray-2.3.1/code/Searcher/SearchDirectory.cpp
Examining data/ray-2.3.1/code/Searcher/ColorSet.cpp
Examining data/ray-2.3.1/code/Searcher/ContigHit.h
Examining data/ray-2.3.1/code/Searcher/VirtualKmerColor.cpp
Examining data/ray-2.3.1/code/Searcher/QualityCaller.cpp
Examining data/ray-2.3.1/code/Searcher/ColoredPeakFinder.h
Examining data/ray-2.3.1/code/Searcher/DistributionWriter.h
Examining data/ray-2.3.1/code/Searcher/ColoredPeakFinder.cpp
Examining data/ray-2.3.1/code/Searcher/ContigSearchEntry.h
Examining data/ray-2.3.1/code/Searcher/ColorSet.h
Examining data/ray-2.3.1/code/KmerAcademyBuilder/KmerAcademyBuilder.cpp
Examining data/ray-2.3.1/code/KmerAcademyBuilder/Kmer.cpp
Examining data/ray-2.3.1/code/KmerAcademyBuilder/KmerAcademyBuilder.h
Examining data/ray-2.3.1/code/KmerAcademyBuilder/Kmer.h
Examining data/ray-2.3.1/code/KmerAcademyBuilder/BloomFilter.cpp
Examining data/ray-2.3.1/code/KmerAcademyBuilder/BloomFilter.h
Examining data/ray-2.3.1/code/SequencesLoader/ColorSpaceLoader.h
Examining data/ray-2.3.1/code/SequencesLoader/BzReader.cpp
Examining data/ray-2.3.1/code/SequencesLoader/SequencesLoader.h
Examining data/ray-2.3.1/code/SequencesLoader/FastaLoaderForReads.h
Examining data/ray-2.3.1/code/SequencesLoader/FastqBz2Loader.h
Examining data/ray-2.3.1/code/SequencesLoader/LoaderFactory.h
Examining data/ray-2.3.1/code/SequencesLoader/FastaGzLoader.cpp
Examining data/ray-2.3.1/code/SequencesLoader/BzReader.h
Examining data/ray-2.3.1/code/SequencesLoader/ExportLoader.cpp
Examining data/ray-2.3.1/code/SequencesLoader/LoaderFactory.cpp
Examining data/ray-2.3.1/code/SequencesLoader/Read.h
Examining data/ray-2.3.1/code/SequencesLoader/FastqLoader.cpp
Examining data/ray-2.3.1/code/SequencesLoader/FastqGzLoader.cpp
Examining data/ray-2.3.1/code/SequencesLoader/LoaderInterface.cpp
Examining data/ray-2.3.1/code/SequencesLoader/FastaBz2Loader.cpp
Examining data/ray-2.3.1/code/SequencesLoader/FastaBz2Loader.h
Examining data/ray-2.3.1/code/SequencesLoader/SffLoader.cpp
Examining data/ray-2.3.1/code/SequencesLoader/FastaLoader.cpp
Examining data/ray-2.3.1/code/SequencesLoader/ColorSpaceLoader.cpp
Examining data/ray-2.3.1/code/SequencesLoader/SffLoader.h
Examining data/ray-2.3.1/code/SequencesLoader/ExportLoader.h
Examining data/ray-2.3.1/code/SequencesLoader/LoaderInterface.h
Examining data/ray-2.3.1/code/SequencesLoader/Loader.h
Examining data/ray-2.3.1/code/SequencesLoader/ColorSpaceDecoder.cpp
Examining data/ray-2.3.1/code/SequencesLoader/FastqBz2Loader.cpp
Examining data/ray-2.3.1/code/SequencesLoader/ArrayOfReads.cpp
Examining data/ray-2.3.1/code/SequencesLoader/BufferedReader.cpp
Examining data/ray-2.3.1/code/SequencesLoader/BufferedReader.h
Examining data/ray-2.3.1/code/SequencesLoader/ReadHandle.cpp
Examining data/ray-2.3.1/code/SequencesLoader/ArrayOfReads.h
Examining data/ray-2.3.1/code/SequencesLoader/SequenceFileDetector.h
Examining data/ray-2.3.1/code/SequencesLoader/FastaLoaderForReads.cpp
Examining data/ray-2.3.1/code/SequencesLoader/FastqLoader.h
Examining data/ray-2.3.1/code/SequencesLoader/ColorSpaceDecoder.h
Examining data/ray-2.3.1/code/SequencesLoader/SequenceFileDetector.cpp
Examining data/ray-2.3.1/code/SequencesLoader/ReadHandle.h
Examining data/ray-2.3.1/code/SequencesLoader/FastqGzLoader.h
Examining data/ray-2.3.1/code/SequencesLoader/Read.cpp
Examining data/ray-2.3.1/code/SequencesLoader/FastaLoader.h
Examining data/ray-2.3.1/code/SequencesLoader/SequencesLoader.cpp
Examining data/ray-2.3.1/code/SequencesLoader/FastaGzLoader.h
Examining data/ray-2.3.1/code/SequencesLoader/Loader.cpp
Examining data/ray-2.3.1/code/JoinerTaskCreator/JoinerTaskCreator.h
Examining data/ray-2.3.1/code/JoinerTaskCreator/JoinerWorker.h
Examining data/ray-2.3.1/code/JoinerTaskCreator/JoinerTaskCreator.cpp
Examining data/ray-2.3.1/code/JoinerTaskCreator/JoinerWorker.cpp
Examining data/ray-2.3.1/code/SeedExtender/ExtensionElement.cpp
Examining data/ray-2.3.1/code/SeedExtender/SeedExtender.h
Examining data/ray-2.3.1/code/SeedExtender/ExtensionElement.h
Examining data/ray-2.3.1/code/SeedExtender/ReadFetcher.cpp
Examining data/ray-2.3.1/code/SeedExtender/OpenAssemblerChooser.cpp
Examining data/ray-2.3.1/code/SeedExtender/TipWatchdog.h
Examining data/ray-2.3.1/code/SeedExtender/ReadFetcher.h
Examining data/ray-2.3.1/code/SeedExtender/ExtensionData.h
Examining data/ray-2.3.1/code/SeedExtender/NovaEngine.h
Examining data/ray-2.3.1/code/SeedExtender/VertexMessenger.cpp
Examining data/ray-2.3.1/code/SeedExtender/BubbleData.h
Examining data/ray-2.3.1/code/SeedExtender/TipWatchdog.cpp
Examining data/ray-2.3.1/code/SeedExtender/NovaEngine.cpp
Examining data/ray-2.3.1/code/SeedExtender/BubbleTool.cpp
Examining data/ray-2.3.1/code/SeedExtender/Chooser.cpp
Examining data/ray-2.3.1/code/SeedExtender/VertexMessenger.h
Examining data/ray-2.3.1/code/SeedExtender/OpenAssemblerChooser.h
Examining data/ray-2.3.1/code/SeedExtender/SeedExtender.cpp
Examining data/ray-2.3.1/code/SeedExtender/DepthFirstSearchData.h
Examining data/ray-2.3.1/code/SeedExtender/Direction.cpp
Examining data/ray-2.3.1/code/SeedExtender/ExtensionData.cpp
Examining data/ray-2.3.1/code/SeedExtender/Direction.h
Examining data/ray-2.3.1/code/SeedExtender/BubbleTool.h
Examining data/ray-2.3.1/code/SeedExtender/Chooser.h
Examining data/ray-2.3.1/code/SeedExtender/DepthFirstSearchData.cpp
Examining data/ray-2.3.1/code/Library/Library.cpp
Examining data/ray-2.3.1/code/Library/Library.h
Examining data/ray-2.3.1/code/Library/LibraryPeakFinder.h
Examining data/ray-2.3.1/code/Library/LibraryWorker.cpp
Examining data/ray-2.3.1/code/Library/LibraryWorker.h
Examining data/ray-2.3.1/code/Library/LibraryPeakFinder.cpp
Examining data/ray-2.3.1/code/Mock/Parameters.h
Examining data/ray-2.3.1/code/Mock/Mock.cpp
Examining data/ray-2.3.1/code/Mock/common_functions.h
Examining data/ray-2.3.1/code/Mock/common_functions.cpp
Examining data/ray-2.3.1/code/Mock/constants.h
Examining data/ray-2.3.1/code/Mock/Mock.h
Examining data/ray-2.3.1/code/Mock/Parameters.cpp
Examining data/ray-2.3.1/code/Example/Example.h
Examining data/ray-2.3.1/code/Example/Example.cpp
Examining data/ray-2.3.1/code/TaxonomyViewer/types.h
Examining data/ray-2.3.1/code/TaxonomyViewer/TaxonomyViewer.cpp
Examining data/ray-2.3.1/code/TaxonomyViewer/TaxonomicTreeLoader.cpp
Examining data/ray-2.3.1/code/TaxonomyViewer/GenomeToTaxonLoader.h
Examining data/ray-2.3.1/code/TaxonomyViewer/TaxonNameLoader.cpp
Examining data/ray-2.3.1/code/TaxonomyViewer/TaxonomyViewer.h
Examining data/ray-2.3.1/code/TaxonomyViewer/TaxonNameLoader.h
Examining data/ray-2.3.1/code/TaxonomyViewer/TaxonomicTreeLoader.h
Examining data/ray-2.3.1/code/TaxonomyViewer/GenomeToTaxonLoader.cpp
Examining data/ray-2.3.1/code/GeneOntology/KeyEncoder.cpp
Examining data/ray-2.3.1/code/GeneOntology/types.h
Examining data/ray-2.3.1/code/GeneOntology/KeyEncoder.h
Examining data/ray-2.3.1/code/GeneOntology/GeneOntology.h
Examining data/ray-2.3.1/code/GeneOntology/GeneOntology.cpp
Examining data/ray-2.3.1/code/MessageProcessor/MessageProcessor.cpp
Examining data/ray-2.3.1/code/MessageProcessor/MessageProcessor.h
Examining data/ray-2.3.1/code/PathEvaluator/PathEvaluator.cpp
Examining data/ray-2.3.1/code/PathEvaluator/PathEvaluator.h
Examining data/ray-2.3.1/code/VerticesExtractor/VerticesExtractor.cpp
Examining data/ray-2.3.1/code/VerticesExtractor/Vertex.h
Examining data/ray-2.3.1/code/VerticesExtractor/GridTableIterator.h
Examining data/ray-2.3.1/code/VerticesExtractor/VerticesExtractor.h
Examining data/ray-2.3.1/code/VerticesExtractor/Vertex.cpp
Examining data/ray-2.3.1/code/VerticesExtractor/GridTableIterator.cpp
Examining data/ray-2.3.1/code/VerticesExtractor/GridTable.h
Examining data/ray-2.3.1/code/VerticesExtractor/GridTable.cpp
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/AttributeFetcher.cpp
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/GraphExplorer.h
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/AttributeFetcher.h
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/SeedFilteringWorkflow.h
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/NanoMerger.h
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/SeedFilteringWorkflow.cpp
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/AnnotationFetcher.cpp
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/GraphSearchResult.cpp
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/NanoMerger.cpp
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/SeedMergingWorkflow.cpp
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/GraphSearchResult.h
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/SpuriousSeedAnnihilator.cpp
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/GraphExplorer.cpp
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/SeedGossipSolver.h
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/AnnihilationWorker.h
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/AnnotationFetcher.h
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/SeedGossipSolver.cpp
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/SpuriousSeedAnnihilator.h
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/GossipAssetManager.h
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/SeedMergingWorkflow.h
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/GossipAssetManager.cpp
Examining data/ray-2.3.1/code/SpuriousSeedAnnihilator/AnnihilationWorker.cpp
Examining data/ray-2.3.1/code/MachineHelper/MachineHelper.h
Examining data/ray-2.3.1/code/MachineHelper/MachineHelper.cpp
Examining data/ray-2.3.1/code/Surveyor/CoalescenceManager.h
Examining data/ray-2.3.1/code/Surveyor/GenomeGraphReader.h
Examining data/ray-2.3.1/code/Surveyor/Mother.h
Examining data/ray-2.3.1/code/Surveyor/MatrixOwner.cpp
Examining data/ray-2.3.1/code/Surveyor/StoreKeeper.h
Examining data/ray-2.3.1/code/Surveyor/StoreKeeper.cpp
Examining data/ray-2.3.1/code/Surveyor/CoalescenceManager.cpp
Examining data/ray-2.3.1/code/Surveyor/ExperimentVertex.cpp
Examining data/ray-2.3.1/code/Surveyor/Mother.cpp
Examining data/ray-2.3.1/code/Surveyor/MatrixOwner.h
Examining data/ray-2.3.1/code/Surveyor/ExperimentVertex.h
Examining data/ray-2.3.1/code/Surveyor/GenomeGraphReader.cpp
Examining data/ray-2.3.1/code/FusionTaskCreator/FusionWorker.cpp
Examining data/ray-2.3.1/code/FusionTaskCreator/FusionTaskCreator.cpp
Examining data/ray-2.3.1/code/FusionTaskCreator/FusionTaskCreator.h
Examining data/ray-2.3.1/code/FusionTaskCreator/FusionWorker.h
Examining data/ray-2.3.1/code/Amos/Amos.h
Examining data/ray-2.3.1/code/Amos/Amos.cpp
Examining data/ray-2.3.1/code/Scaffolder/Scaffolder.cpp
Examining data/ray-2.3.1/code/Scaffolder/Scaffolder.h
Examining data/ray-2.3.1/code/Scaffolder/SummarizedLink.h
Examining data/ray-2.3.1/code/Scaffolder/ScaffoldingEdge.h
Examining data/ray-2.3.1/code/Scaffolder/ScaffoldingEdge.cpp
Examining data/ray-2.3.1/code/Scaffolder/ScaffoldingVertex.cpp
Examining data/ray-2.3.1/code/Scaffolder/ScaffoldingVertex.h
Examining data/ray-2.3.1/code/Scaffolder/ScaffoldingLink.cpp
Examining data/ray-2.3.1/code/Scaffolder/ScaffoldingLink.h
Examining data/ray-2.3.1/code/Scaffolder/SummarizedLink.cpp
Examining data/ray-2.3.1/code/Scaffolder/ScaffoldingAlgorithm.cpp
Examining data/ray-2.3.1/code/Scaffolder/ScaffoldingAlgorithm.h
Examining data/ray-2.3.1/code/GenomeNeighbourhood/GenomeNeighbourhood.cpp
Examining data/ray-2.3.1/code/GenomeNeighbourhood/NeighbourPair.h
Examining data/ray-2.3.1/code/GenomeNeighbourhood/GenomeNeighbourhood.h
Examining data/ray-2.3.1/code/GenomeNeighbourhood/Neighbour.cpp
Examining data/ray-2.3.1/code/GenomeNeighbourhood/Neighbour.h
Examining data/ray-2.3.1/code/GenomeNeighbourhood/NeighbourPair.cpp
Examining data/ray-2.3.1/code/EdgePurger/EdgePurgerWorker.h
Examining data/ray-2.3.1/code/EdgePurger/EdgePurger.cpp
Examining data/ray-2.3.1/code/EdgePurger/EdgePurgerWorker.cpp
Examining data/ray-2.3.1/code/EdgePurger/EdgePurger.h
Examining data/ray-2.3.1/code/NetworkTest/NetworkTest.h
Examining data/ray-2.3.1/code/NetworkTest/NetworkTest.cpp
Examining data/ray-2.3.1/code/SequencesIndexer/ReadAnnotation.cpp
Examining data/ray-2.3.1/code/SequencesIndexer/PairedRead.h
Examining data/ray-2.3.1/code/SequencesIndexer/DynamicVector.h
Examining data/ray-2.3.1/code/SequencesIndexer/PairedRead.cpp
Examining data/ray-2.3.1/code/SequencesIndexer/IndexerWorker.h
Examining data/ray-2.3.1/code/SequencesIndexer/SequencesIndexer.h
Examining data/ray-2.3.1/code/SequencesIndexer/ReadAnnotation.h
Examining data/ray-2.3.1/code/SequencesIndexer/IndexerWorker.cpp
Examining data/ray-2.3.1/code/SequencesIndexer/SequencesIndexer.cpp
Examining data/ray-2.3.1/code/FusionData/FusionData.h
Examining data/ray-2.3.1/code/FusionData/FusionData.cpp
Examining data/ray-2.3.1/code/CoverageGatherer/CoverageDistribution.h
Examining data/ray-2.3.1/code/CoverageGatherer/CoverageGatherer.cpp
Examining data/ray-2.3.1/code/CoverageGatherer/CoverageGatherer.h
Examining data/ray-2.3.1/code/CoverageGatherer/CoverageDistribution.cpp
Examining data/ray-2.3.1/code/SeedingData/GraphPath.h
Examining data/ray-2.3.1/code/SeedingData/PathHandle.h
Examining data/ray-2.3.1/code/SeedingData/SeedingData.cpp
Examining data/ray-2.3.1/code/SeedingData/SeedWorker.cpp
Examining data/ray-2.3.1/code/SeedingData/SeedWorker.h
Examining data/ray-2.3.1/code/SeedingData/PathHandle.cpp
Examining data/ray-2.3.1/code/SeedingData/SeedingData.h
Examining data/ray-2.3.1/code/SeedingData/GraphPath.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/cryptography/crypto.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/cryptography/crypto.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/plugins/RegisteredPlugin.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/plugins/CorePlugin.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/plugins/RegisteredPlugin.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/plugins/CorePlugin.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/actors/Playground.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/actors/Playground.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/actors/Actor.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/actors/Actor.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/profiling/TimePrinter.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/profiling/Profiler.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/profiling/Profiler.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/profiling/Derivative.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/profiling/ProcessStatus.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/profiling/TickLogger.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/profiling/Derivative.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/profiling/ProcessStatus.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/profiling/TickLogger.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/profiling/TimePrinter.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStore.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStoreItem.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStoreItem.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStoreRequest.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStoreRequest.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/store/CarriageableItem.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStore.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/ReusableMemoryStore.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/MyAllocator.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/DirtyBuffer.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/MyAllocator.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/allocator.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/RingAllocator.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/RingAllocator.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/allocator.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/DefragmentationGroup.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/ChunkAllocatorWithDefragmentation.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/DefragmentationLane.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/DefragmentationLane.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/ReusableMemoryStore.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/ChunkAllocatorWithDefragmentation.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/DirtyBuffer.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/memory/DefragmentationGroup.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/core/statistics.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/core/types.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/core/slave_modes.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/core/ComputeCore.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/core/OperatingSystem.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/core/ComputeCore.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/core/MiniRank.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/core/master_modes.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/core/master_modes.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/core/RankProcess.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/core/OperatingSystem.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/core/MiniRank.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/core/statistics.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/core/slave_modes.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/handlers/MessageTagHandler.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/handlers/MessageTagExecutor.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/handlers/MasterModeExecutor.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/handlers/SlaveModeExecutor.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/handlers/SlaveModeHandler.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/handlers/MasterModeHandler.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/handlers/MasterModeExecutor.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/handlers/MessageTagExecutor.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/handlers/SlaveModeExecutor.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/scheduling/Worker.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/scheduling/SwitchMan.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/scheduling/TaskCreator.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/scheduling/TaskCreator.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/scheduling/VirtualProcessor.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/scheduling/SwitchMan.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/scheduling/VirtualProcessor.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/files/FileReader.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/files/FileReader.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/structures/SplayTree.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/structures/MyHashTableIterator.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/structures/StaticVector.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/structures/SplayNode.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/structures/StaticVector.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/structures/MyHashTableGroup.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/structures/SplayTreeIterator.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/structures/MyHashTable.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/structures/MyStack.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessageRouter.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessageQueue.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessagesHandler.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/communication/BufferedData.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/communication/Message.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/communication/Message.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessageQueue.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/communication/VirtualCommunicator.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessagesHandler.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/communication/VirtualCommunicator.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/communication/mpi_tags.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/communication/BufferedData.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/communication/mpi_tags.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessageRouter.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/Torus.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementationRandom.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/ConnectionGraph.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementationGroup.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/Polytope.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/Torus.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/Polytope.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementation.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementationKautz.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementationDeBruijn.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementationComplete.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementationExperimental.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementationRandom.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/ConnectionGraph.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementationExperimental.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementationDeBruijn.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementationGroup.cpp
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementationKautz.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementationComplete.h
Examining data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementation.h

FINAL RESULTS:

data/ray-2.3.1/RayPlatform/RayPlatform/communication/BufferedData.cpp:42:2:  [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(m_type,type);
data/ray-2.3.1/RayPlatform/RayPlatform/core/ComputeCore.cpp:1515:2:  [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(SLAVE_MODES[mode],symbol);
data/ray-2.3.1/RayPlatform/RayPlatform/core/ComputeCore.cpp:1559:2:  [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(MASTER_MODES[mode],symbol);
data/ray-2.3.1/RayPlatform/RayPlatform/core/ComputeCore.cpp:1598:2:  [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(MESSAGE_TAGS[tag],symbol);
data/ray-2.3.1/RayPlatform/RayPlatform/memory/MyAllocator.cpp:47:2:  [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(m_type,type);
data/ray-2.3.1/RayPlatform/RayPlatform/memory/RingAllocator.cpp:63:2:  [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(m_type,type);
data/ray-2.3.1/RayPlatform/RayPlatform/structures/MyHashTable.h:545:2:  [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(m_mallocType,mallocType);
data/ray-2.3.1/RayPlatform/RayPlatform/structures/StaticVector.cpp:30:2:  [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(m_type,type);
data/ray-2.3.1/code/Amos/Amos.cpp:125:5:  [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(qlt,seq.c_str());
data/ray-2.3.1/code/NetworkTest/NetworkTest.cpp:211:3:  [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(destination,m_name->c_str());
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:252:4:  [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(m_currentSequenceHeader,line);
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:293:3:  [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(line,m_bufferedLine);
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:577:4:  [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(m_bufferedLine,line);
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:590:4:  [4] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused).
			strcat(newContent,line);
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:606:2:  [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(m_currentSequenceBuffer,newContent);
data/ray-2.3.1/code/Searcher/Searcher.cpp:1677:4:  [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(sequence,sequenceName.c_str());
data/ray-2.3.1/code/Searcher/Searcher.cpp:2001:5:  [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(sequenceNameFromMessage,sequenceName.c_str());
data/ray-2.3.1/code/SequencesLoader/Read.cpp:34:2:  [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,sequence);
data/ray-2.3.1/code/SequencesLoader/SequencesLoader.cpp:225:5:  [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(qlt,seq);
data/ray-2.3.1/RayPlatform/RayPlatform/core/ComputeCore.cpp:1124:2:  [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(portableProcessId() * getMicroseconds());
data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementation.cpp:251:3:  [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(i*i + i*i*i);
data/ray-2.3.1/RayPlatform/RayPlatform/routing/GraphImplementationRandom.cpp:66:3:  [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(i*i*i+2*i);
data/ray-2.3.1/code/Mock/Parameters.cpp:54:2:  [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(99);
data/ray-2.3.1/code/NetworkTest/NetworkTest.cpp:90:2:  [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(time(NULL)*(1+m_rank));
data/ray-2.3.1/RayPlatform/RayPlatform/actors/Actor.cpp:56:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(newBuffer, oldBuffer, bytes * sizeof(char));
data/ray-2.3.1/RayPlatform/RayPlatform/communication/BufferedData.h:49:2:  [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 m_type[100];
data/ray-2.3.1/RayPlatform/RayPlatform/communication/Message.cpp:277:2:  [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(memory + offset + MESSAGE_META_DATA_ACTOR_SOURCE, &m_sourceActor, sizeof(int));
data/ray-2.3.1/RayPlatform/RayPlatform/communication/Message.cpp:278:2:  [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(memory + offset + MESSAGE_META_DATA_ACTOR_DESTINATION, &m_destinationActor, sizeof(int));
data/ray-2.3.1/RayPlatform/RayPlatform/communication/Message.cpp:318:2:  [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(&m_sourceActor, memory + offset + MESSAGE_META_DATA_ACTOR_SOURCE, sizeof(int));
data/ray-2.3.1/RayPlatform/RayPlatform/communication/Message.cpp:319:2:  [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(&m_destinationActor, memory + offset + MESSAGE_META_DATA_ACTOR_DESTINATION, sizeof(int));
data/ray-2.3.1/RayPlatform/RayPlatform/communication/Message.cpp:383:2:  [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(memory + offset + MESSAGE_META_DATA_ROUTE_SOURCE, &m_routingSource, sizeof(int));
data/ray-2.3.1/RayPlatform/RayPlatform/communication/Message.cpp:384:2:  [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(memory + offset + MESSAGE_META_DATA_ROUTE_DESTINATION, &m_routingDestination, sizeof(int));
data/ray-2.3.1/RayPlatform/RayPlatform/communication/Message.cpp:432:2:  [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(&m_routingSource, memory + offset + MESSAGE_META_DATA_ROUTE_SOURCE, sizeof(int));
data/ray-2.3.1/RayPlatform/RayPlatform/communication/Message.cpp:433:2:  [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(&m_routingDestination, memory + offset + MESSAGE_META_DATA_ROUTE_DESTINATION, sizeof(int));
data/ray-2.3.1/RayPlatform/RayPlatform/communication/Message.cpp:619:2:  [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(getBufferBytes() + getNumberOfBytes() + MESSAGE_META_DATA_MINIRANK_SOURCE,
data/ray-2.3.1/RayPlatform/RayPlatform/communication/Message.cpp:622:2:  [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(getBufferBytes() + getNumberOfBytes() + MESSAGE_META_DATA_MINIRANK_DESTINATION,
data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessageRouter.cpp:333:2:  [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(outgoingMessage, message->getBuffer(), count*sizeof(char));
data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessagesHandler.cpp:233:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(copiedBuffer, buffer, bytes);
data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessagesHandler.cpp:361:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(incoming,filledBuffer,count*sizeof(MessageUnit));
data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessagesHandler.cpp:501:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(incoming, m_staticBuffer,count*sizeof(char));
data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessagesHandler.cpp:653:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(incoming,populatedBuffer,count*sizeof(MessageUnit));
data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessagesHandler.cpp:754:2:  [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 staticBuffer[MAXIMUM_MESSAGE_SIZE_IN_BYTES + MESSAGE_META_DATA_SIZE];
data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessagesHandler.cpp:784:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(incoming,staticBuffer,count);
data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessagesHandler.cpp:883:2:  [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 serverName[1000];
data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessagesHandler.cpp:968:5:  [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).
	fp.open(file,ios_base::out|ios_base::app);
data/ray-2.3.1/RayPlatform/RayPlatform/communication/MessagesHandler.cpp:1300:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(incoming,message.getBuffer(), count*sizeof(char));
data/ray-2.3.1/RayPlatform/RayPlatform/communication/mpi_tags.cpp:27:1:  [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_TAGS[MAXIMUM_NUMBER_OF_TAG_HANDLERS][128];
data/ray-2.3.1/RayPlatform/RayPlatform/communication/mpi_tags.h:31:8:  [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.
extern char MESSAGE_TAGS[MAXIMUM_NUMBER_OF_TAG_HANDLERS][128];
data/ray-2.3.1/RayPlatform/RayPlatform/core/ComputeCore.cpp:698:5:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
				memcpy(buffer, aMessage->getBuffer(), aMessage->getNumberOfBytes() * sizeof(char));
data/ray-2.3.1/RayPlatform/RayPlatform/core/ComputeCore.cpp:902:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(bytes + numberOfBytes, &crc32, sizeof(crc32));
data/ray-2.3.1/RayPlatform/RayPlatform/core/ComputeCore.cpp:1136:3:  [2] (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). Risk is low because the source is a constant string.
		strcpy(MASTER_MODES[i],"UnnamedMasterMode");
data/ray-2.3.1/RayPlatform/RayPlatform/core/ComputeCore.cpp:1139:3:  [2] (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). Risk is low because the source is a constant string.
		strcpy(SLAVE_MODES[i],"UnnamedSlaveMode");
data/ray-2.3.1/RayPlatform/RayPlatform/core/ComputeCore.cpp:1142:3:  [2] (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). Risk is low because the source is a constant string.
		strcpy(MESSAGE_TAGS[i],"UnnamedMessageTag");
data/ray-2.3.1/RayPlatform/RayPlatform/core/RankProcess.h:137:21:  [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).
			miniRanksPerRank=atoi(argv[i+1]);
data/ray-2.3.1/RayPlatform/RayPlatform/core/master_modes.cpp:24:1:  [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 MASTER_MODES[MAXIMUM_NUMBER_OF_MASTER_HANDLERS][128];
data/ray-2.3.1/RayPlatform/RayPlatform/core/master_modes.h: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.
extern char MASTER_MODES[MAXIMUM_NUMBER_OF_MASTER_HANDLERS][128];
data/ray-2.3.1/RayPlatform/RayPlatform/core/slave_modes.cpp:24:1:  [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 SLAVE_MODES[MAXIMUM_NUMBER_OF_SLAVE_HANDLERS][128];
data/ray-2.3.1/RayPlatform/RayPlatform/core/slave_modes.h: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.
extern char SLAVE_MODES[MAXIMUM_NUMBER_OF_SLAVE_HANDLERS][128];
data/ray-2.3.1/RayPlatform/RayPlatform/files/FileReader.cpp:49:18:  [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).
void FileReader::open(const char * file) {
data/ray-2.3.1/RayPlatform/RayPlatform/files/FileReader.cpp:54:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	m_reader.open(file);
data/ray-2.3.1/RayPlatform/RayPlatform/files/FileReader.cpp:98:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(buffer, availableBuffer, i);
data/ray-2.3.1/RayPlatform/RayPlatform/files/FileReader.h:54:7:  [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).
	void open(const char * file);
data/ray-2.3.1/RayPlatform/RayPlatform/memory/MyAllocator.h:40:2:  [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 m_type[101];
data/ray-2.3.1/RayPlatform/RayPlatform/memory/RingAllocator.h:85:2:  [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 m_type[100];
data/ray-2.3.1/RayPlatform/RayPlatform/profiling/ProcessStatus.cpp:24:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char line[1024];
data/ray-2.3.1/RayPlatform/RayPlatform/profiling/TimePrinter.cpp:68:2:  [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 buffer[20];
data/ray-2.3.1/RayPlatform/RayPlatform/profiling/TimePrinter.cpp:106:9:  [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).
	m_file.open(fileName.str().c_str(),ios_base::out);
data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStore.cpp:73:2:  [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 buffer[MAXIMUM_KEY_LENGTH];
data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStore.cpp:82:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(buffer, key, keyLength);
data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStore.cpp:302:2:  [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(&valueSize, buffer + inputPosition, size);
data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStore.cpp:305:2:  [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(&offset, buffer + inputPosition, size);
data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStore.cpp:322:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(buffer + outputPosition, key, size);
data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStore.cpp:328:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(buffer + outputPosition, &valueLength, size);
data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStore.cpp:330:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(buffer + outputPosition, &offset, size);
data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStore.cpp:421:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(responseBuffer + outputPosition, value + offset, size);
data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStore.cpp:546:2:  [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(value + offset, buffer + inputPosition, bytesToCopy);
data/ray-2.3.1/RayPlatform/RayPlatform/structures/MyHashTable.h:162:2:  [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 m_mallocType[100];
data/ray-2.3.1/RayPlatform/RayPlatform/structures/StaticVector.h:39:2:  [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 m_type[100];
data/ray-2.3.1/code/Amos/Amos.cpp:82:14:  [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).
		m_amosFile=fopen(m_parameters->getAmosFile().c_str(),"a+");
data/ray-2.3.1/code/CoverageGatherer/CoverageDistribution.cpp:37:5:  [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).
		f.open(file->c_str());
data/ray-2.3.1/code/CoverageGatherer/CoverageGatherer.cpp:66:12:  [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).
		kmerFile=fopen(name.str().c_str(),"w"); // create empty file
data/ray-2.3.1/code/CoverageGatherer/CoverageGatherer.cpp:68:12:  [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).
		kmerFile=fopen(name.str().c_str(),"a"); // append to file
data/ray-2.3.1/code/GeneOntology/GeneOntology.cpp:261:4:  [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).
	f.open(m_annotationFileName.c_str());
data/ray-2.3.1/code/GeneOntology/GeneOntology.cpp:452:10:  [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(file2.c_str());
data/ray-2.3.1/code/GeneOntology/GeneOntology.cpp:795:25:  [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).
			tsvFiles[domainName]=fopen(tsvFile.c_str(),"a");
data/ray-2.3.1/code/GeneOntology/GeneOntology.cpp:904:2:  [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 line[2048];
data/ray-2.3.1/code/KmerAcademyBuilder/Kmer.cpp:329:2:  [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 a[CONFIG_MAXKMERLENGTH+1];
data/ray-2.3.1/code/KmerAcademyBuilder/Kmer.cpp:423:2:  [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 buffer[CONFIG_MAXKMERLENGTH+1];
data/ray-2.3.1/code/KmerAcademyBuilder/KmerAcademyBuilder.cpp:136:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char memory[CONFIG_MAXKMERLENGTH+1];
data/ray-2.3.1/code/KmerAcademyBuilder/KmerAcademyBuilder.cpp:145:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(memory,m_readSequence+position,m_parameters->getWordSize());
data/ray-2.3.1/code/KmerAcademyBuilder/KmerAcademyBuilder.h:72:2:  [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 m_readSequence[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/Library/Library.cpp:387:22:  [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(name.str().c_str(), "w");
data/ray-2.3.1/code/MachineHelper/MachineHelper.cpp:814:5:  [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).
	fp.open(fileName, std::ios::app);
data/ray-2.3.1/code/MessageProcessor/MessageProcessor.cpp:2444:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(dest,m_myReads->at(index)->getRawSequence(),m_myReads->at(index)->getRequiredBytes());
data/ray-2.3.1/code/Mock/Parameters.cpp:132:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char buffer[__BLOCK_SIZE];
data/ray-2.3.1/code/Mock/Parameters.cpp:564:24:  [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).
				meanFragmentLength=atoi(token.c_str());
data/ray-2.3.1/code/Mock/Parameters.cpp:567:23:  [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).
				standardDeviation=atoi(token.c_str());
data/ray-2.3.1/code/Mock/Parameters.cpp:611:26:  [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).
			m_maximumSeedCoverage=atoi(token.c_str());
data/ray-2.3.1/code/Mock/Parameters.cpp:689:25:  [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).
					meanFragmentLength=atoi(token.c_str());
data/ray-2.3.1/code/Mock/Parameters.cpp:692:24:  [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).
					standardDeviation=atoi(token.c_str());
data/ray-2.3.1/code/Mock/Parameters.cpp:749:21:  [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).
				m_reducerPeriod=atoi(m_commands[i+1].c_str());
data/ray-2.3.1/code/Mock/Parameters.cpp:763:21:  [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).
			m_repeatCoverage=atoi(token.c_str());
data/ray-2.3.1/code/Mock/Parameters.cpp:777:22:  [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).
			m_minimumCoverage=atoi(token.c_str());
data/ray-2.3.1/code/Mock/Parameters.cpp:791:19:  [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).
			m_peakCoverage=atoi(token.c_str());
data/ray-2.3.1/code/Mock/Parameters.cpp:820:13:  [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).
			m_degree=atoi(token.c_str());
data/ray-2.3.1/code/Mock/Parameters.cpp:872:26:  [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).
			m_minimumContigLength=atoi(token.c_str());
data/ray-2.3.1/code/Mock/Parameters.cpp:892:15:  [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).
			m_wordSize=atoi(token.c_str());
data/ray-2.3.1/code/Mock/common_functions.cpp:102:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char sequence[CONFIG_MAXKMERLENGTH];
data/ray-2.3.1/code/Mock/common_functions.cpp:103:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(sequence,m_sequence+pos,w);
data/ray-2.3.1/code/Mock/common_functions.cpp:108:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char sequence[CONFIG_MAXKMERLENGTH];
data/ray-2.3.1/code/Mock/common_functions.cpp:109:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(sequence,m_sequence+length-pos-w,w);
data/ray-2.3.1/code/Scaffolder/Scaffolder.cpp:667:7:  [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).
			fp.open(fileName.str().c_str());
data/ray-2.3.1/code/Scaffolder/Scaffolder.cpp:669:7:  [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).
			fp.open(fileName.str().c_str(),ios_base::out|ios_base::app);
data/ray-2.3.1/code/Scaffolder/Scaffolder.cpp:1608:8:  [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).
		m_fp.open(file.c_str(),ios_base::out|ios_base::app);
data/ray-2.3.1/code/Searcher/DistributionWriter.cpp:119:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	m_output.open(rawDistribution.str().c_str());
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:125:2:  [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 line[10000];
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:210:23:  [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).
		m_currentFileStream=fopen(fileName.str().c_str(),"r");
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:242:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char line[CONFIG_COLORED_LINE_MAX_LENGTH];
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:426:2:  [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 sequenceBuffer[400];
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:427:2:  [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(sequenceBuffer,m_currentSequenceBuffer+m_currentSequencePosition,kmerLength);
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:530:2:  [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 newContent[CONFIG_COLORED_LINE_MAX_LENGTH];
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:563:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char line[CONFIG_COLORED_LINE_MAX_LENGTH];
data/ray-2.3.1/code/Searcher/SearchDirectory.h:51:2:  [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 m_bufferedLine[CONFIG_COLORED_LINE_MAX_LENGTH];
data/ray-2.3.1/code/Searcher/SearchDirectory.h:65:2:  [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 m_currentSequenceHeader[CONFIG_COLORED_LINE_MAX_LENGTH];
data/ray-2.3.1/code/Searcher/SearchDirectory.h:66:2:  [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 m_currentSequenceBuffer[CONFIG_COLORED_LINE_MAX_LENGTH];
data/ray-2.3.1/code/Searcher/Searcher.cpp:719:21:  [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).
		contigSummaryFile.open(summary.str().c_str(), ios_base::app);
data/ray-2.3.1/code/Searcher/Searcher.cpp:819:26:  [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).
			m_currentCoverageFile.open(file2.str().c_str(),ios_base::app);
data/ray-2.3.1/code/Searcher/Searcher.cpp:1493:6:  [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).
		f1.open(summaryFile.str().c_str(),ios_base::app);
data/ray-2.3.1/code/Searcher/Searcher.cpp:1504:6:  [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).
		f2.open(virtualStuff.str().c_str(),ios_base::app);
data/ray-2.3.1/code/Searcher/Searcher.cpp:2443:19:  [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).
		directoriesFile.open(directory6.str().c_str(),ios_base::app);
data/ray-2.3.1/code/Searcher/Searcher.cpp:2467:10:  [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).
			files.open(fileForFiles.str().c_str(),ios_base::app);
data/ray-2.3.1/code/Searcher/Searcher.cpp:3529:37:  [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).
		m_arrayOfFiles[directoryIterator]=fopen(fileName.str().c_str(),"a");
data/ray-2.3.1/code/Searcher/Searcher.cpp:3538:41:  [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).
		m_arrayOfFiles_tsv[directoryIterator]=fopen(fileName_tsv.str().c_str(),"a");
data/ray-2.3.1/code/Searcher/Searcher.cpp:3802:51:  [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).
       		m_identificationFiles[directoryIterator]=fopen(identifications.str().c_str(),"a");
data/ray-2.3.1/code/Searcher/Searcher.cpp:3969:5:  [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).
	f1.open(summaryFile.str().c_str(),ios_base::app);
data/ray-2.3.1/code/SeedExtender/SeedExtender.cpp:2179:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char readSequence[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SeedExtender/SeedExtender.cpp:2612:14:  [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).
		m_pathFile.open(file.c_str(),ios_base::app);
data/ray-2.3.1/code/SeedExtender/SeedExtender.h:262:2:  [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 m_receivedString[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SeedingData/GraphPath.cpp:481:2:  [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 kmer[CONFIG_MAXKMERLENGTH+1];
data/ray-2.3.1/code/SeedingData/GraphPath.cpp:591:2:  [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(&elements, buffer + position, operationSize);
data/ray-2.3.1/code/SeedingData/GraphPath.cpp:595:2:  [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(&kmerLength, buffer + position, operationSize);
data/ray-2.3.1/code/SeedingData/GraphPath.cpp:618:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(buffer + position, &elements, operationSize);
data/ray-2.3.1/code/SeedingData/GraphPath.cpp:627:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(buffer + position, &kmerLength, operationSize);
data/ray-2.3.1/code/SeedingData/PathHandle.cpp:129:2:  [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(&m_value, buffer, size);
data/ray-2.3.1/code/SeedingData/PathHandle.cpp:136:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(buffer, &m_value, size);
data/ray-2.3.1/code/SequencesIndexer/DynamicVector.h:79:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(newArray,m_array,currentBytes); /* this is fast */
data/ray-2.3.1/code/SequencesIndexer/SequencesIndexer.cpp:248:20:  [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).
		m_readMarkerFile.open(fileName.c_str());
data/ray-2.3.1/code/SequencesLoader/BufferedReader.cpp:192:2:  [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(content, buffer, count);
data/ray-2.3.1/code/SequencesLoader/BzReader.cpp:33:16:  [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).
void BzReader::open(const char*file){
data/ray-2.3.1/code/SequencesLoader/BzReader.cpp:34:9:  [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).
	m_file=fopen(file,"r");
data/ray-2.3.1/code/SequencesLoader/BzReader.cpp:130:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(m_unused,m_unused1,m_nUnused);
data/ray-2.3.1/code/SequencesLoader/BzReader.h:42:2:  [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 m_unused[BZ_MAX_UNUSED];
data/ray-2.3.1/code/SequencesLoader/BzReader.h:49:7:  [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).
	void open(const char*file);
data/ray-2.3.1/code/SequencesLoader/ColorSpaceDecoder.cpp:77:2:  [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 v[1024];
data/ray-2.3.1/code/SequencesLoader/ColorSpaceLoader.cpp:38:23:  [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).
int ColorSpaceLoader::open(string file){
data/ray-2.3.1/code/SequencesLoader/ColorSpaceLoader.cpp:39:6:  [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).
	m_f=fopen(file.c_str(),"r");
data/ray-2.3.1/code/SequencesLoader/ColorSpaceLoader.cpp:42:2:  [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 bufferForLine[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SequencesLoader/ColorSpaceLoader.cpp:57:6:  [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).
	m_f=fopen(file.c_str(),"r");
data/ray-2.3.1/code/SequencesLoader/ColorSpaceLoader.cpp:62:2:  [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 bufferForLine[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SequencesLoader/ColorSpaceLoader.h:51:6:  [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).
	int open(string file);
data/ray-2.3.1/code/SequencesLoader/ExportLoader.cpp:35:19:  [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).
int ExportLoader::open(string file){
data/ray-2.3.1/code/SequencesLoader/ExportLoader.cpp:36:6:  [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).
	m_f=fopen(file.c_str(),"r");
data/ray-2.3.1/code/SequencesLoader/ExportLoader.cpp:39:2:  [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 buffer[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SequencesLoader/ExportLoader.cpp:46:6:  [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).
	m_f=fopen(file.c_str(),"r");
data/ray-2.3.1/code/SequencesLoader/ExportLoader.cpp:51:2:  [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 buffer[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SequencesLoader/ExportLoader.h:53:6:  [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).
	int open(string file);
data/ray-2.3.1/code/SequencesLoader/FastaBz2Loader.cpp:39:21:  [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).
int FastaBz2Loader::open(string file){
data/ray-2.3.1/code/SequencesLoader/FastaBz2Loader.h:45:6:  [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).
	int open(string file);
data/ray-2.3.1/code/SequencesLoader/FastaGzLoader.cpp:36:20:  [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).
int FastaGzLoader::open(string file){
data/ray-2.3.1/code/SequencesLoader/FastaGzLoader.h:48:6:  [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).
	int open(string file);
data/ray-2.3.1/code/SequencesLoader/FastaLoader.cpp:40:4:  [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 bufferForLine[1024];
data/ray-2.3.1/code/SequencesLoader/FastaLoaderForReads.cpp:35:26:  [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).
int FastaLoaderForReads::open(string file){
data/ray-2.3.1/code/SequencesLoader/FastaLoaderForReads.h:47:6:  [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).
	int open(string file);
data/ray-2.3.1/code/SequencesLoader/FastqBz2Loader.cpp:40:21:  [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).
int FastqBz2Loader::open(string file){
data/ray-2.3.1/code/SequencesLoader/FastqBz2Loader.cpp:45:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	m_reader.open(file.c_str());
data/ray-2.3.1/code/SequencesLoader/FastqBz2Loader.cpp:46:2:  [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 buffer[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SequencesLoader/FastqBz2Loader.cpp:62:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	m_reader.open(file.c_str());
data/ray-2.3.1/code/SequencesLoader/FastqBz2Loader.cpp:72:2:  [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 buffer[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SequencesLoader/FastqBz2Loader.h:48:6:  [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).
	int open(string file);
data/ray-2.3.1/code/SequencesLoader/FastqGzLoader.cpp:41:20:  [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).
int FastqGzLoader::open(string file){
data/ray-2.3.1/code/SequencesLoader/FastqGzLoader.cpp:58:2:  [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 buffer[CONFIG_ZLIB_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SequencesLoader/FastqGzLoader.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 buffer[CONFIG_ZLIB_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SequencesLoader/FastqGzLoader.cpp:282:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(buffer,source,bytesToCopy);
data/ray-2.3.1/code/SequencesLoader/FastqGzLoader.h:68:6:  [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).
	int open(string file);
data/ray-2.3.1/code/SequencesLoader/FastqLoader.cpp:37:18:  [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).
int FastqLoader::open(string file){
data/ray-2.3.1/code/SequencesLoader/FastqLoader.cpp:42:6:  [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).
	m_f=fopen(file.c_str(),"r");
data/ray-2.3.1/code/SequencesLoader/FastqLoader.cpp:51:2:  [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 buffer[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SequencesLoader/FastqLoader.cpp:77:6:  [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).
	m_f=fopen(file.c_str(),"r");
data/ray-2.3.1/code/SequencesLoader/FastqLoader.cpp:92:2:  [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 buffer[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SequencesLoader/FastqLoader.h:54:6:  [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).
	int open(string file);
data/ray-2.3.1/code/SequencesLoader/Loader.cpp:75:16:  [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).
		m_interface->open(file);
data/ray-2.3.1/code/SequencesLoader/LoaderInterface.h:42:14:  [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).
	virtual int open(string file) = 0;
data/ray-2.3.1/code/SequencesLoader/Read.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 buffer[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SequencesLoader/Read.cpp:157:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(m_sequence,workingBuffer,requiredBytes);
data/ray-2.3.1/code/SequencesLoader/Read.cpp:186:2:  [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 buffer[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SequencesLoader/SequencesLoader.cpp:63:2:  [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 read[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SequencesLoader/SequencesLoader.cpp:195:6:  [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).
		fp=fopen(m_parameters->getAmosFile().c_str(),"w");
data/ray-2.3.1/code/SequencesLoader/SffLoader.cpp:84:16:  [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).
int SffLoader::open(string file){
data/ray-2.3.1/code/SequencesLoader/SffLoader.cpp:96:7:  [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).
	m_fp=fopen(file.c_str(),"r");
data/ray-2.3.1/code/SequencesLoader/SffLoader.h:55:6:  [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).
	int open(string file);
data/ray-2.3.1/code/SpuriousSeedAnnihilator/GraphSearchResult.cpp:76:2:  [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(&paths, buffer + position, size);
data/ray-2.3.1/code/SpuriousSeedAnnihilator/GraphSearchResult.cpp:90:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(&strand, buffer + position, size);
data/ray-2.3.1/code/SpuriousSeedAnnihilator/GraphSearchResult.cpp:117:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(buffer + position, &paths, size);
data/ray-2.3.1/code/SpuriousSeedAnnihilator/GraphSearchResult.cpp:127:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(buffer + position, &value, size);
data/ray-2.3.1/code/Surveyor/CoalescenceManager.cpp:343:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(buffer + offset, &sample, sizeof(sample));
data/ray-2.3.1/code/Surveyor/CoalescenceManager.cpp:407:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(buffer + offset, &producer, sizeof(producer));
data/ray-2.3.1/code/Surveyor/GenomeGraphReader.cpp:74:2:  [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(&m_aggregator, buffer, sizeof(int));
data/ray-2.3.1/code/Surveyor/GenomeGraphReader.cpp:77:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	m_reader.open(m_fileName.c_str());
data/ray-2.3.1/code/Surveyor/GenomeGraphReader.cpp:112:2:  [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 buffer[1024];
data/ray-2.3.1/code/Surveyor/GenomeGraphReader.cpp:239:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char messageBuffer[100];
data/ray-2.3.1/code/Surveyor/GenomeGraphReader.cpp:243:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(messageBuffer + position, &m_sample, sizeof(m_sample));
data/ray-2.3.1/code/Surveyor/MatrixOwner.cpp:125:19:  [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).
			similarityFile.open(similarityMatrix.c_str());
data/ray-2.3.1/code/Surveyor/MatrixOwner.cpp:144:17:  [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).
			distanceFile.open(distanceMatrix.c_str());
data/ray-2.3.1/code/Surveyor/Mother.cpp:223:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char buffer[32];
data/ray-2.3.1/code/Surveyor/Mother.cpp:225:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(buffer + offset, &m_parameters, sizeof(m_parameters));
data/ray-2.3.1/code/Surveyor/Mother.cpp:227:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(buffer + offset, &names, sizeof(names));
data/ray-2.3.1/code/Surveyor/StoreKeeper.cpp:171:4:  [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[20];
data/ray-2.3.1/code/Surveyor/StoreKeeper.cpp:173:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(buffer + offset, &sample1, sizeof(sample1));
data/ray-2.3.1/code/Surveyor/StoreKeeper.cpp:175:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(buffer + offset, &sample2, sizeof(sample2));
data/ray-2.3.1/code/Surveyor/StoreKeeper.cpp:177:4:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
			memcpy(buffer + offset, &count, sizeof(count));
data/ray-2.3.1/code/TaxonomyViewer/GenomeToTaxonLoader.cpp:35:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	m_stream.open(file.c_str());
data/ray-2.3.1/code/TaxonomyViewer/GenomeToTaxonLoader.cpp:68:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	m_stream.open(file.c_str());
data/ray-2.3.1/code/TaxonomyViewer/TaxonNameLoader.cpp:35:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	m_stream.open(file.c_str());
data/ray-2.3.1/code/TaxonomyViewer/TaxonNameLoader.cpp:45:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char line[1024];
data/ray-2.3.1/code/TaxonomyViewer/TaxonNameLoader.cpp:56:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	m_stream.open(file.c_str());
data/ray-2.3.1/code/TaxonomyViewer/TaxonNameLoader.cpp:67:2:  [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 line[1024];
data/ray-2.3.1/code/TaxonomyViewer/TaxonomicTreeLoader.cpp:33:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	m_stream.open(file.c_str());
data/ray-2.3.1/code/TaxonomyViewer/TaxonomicTreeLoader.cpp:62:11:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	m_stream.open(file.c_str());
data/ray-2.3.1/code/TaxonomyViewer/TaxonomyViewer.cpp:116:5:  [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).
		f.open(file.c_str(),ios_base::app);
data/ray-2.3.1/code/TaxonomyViewer/TaxonomyViewer.cpp:721:19:  [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).
			tsvFiles[rank]=fopen(tsvFile.c_str(),"a");
data/ray-2.3.1/code/VerticesExtractor/Vertex.cpp:427:2:  [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(&m_coverage_lower, buffer + position, bytes);
data/ray-2.3.1/code/VerticesExtractor/Vertex.cpp:431:2:  [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(&m_edges_lower, buffer + position, bytes);
data/ray-2.3.1/code/VerticesExtractor/Vertex.cpp:444:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(buffer + position, &m_coverage_lower, bytes);
data/ray-2.3.1/code/VerticesExtractor/Vertex.cpp:450:2:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
	memcpy(buffer + position, &edges, bytes);
data/ray-2.3.1/code/VerticesExtractor/VerticesExtractor.cpp:134:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char memory[1000];
data/ray-2.3.1/code/VerticesExtractor/VerticesExtractor.cpp:143:3:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
		memcpy(memory,m_readSequence+p,m_parameters->getWordSize());
data/ray-2.3.1/code/VerticesExtractor/VerticesExtractor.h:83:2:  [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 m_readSequence[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/RayPlatform/RayPlatform/core/ComputeCore.cpp:254:3:  [1] (obsolete) usleep:
  This C routine is considered obsolete (as opposed to the shell command by
  the same name). The interaction of this function with SIGALRM and other
  timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
  unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
		usleep(10);
data/ray-2.3.1/RayPlatform/RayPlatform/files/FileReader.cpp:82:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		this->read();
data/ray-2.3.1/RayPlatform/RayPlatform/files/FileReader.cpp:118:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void FileReader::read() {
data/ray-2.3.1/RayPlatform/RayPlatform/files/FileReader.cpp:143:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	m_reader.read(destinationBuffer, bytes);
data/ray-2.3.1/RayPlatform/RayPlatform/files/FileReader.h:48:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	void read();
data/ray-2.3.1/RayPlatform/RayPlatform/store/KeyValueStore.cpp:320:13:  [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).
	int size = strlen(key);
data/ray-2.3.1/code/Amos/Amos.cpp:126:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
				for(int i=0;i<(int)strlen(qlt);i++){
data/ray-2.3.1/code/FusionData/FusionData.cpp:57:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			f.read((char*)&theSize,sizeof(int));
data/ray-2.3.1/code/FusionData/FusionData.cpp:63:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				f.read((char*)&name,sizeof(PathHandle));
data/ray-2.3.1/code/FusionData/FusionData.cpp:64:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				f.read((char*)&vertices,sizeof(int));
data/ray-2.3.1/code/FusionData/FusionData.cpp:69:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
					kmer.read(&f);
data/ray-2.3.1/code/GeneOntology/KeyEncoder.cpp:86:9:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	assert(strlen(identifier)==3+5);
data/ray-2.3.1/code/GeneOntology/KeyEncoder.cpp:206:19:  [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).
	int actualLength=strlen(identifier);
data/ray-2.3.1/code/GeneOntology/KeyEncoder.cpp:214:14:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	assert((int)strlen(identifier)== (start+length));
data/ray-2.3.1/code/KmerAcademyBuilder/Kmer.cpp:373:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void Kmer::read(istream*f){
data/ray-2.3.1/code/KmerAcademyBuilder/Kmer.cpp:376:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		f->read((char*)&a,sizeof(uint64_t));
data/ray-2.3.1/code/KmerAcademyBuilder/Kmer.h:149:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	void read(istream*f);
data/ray-2.3.1/code/KmerAcademyBuilder/KmerAcademyBuilder.cpp:128:11:  [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).
		int len=strlen(m_readSequence);
data/ray-2.3.1/code/Library/Library.cpp:97:4:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	f.read((char*)&entries,sizeof(uint32_t));
data/ray-2.3.1/code/Library/Library.cpp:111:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		f.read((char*)&library,sizeof(uint32_t));
data/ray-2.3.1/code/Library/Library.cpp:112:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		f.read((char*)&distance,sizeof(uint32_t));
data/ray-2.3.1/code/Library/Library.cpp:113:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		f.read((char*)&count,sizeof(uint32_t));
data/ray-2.3.1/code/MachineHelper/MachineHelper.cpp:231:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		f.read((char*)&n,sizeof(int));
data/ray-2.3.1/code/MachineHelper/MachineHelper.cpp:236:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			f.read((char*)&coverage,sizeof(int));
data/ray-2.3.1/code/MachineHelper/MachineHelper.cpp:237:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			f.read((char*)&count,sizeof(LargeCount));
data/ray-2.3.1/code/MessageProcessor/MessageProcessor.cpp:600:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		f.read((char*)&n,sizeof(LargeCount));
data/ray-2.3.1/code/MessageProcessor/MessageProcessor.cpp:607:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			kmer.read(&f);
data/ray-2.3.1/code/MessageProcessor/MessageProcessor.cpp:609:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			f.read((char*)&coverage,sizeof(int));
data/ray-2.3.1/code/MessageProcessor/MessageProcessor.cpp:618:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			f.read((char*)&parents,sizeof(int));
data/ray-2.3.1/code/MessageProcessor/MessageProcessor.cpp:621:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				parent.read(&f);
data/ray-2.3.1/code/MessageProcessor/MessageProcessor.cpp:625:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			f.read((char*)&children,sizeof(int));
data/ray-2.3.1/code/MessageProcessor/MessageProcessor.cpp:629:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				child.read(&f);
data/ray-2.3.1/code/MessageProcessor/MessageProcessor.cpp:1097:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		f.read((char*)&n,sizeof(LargeCount));
data/ray-2.3.1/code/MessageProcessor/MessageProcessor.cpp:1107:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		f2.read((char*)&n,sizeof(LargeCount));
data/ray-2.3.1/code/MessageProcessor/MessageProcessor.cpp:1111:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			kmer.read(&f2);
data/ray-2.3.1/code/MessageProcessor/MessageProcessor.cpp:1117:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			f2.read((char*)&markers,sizeof(int));
data/ray-2.3.1/code/MessageProcessor/MessageProcessor.cpp:1127:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				marker->read(&f2,isLower);
data/ray-2.3.1/code/MessageProcessor/MessageProcessor.cpp:1596:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	assert(read!=NULL);
data/ray-2.3.1/code/Mock/Parameters.cpp:134:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		f.read(buffer,__BLOCK_SIZE);
data/ray-2.3.1/code/Mock/Parameters.cpp:2420:16:  [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).
	int theLength=strlen(textMessage);
data/ray-2.3.1/code/Mock/common_functions.cpp:42:10:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	int len=strlen(x);
data/ray-2.3.1/code/Mock/common_functions.cpp:92:13:  [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).
	int length=strlen(m_sequence);
data/ray-2.3.1/code/Mock/common_functions.cpp:191:13:  [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).
	int theLen=strlen(a);
data/ray-2.3.1/code/Mock/common_functions.cpp:199:66:  [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).
			cout<<"Chunk="<<chunk<<" positionInKmer="<<j<<" KmerLength="<<strlen(a)<<" bitPosition=" <<bitPosition<<" Chunks="<<i.getNumberOfU64()<<endl;
data/ray-2.3.1/code/Partitioner/Partitioner.cpp:251:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			f.read((char*)&count,sizeof(int));
data/ray-2.3.1/code/Partitioner/Partitioner.cpp:255:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				f.read((char*)&file,sizeof(int));
data/ray-2.3.1/code/Partitioner/Partitioner.cpp:256:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				f.read((char*)&sequences,sizeof(LargeCount));
data/ray-2.3.1/code/Scaffolder/ScaffoldingEdge.cpp:103:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void ScaffoldingEdge::read(ifstream*f){
data/ray-2.3.1/code/Scaffolder/ScaffoldingEdge.h:73:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	void read(ifstream*f);
data/ray-2.3.1/code/Scaffolder/ScaffoldingVertex.cpp:41:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void ScaffoldingVertex::read(ifstream*f){
data/ray-2.3.1/code/Scaffolder/ScaffoldingVertex.h:42:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	void read(ifstream*f);
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:46:2:  [1] (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). Risk is low because the source is a constant character.
	strcpy(m_bufferedLine,"");
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:243:3:  [1] (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). Risk is low because the source is a constant character.
		strcpy(line,"");
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:263:2:  [1] (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). Risk is low because the source is a constant character.
	strcpy(m_currentSequenceBuffer,"");
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:278:9:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	assert(strlen(m_currentSequenceHeader)>0);
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:280:9:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	assert(strlen(m_currentSequenceBuffer)==0);
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:294:3:  [1] (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). Risk is low because the source is a constant character.
		strcpy(m_bufferedLine,"");
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:309:9:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	assert(strlen(m_bufferedLine)==0);
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:324:10:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	if(line[strlen(line)-1]=='\n'){
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:325:8:  [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).
		line[strlen(line)-1]='\0';
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:341:34:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	if( !m_noMoreSequence  && ((int)strlen(m_currentSequenceBuffer) - m_currentSequencePosition) < kmerLength
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:354:22:  [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).
		cout<<" buffer: "<<strlen(m_currentSequenceBuffer)<<endl;
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:364:11:  [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).
	if(((int)strlen(m_currentSequenceBuffer) - m_currentSequencePosition) <kmerLength){
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:403:21:  [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).
	cout<<" buffer: "<<strlen(m_currentSequenceBuffer)<<endl;
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:431:14:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	assert((int)strlen(sequenceBuffer)==kmerLength);
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:532:2:  [1] (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). Risk is low because the source is a constant character.
	strcpy(newContent,"");
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:539:16:  [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).
	int theLength=strlen(m_currentSequenceBuffer);
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:558:52:  [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).
	cout<<"after copying remainings, newContent is "<<strlen(newContent)<<endl;
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:564:3:  [1] (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). Risk is low because the source is a constant character.
		strcpy(line,"");
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:573:11:  [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).
			assert(strlen(m_bufferedLine)==0);
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:613:44:  [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).
	cout<<"new m_currentSequenceBuffer has "<<strlen(m_currentSequenceBuffer)<<" nucleotides"<<endl;
data/ray-2.3.1/code/Searcher/SearchDirectory.cpp:619:9:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	return strlen(line)>0 && line[0]=='>';
data/ray-2.3.1/code/SeedExtender/SeedExtender.cpp:393:36:  [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).
				ed->m_EXTENSION_receivedLength=strlen(theSequence);
data/ray-2.3.1/code/SeedExtender/SeedExtender.cpp:396:58:  [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).
					cout<<"OutOfRange UniqueId="<<uniqueId<<" Length="<<strlen(theSequence)<<" StartPosition="<<element->getPosition()<<" CurrentPosition="<<ed->m_EXTENSION_extension.size()-1<<" StrandPosition="<<element->getStrandPosition()<<endl;
data/ray-2.3.1/code/SeedExtender/SeedExtender.cpp:1513:32:  [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).
						int rightReadLength=(int)strlen(m_receivedString);
data/ray-2.3.1/code/SeedExtender/SeedExtender.cpp:1612:20:  [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).
				int readLength=strlen(m_receivedString);
data/ray-2.3.1/code/SeedExtender/SeedExtender.cpp:1730:30:  [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).
					assert(readLength==(int)strlen(m_receivedString));
data/ray-2.3.1/code/SeedExtender/SeedExtender.cpp:2101:4:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	f.read((char*)&count,sizeof(int));
data/ray-2.3.1/code/SeedExtender/SeedExtender.cpp:2105:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		f.read((char*)&length,sizeof(int));
data/ray-2.3.1/code/SeedExtender/SeedExtender.cpp:2114:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			kmer.read(&f);
data/ray-2.3.1/code/SeedingData/SeedingData.cpp:430:4:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	f.read((char*)&n,sizeof(int));
data/ray-2.3.1/code/SeedingData/SeedingData.cpp:435:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		f.read((char*)&vertices,sizeof(int));
data/ray-2.3.1/code/SeedingData/SeedingData.cpp:438:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			kmer.read(&f);
data/ray-2.3.1/code/SeedingData/SeedingData.cpp:443:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			f.read((char*)&coverageValue,sizeof(CoverageDepth));
data/ray-2.3.1/code/SequencesIndexer/IndexerWorker.cpp:71:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	assert(read!=NULL);
data/ray-2.3.1/code/SequencesIndexer/PairedRead.cpp:59:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void PairedRead::read(istream*f){
data/ray-2.3.1/code/SequencesIndexer/PairedRead.cpp:60:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	f->read((char*)&m_readIndex,sizeof(uint32_t));
data/ray-2.3.1/code/SequencesIndexer/PairedRead.cpp:61:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	f->read((char*)&m_rank,sizeof(uint16_t));
data/ray-2.3.1/code/SequencesIndexer/PairedRead.cpp:62:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	f->read((char*)&m_library,sizeof(uint16_t));
data/ray-2.3.1/code/SequencesIndexer/PairedRead.h:51:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	void read(istream*f);
data/ray-2.3.1/code/SequencesIndexer/ReadAnnotation.cpp:83:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void ReadAnnotation::read(istream*f,bool isLower){
data/ray-2.3.1/code/SequencesIndexer/ReadAnnotation.cpp:88:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	f->read((char*)&rank,sizeof(int));
data/ray-2.3.1/code/SequencesIndexer/ReadAnnotation.cpp:89:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	f->read((char*)&readIndex,sizeof(int));
data/ray-2.3.1/code/SequencesIndexer/ReadAnnotation.cpp:90:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	f->read((char*)&positionOnStrand,sizeof(int));
data/ray-2.3.1/code/SequencesIndexer/ReadAnnotation.cpp:91:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	f->read((char*)&strand,sizeof(char));
data/ray-2.3.1/code/SequencesIndexer/ReadAnnotation.h:55:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	void read(istream*f,bool isLower);
data/ray-2.3.1/code/SequencesLoader/ColorSpaceDecoder.cpp:76:10:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	int len=strlen(x);
data/ray-2.3.1/code/SequencesLoader/ColorSpaceLoader.cpp:76:23:  [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).
			for(int j=0;j<(int)strlen(bufferForLine);j++){
data/ray-2.3.1/code/SequencesLoader/ExportLoader.cpp:65:17:  [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).
		int theLength=strlen(buffer);
data/ray-2.3.1/code/SequencesLoader/LoaderInterface.cpp:25:21:  [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).
	int fileNameLength=strlen(fileName);
data/ray-2.3.1/code/SequencesLoader/LoaderInterface.cpp:26:26:  [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).
        int suffixLength=strlen(suffix);
data/ray-2.3.1/code/SequencesLoader/Read.cpp:33:13:  [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).
	int theLen=strlen(sequence);
data/ray-2.3.1/code/SequencesLoader/Read.cpp:55:10:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
	int len=strlen(corrected);
data/ray-2.3.1/code/SequencesLoader/Read.cpp:72:11:  [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).
	m_length=strlen(seq);
data/ray-2.3.1/code/SequencesLoader/Read.cpp:93:17:  [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(trimFlag && strlen(sequence)<RAY_MAXIMUM_READ_LENGTH){
data/ray-2.3.1/code/SequencesLoader/Read.cpp:101:13:  [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).
	int length=strlen(sequence);
data/ray-2.3.1/code/SequencesLoader/Read.cpp:269:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	f->read((char*)&forwardOffset,sizeof(int));
data/ray-2.3.1/code/SequencesLoader/Read.cpp:270:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	f->read((char*)&reverseOffset,sizeof(int));
data/ray-2.3.1/code/SequencesLoader/Read.cpp:283:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
void Read::read(istream*f,MyAllocator*seqMyAllocator){
data/ray-2.3.1/code/SequencesLoader/Read.cpp:284:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	m_pairedRead.read(f);
data/ray-2.3.1/code/SequencesLoader/Read.cpp:285:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	f->read((char*)&m_type,sizeof(uint8_t));
data/ray-2.3.1/code/SequencesLoader/Read.cpp:286:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	f->read((char*)&m_length,sizeof(uint16_t));
data/ray-2.3.1/code/SequencesLoader/Read.cpp:290:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		f->read((char*)m_sequence,getRequiredBytes());
data/ray-2.3.1/code/SequencesLoader/Read.h:82:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	void read(istream*f,MyAllocator*seqMyAllocator);
data/ray-2.3.1/code/SequencesLoader/SequencesLoader.cpp:63:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	char read[RAY_MAXIMUM_READ_LENGTH];
data/ray-2.3.1/code/SequencesLoader/SequencesLoader.cpp:64:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	theRead->getSeq(read,m_parameters->getColorSpaceMode(),false);
data/ray-2.3.1/code/SequencesLoader/SequencesLoader.cpp:69:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	myRead.constructor(read,&(*m_persistentAllocator),true);
data/ray-2.3.1/code/SequencesLoader/SequencesLoader.cpp:227:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
				for(int j=0;j<(int)strlen(qlt);j++){
data/ray-2.3.1/code/SequencesLoader/SequencesLoader.cpp:262:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		f.read((char*)&count,sizeof(LargeCount));
data/ray-2.3.1/code/SequencesLoader/SequencesLoader.cpp:265:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			myRead.read(&f,m_persistentAllocator);
data/ray-2.3.1/code/SequencesLoader/SffLoader.cpp:148:3:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		fgetc(m_fp);
data/ray-2.3.1/code/SequencesLoader/SffLoader.cpp:198:4:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			fgetc(m_fp);
data/ray-2.3.1/code/SequencesLoader/SffLoader.cpp:202:4:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			fgetc(m_fp);
data/ray-2.3.1/code/SequencesLoader/SffLoader.cpp:205:4:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			fgetc(m_fp);
data/ray-2.3.1/code/SequencesLoader/SffLoader.cpp:211:4:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			fgetc(m_fp);
data/ray-2.3.1/code/SequencesLoader/SffLoader.cpp:215:4:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			fgetc(m_fp);
data/ray-2.3.1/code/SequencesLoader/SffLoader.cpp:224:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		Read read;
data/ray-2.3.1/code/SequencesLoader/SffLoader.cpp:225:3:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		read.constructor(sequence.substr(first-1,last-first+1).c_str(),seqMyAllocator,true);
data/ray-2.3.1/code/SequencesLoader/SffLoader.cpp:226:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		reads->push_back(&read);
data/ray-2.3.1/code/Surveyor/GenomeGraphReader.cpp:119:6:  [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(strlen(buffer) > 0 && buffer[0] == '#')
data/ray-2.3.1/code/Surveyor/GenomeGraphReader.cpp:154:29:  [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).
		for(int i = 0 ; i < (int) strlen(buffer) ; ++i) {
data/ray-2.3.1/code/TaxonomyViewer/TaxonNameLoader.cpp:49:6:  [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(strlen(line)>0){
data/ray-2.3.1/code/VerticesExtractor/VerticesExtractor.cpp:123:11:  [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).
		int len=strlen(m_readSequence);

ANALYSIS SUMMARY:

Hits = 370
Lines analyzed = 85448 in approximately 1.96 seconds (43685 lines/second)
Physical Source Lines of Code (SLOC) = 49985
Hits@level = [0] 117 [1] 133 [2] 213 [3]   5 [4]  19 [5]   0
Hits@level+ = [0+] 487 [1+] 370 [2+] 237 [3+]  24 [4+]  19 [5+]   0
Hits/KSLOC@level+ = [0+] 9.74292 [1+] 7.40222 [2+] 4.74142 [3+] 0.480144 [4+] 0.380114 [5+]   0
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.