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/gatb-core-1.4.2+dfsg/gatb-core/doc/doxygen/src/dbgh5page.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/doc/doxygen/src/designpage.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/doc/doxygen/src/downloadpage.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/doc/doxygen/src/mainpage.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/doc/doxygen/src/snippetspage.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/doc/doxygen/src/testspage.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank1.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank10.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank11.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank12.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank13.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank14.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank15.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank16.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank17.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank18.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank19.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank2.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank20.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank21.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank22.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank23.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank24.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank25.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank26.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank27.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank28.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank3.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank4.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank5.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank6.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank7.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank8.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank9.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn1.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn10.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn11.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn12.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn13.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn14.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn15.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn16.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn17.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn18.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn19.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn2.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn20.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn21.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn22.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn23.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn24.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn25.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn26.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn27.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn3.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn4.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn5.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn6.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn7.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn8.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn9.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/traversal1.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/traversal2.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer1.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer10.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer11.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer12.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer13.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer14.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer15.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer16.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer17.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer2.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer3.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer4.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer5.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer6.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer7.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer8.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer9.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/protos/MicroSNP.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/protos/histo2D.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/storage/storage1.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/storage/storage10.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/storage/storage2.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/storage/storage3.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/storage/storage4.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/storage/storage5.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/storage/storage6.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/storage/storage7.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/storage/storage8.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/storage/storage9.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/ToyTool.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/iterators1.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/iterators2.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/iterators3.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/iterators4.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/iterators5.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/iterators6.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/iterators7.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/iterators8.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/iterators9.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading1.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading2.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading3.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading4.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading5.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading6.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading7.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading8.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/observer1.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/optionsparser1.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/optionsparser2.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/scripts/NewProject/XXX.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/scripts/NewProject/XXX.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/scripts/NewProject/main.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/api/IAlphabet.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/api/IBank.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/api/Sequence.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/AbstractBank.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/Alphabet.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/Bank.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankComposite.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankHelpers.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankHelpers.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankStrings.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/Banks.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/ThreadPool.h
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/binSeq.h
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/logging.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/ograph.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/ograph.h
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/ographBin.h
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/unionFind.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/api/IContainerNode.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/ContainerNode.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/ExtremityInfo.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Frontline.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/NodesDeleter.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/dag_vector.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/rank_vector.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/gatb_core.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/api/IModel.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/BankKmerIterator.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/BankKmers.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/BloomBuilder.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/BloomBuilder.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessor.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorAbstract.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorChain.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorCutoff.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorProxy.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithmFactory.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/DebloomMinimizerAlgorithm.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/LinearCounter.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/LinearCounter.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Model.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/RepartitionAlgorithm.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/RepartitionAlgorithm.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Sequence2SuperKmer.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/Exception.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/IFileSystem.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/IMemory.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/ISmartPointer.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/ISystemInfo.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/IThread.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/ITime.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/config_sha1.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/types.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/MemoryCommon.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/ThreadMacos.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/ThreadMacos.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/TimeCommon.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/api/Bag.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/api/Collection.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/api/Container.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/api/Iterable.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagPartition.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/CollectionAbstract.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/CollectionCache.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/ContainerSet.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Hash16.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IterableHelpers.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/OAHash.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/CompressionUtils.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/HeaderCoder.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/RangeCoder.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/RangeCoder.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/api/IObserver.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/api/Iterator.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/IteratorHelpers.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Observer.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Observer.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/FastMinimizer.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/NativeInt128.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/NativeInt16.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/NativeInt32.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/NativeInt8.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Data.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Data.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Enums.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/IOptionsParser.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/IProperty.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Macros.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Range.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/StringsRepository.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Vector.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/OptionsParser.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Pool.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/StringLine.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Stringify.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Tokenizer.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Tool.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Tool.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/XmlReader.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/api/ICell.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Cell.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageTools.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench1.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_bagfile.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_bloom.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_graph.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_minim.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_mphf.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/CppunitCommon.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestSequence.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bcalm/TestBcalm.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestSimplifications.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestSimplificationsUnitigs.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestDSK.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestDebloom.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestKmer.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestKmerBank.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestMPHF.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/main.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/collections/TestBag.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/collections/TestCollection.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/collections/TestContainer.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/collections/TestIterable.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/collections/TestMap.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/designpattern/TestIterators.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/math/TestMath.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/misc/TestMisc.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h
Examining data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/json/json.hpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/tools/BankDownload.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/tools/ClearCache.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/tools/KmerChecksum.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/tools/bankgen.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/tools/dbgcheck.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/tools/dbgh5.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/tools/dbginfo.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/tools/dbgtopology.cpp
Examining data/gatb-core-1.4.2+dfsg/gatb-core/tools/leon.cpp
FINAL RESULTS:
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:64:29: [5] (buffer) gets:
Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
int len = file->gets (buffer, sizeof(buffer));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/IFileSystem.hpp:89:17: [5] (buffer) gets:
Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
virtual int gets (char* s, int size) = 0;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:89:9: [5] (buffer) gets:
Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
int gets (char *s, int size)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:481:26: [5] (buffer) gets:
Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
while (file->gets (buffer, sizeof(buffer) ) != 0)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/api/IBank.hpp:161:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IBankFactory : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/AbstractBank.hpp:49:43: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class AbstractBank : public IBank, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp:97:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Bank factory '%s already registered", name.c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/Bank.cpp:157:30: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (result == 0) { throw system::Exception ("Unable to open bank '%s' (if it is a list of files, perhaps some of the files inside don't exist)", uri.c_str()); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:51:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = getFile (name, deleteIfExists ? "w+" : NULL);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:190:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = getFile (_name);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:228:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = getFile (_name, "a+");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:262:1: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* BankAlbum::getFile (const std::string& name, const char* mode)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.hpp:119:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* getFile (const std::string& name, const char* mode=NULL);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:28:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:250:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw gatb::core::system::ExceptionErrno (STR_BANK_unable_write_file);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:273:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw gatb::core::system::ExceptionErrno (STR_BANK_unable_open_file, _filename.c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:404:58: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (binary_read_file == 0) { throw gatb::core::system::ExceptionErrno (STR_BANK_unable_open_file, _ref._filename.c_str()); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:412:72: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (checkMagic(binary_read_file)==false) { throw gatb::core::system::ExceptionErrno (STR_BANK_unable_open_file, _ref._filename.c_str()); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:505:60: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (checkMagic(file)==false) { throw gatb::core::system::ExceptionErrno (STR_BANK_unable_open_file, _ref._filename.c_str()); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankComposite.hpp:127:51: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void insert (const Sequence& item) { throw system::Exception ("Can't insert sequence in a composite bank."); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp:31:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp:32:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp:36:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp:37:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp:161:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw gatb::core::system::Exception (STR_BANK_bad_file_number, _filenames.size(), getMaxNbFiles());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp:313:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw gatb::core::system::ExceptionErrno (STR_BANK_unable_open_file, _ref._filenames[0].c_str()); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp:666:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw gatb::core::system::ExceptionErrno (STR_BANK_unable_open_file, fname);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankHelpers.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankHelpers.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankSplitter.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:72:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:73:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:45:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:46:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp:29:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
u_int64_t mem = gatb::core::system::impl::System::info().getMemorySelfUsed() / 1024;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp:30:43: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
u_int64_t memMaxProcess = gatb::core::system::impl::System::info().getMemorySelfMaxUsed() / 1024;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:31:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:32:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:173:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class SortCmd : public tools::dp::ICommand, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/ContainerNode.hpp:50:84: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class ContainerNode : public IContainerNode<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/ContainerNode.hpp:109:93: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class ContainerNodeCascading : public IContainerNode<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:56:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:300:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
(props->getStr(STR_URI_OUTPUT_DIR) + "/" + system::impl::System::file().getBaseName (bank->getId()));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:306:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Error: can't create output directory");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:415:51: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (solidCounts->getNbItems() == 0) { throw system::Exception ("This dataset has no solid kmers"); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:438:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Graph construction failure during build_visitor_postsolid, the input _gatb/ folder (or .h5 file) needs to contain at least solid kmers");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:703:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Graph construction failure because of bad parameters (notify a developer)");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:733:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Graph construction failure because of bad parameters (notify a developer)");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:859:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
bool load_from_hdf5 = (system::impl::System::file().getExtension(input) == "h5");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:860:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
bool load_from_file = (system::impl::System::file().isFolderEndingWith(input,"_gatb"));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:1661:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::ExceptionNotImplemented();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:2346:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception("Iteration impossible (no solid nodes available)");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:2367:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception("Iteration impossible (no solid nor branching nodes available)");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:2370:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
else { throw system::Exception("Invalid type"); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:2966:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class Cmd : public tools::dp::ICommand, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:3503:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Cannot precompute adjacency information - MPHF was not constructed");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:3714:117: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void GraphTemplate<Node, Edge, GraphDataVariant>::deleteNodesByIndex(vector<bool> &bitmap, int nbCores, gatb::core::system::ISynchronizer* synchro) const
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:3820:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* synchro = system::impl::System::thread().newSynchronizer();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:3820:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* synchro = system::impl::System::thread().newSynchronizer();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.hpp:912:85: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void deleteNodesByIndex(std::vector<bool> &bitmap, int nbCores = 1, gatb::core::system::ISynchronizer* synchro=NULL) const;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:56:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:134:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Graph construction failure because of bad parameters (notify a developer)");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:164:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Graph construction failure because of bad parameters (notify a developer)");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:258:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Graph construction failure during build_visitor_postsolid, the input h5 file needs to contain at least solid kmers.");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:845:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
bool load_from_gfa = (system::impl::System::file().getExtension(input) == "gfa");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:857:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
bool load_from_hdf5 = (system::impl::System::file().getExtension(input) == "h5");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:858:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
bool load_from_file = (system::impl::System::file().isFolderEndingWith(input,"_gatb"));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:884:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Input file does not exist");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:1400:100: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void GraphUnitigsTemplate<span>::deleteNodesByIndex(vector<bool> &bitmap, int nbCores, gatb::core::system::ISynchronizer* synchro) const
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp:320:85: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void deleteNodesByIndex(std::vector<bool> &bitmap, int nbCores = 1, gatb::core::system::ISynchronizer* synchro=NULL) const;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp:31:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp:27:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp:28:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp:68:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().remove (unitigs_filename);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp:69:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().rename (unitigs_filename+".linked", unitigs_filename);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/LinkTigs.cpp:202:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().remove (unitigs_filename + ".links." + to_string(pass));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/NodesDeleter.hpp:52:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/NodesDeleter.hpp:79:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
synchro = system::impl::System::thread().newSynchronizer();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:52:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system; // for System
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:53:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:402:5: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(buffer, simplprogressFormat0, ++_nbTipRemovalPasses);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:1306:5: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(buffer, simplprogressFormat2, ++_nbBulgeRemovalPasses);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:1629:5: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(buffer, simplprogressFormat3, ++_nbECRemovalPasses);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.hpp:37:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class Simplifications : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:54:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class TerminatorTemplate : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:100:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class TraversalTemplate: public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp:35:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp:36:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/gatb_core.hpp:92:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/gatb_core.hpp:93:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/api/ICountProcessor.hpp:92:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class ICountProcessor : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/BankKmers.hpp:72:55: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void insert (const bank::Sequence& item) { throw system::Exception ("Can't insert sequence to BankKmers"); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/BankKmers.hpp:75:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void flush () { throw system::Exception ("Can't flush BankKmers"); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:53:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:54:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:73:82: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
result.add (1, "estimated_sequence_volume", "%ld", _estimateSeqTotalSize / system::MBYTE);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp:37:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp:38:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp:211:54: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (_config._nbCores == 0) { _config._nbCores = system::impl::System::info().getNbCores(); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp:270:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (_config._abundanceUserNb == 0) { throw system::Exception("Kmer solidity has no defined value"); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp:274:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Kmer solidity has more thresholds (%d) than banks (%d)", _config._abundanceUserNb, _config._nb_banks);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ConfigurationAlgorithm.cpp:281:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Kmer solidity custom has different number of values (%d) than banks (%d)", _config._solidVecUserNb, _config._nb_banks);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorChain.hpp:99:58: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (typedClones.size() != clones.size()) { throw system::Exception("Error in CountProcessorChain::finishClones"); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:63:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* synchronizer = 0,
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:208:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchronizer;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorDump.hpp:209:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void setSynchronizer (system::ISynchronizer* synchronizer) { SP_SETATTR(synchronizer); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:32:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:33:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:217:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:49:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Unable to set abundance min values (%d values for %d banks)", cutoffs.size(), _thresholds.size());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorSolidity.hpp:326:25: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("unable to create CountProcessorSolidity instance for kind %d", kind);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp:57:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp:58:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp:341:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().remove (outputUri);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/DebloomMinimizerAlgorithm.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/LinearCounter.cpp:25:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/LinearCounter.cpp:26:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:31:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:32:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:385:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class ModelAbstract : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:403:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Type '%s' has too low precision (%d bits) for the required %d kmer size",
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:671:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("BAD FORMAT IN 'execute'");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Model.hpp:1014:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (kmerSize < minimizerSize) { throw system::Exception ("Bad values for kmer %d and minimizer %d", kmerSize, minimizerSize); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:250:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (magic != MAGIC_NUMBER) { throw system::Exception("Unable to load Repartitor (minimRepart), possibly due to bad format."); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:259:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (magic != MAGIC_NUMBER) { throw system::Exception("Unable to load Repartitor (minimFrequency), possibly due to bad format."); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.hpp:292:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class Repartitor : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.hpp:304:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (nbpart <= 0) { system::Exception("Repartitor: nbpart (%d) should be > 0", nbpart); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:28:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:345:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().remove(fname);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:718:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().remove(fname);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:924:74: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class ReadSuperKCommand : public gatb::core::tools::dp::ICommand, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp:1390:68: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class SortCommand : public gatb::core::tools::dp::ICommand, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.hpp:109:74: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class PartitionsCommand : public gatb::core::tools::dp::ICommand, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartitionsCommand.hpp:281:84: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class PartitionsCommand_multibank : public gatb::core::tools::dp::ICommand, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/RepartitionAlgorithm.cpp:56:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/RepartitionAlgorithm.cpp:57:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:43:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:44:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:285:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
histo2Dstorage_filename = system::impl::System::file().getBaseName(firstbankname) + ".histo2D";
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:292:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
histo2Dstorage_filename = system::impl::System::file().getBaseName(firstbankname) + ".histo2D";
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:317:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
histo1Dstorage_filename = system::impl::System::file().getBaseName(firstbankname) + ".histo";
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:324:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
histo1Dstorage_filename = system::impl::System::file().getBaseName(firstbankname) + ".histo";
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:504:61: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
(getInput()->getStr(STR_URI_OUTPUT_DIR) + "/" + system::impl::System::file().getBaseName (_bank->getId()));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:559:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
(getInput()->getStr(STR_URI_OUTPUT_DIR) + "/" + system::impl::System::file().getBaseName (_bank->getIdNb(0))) + ".histo2D";
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:52:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:86:10: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf (buffer, sizeof(buffer), format, args);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/IFileSystem.hpp:37:12: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/IMemory.hpp:40:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/ISmartPointer.hpp:34:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/ISmartPointer.hpp:205:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
#define LOCAL(object) gatb::core::system::LocalObject __##object (object)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/ISystemInfo.hpp:36:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:38:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/IThread.hpp:121:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
virtual void addException (system::Exception e) = 0;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/ITime.hpp:38:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:35:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace gatb { namespace core { namespace system { namespace impl {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:44:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:117:15: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf (getHandle(), format, args);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp:37:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace gatb { namespace core { namespace system { namespace impl {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp:165:5: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf (buffer, sizeof(buffer), fmt, ap);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.hpp:36:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp:37:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace gatb { namespace core { namespace system { namespace impl {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp:123:14: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return ::system("purge");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp:161:5: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf (buffer, sizeof(buffer), fmt, ap);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.hpp:36:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/MemoryCommon.hpp:40:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.cpp:23:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace gatb { namespace core { namespace system { namespace impl {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.cpp:64:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
for (std::vector<system::IThread*>::iterator it = _threads.begin(); it != _threads.end(); it++)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.cpp:99:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
for (std::vector<system::IThread*>::iterator it = _threads.begin(); it != _threads.end(); it++)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.hpp:48:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.hpp:170:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class ThreadGroup : public IThreadGroup, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.hpp:207:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void addException (system::Exception e)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.hpp:228:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _startSynchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.hpp:232:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
std::list<system::Exception> _exceptions;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.hpp:273:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_synchro = system::impl::System::thread().newSynchronizer();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.hpp:347:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.hpp:355:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
#define MALLOC gatb::core::system::impl::System::memory().malloc
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.hpp:356:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
#define CALLOC gatb::core::system::impl::System::memory().calloc
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.hpp:357:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
#define REALLOC gatb::core::system::impl::System::memory().realloc
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/System.hpp:358:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
#define FREE gatb::core::system::impl::System::memory().free
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:31:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace gatb { namespace core { namespace system { namespace impl {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.hpp:38:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp:33:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace gatb { namespace core { namespace system { namespace impl {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp:44:44: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class ThreadLinux : public IThread, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.cpp:77:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class SynchronizerLinux : public ISynchronizer, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/ThreadLinux.hpp:34:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/ThreadMacos.cpp:33:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace gatb { namespace core { namespace system { namespace impl {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/ThreadMacos.cpp:44:44: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class ThreadMacos : public IThread, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/ThreadMacos.cpp:78:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class SynchronizerMacos : public ISynchronizer, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/ThreadMacos.hpp:34:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/TimeCommon.hpp:41:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/TimeCommon.hpp:71:9: [4] (format) snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
snprintf (buffer, sizeof(buffer), format,
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/api/Bag.hpp:51:51: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class Bag : public virtual system::ISmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/api/Container.hpp:46:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class Container : public virtual system::ISmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/api/Iterable.hpp:52:55: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class Iterable : public virtual system::ISmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:52:68: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class BagCache : public Bag<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:60:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
BagCache (Bag<Item>* ref, size_t cacheSize, system::ISynchronizer* synchro=0)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:66:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_items, 0, _nbMax*sizeof(Item));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:76:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_items, 0, _nbMax*sizeof(Item));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:119:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:120:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void setSynchro (system::ISynchronizer* synchro) { SP_SETATTR(synchro); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:144:129: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
BagCacheSortedBuffered (Bag<Item>* ref, size_t cacheSize, Item* sharedBuffer, size_t sharedCacheSize, size_t * idxShared, system::ISynchronizer* outsynchro=0, system::ISynchronizer* synchro=0
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:144:166: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
BagCacheSortedBuffered (Bag<Item>* ref, size_t cacheSize, Item* sharedBuffer, size_t sharedCacheSize, size_t * idxShared, system::ISynchronizer* outsynchro=0, system::ISynchronizer* synchro=0
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:194:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _outsynchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:195:25: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void setOutSynchro (system::ISynchronizer* outsynchro) { SP_SETATTR(outsynchro); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:211:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memcpy (_sharedBuffer + *_idxShared, this->_items, this->_idx*sizeof(Item));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:258:55: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
BagCacheSorted (Bag<Item>* ref, size_t cacheSize, system::ISynchronizer* synchro=0)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:50:67: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class BagFile : public Bag<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:63:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (system::impl::System::file().doesExist(filename))
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:64:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (filename, "rb+");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:66:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (filename, "wb");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:104:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* _file;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:111:69: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class BagGzFile : public Bag<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:119:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().remove (filename);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:157:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* _file;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:165:82: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class BagCountCompressedFile : public Bag<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:173:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().remove (filename);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:176:17: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (filename, "wb+");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:288:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* _file;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagPartition.hpp:52:57: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
for (size_t i=0; i<_partitions.size(); i++) { system::impl::System::file().remove (getFilename(i)); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagPartition.hpp:82:30: [4] (format) snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
char filename[128]; snprintf (filename, sizeof(filename), _uriFormat.c_str(), idx);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagPartition.hpp:95:59: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
BagCachePartition (BagFilePartition<Item>& partition, system::ISynchronizer* synchro)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagPartition.hpp:134:73: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
virtual BagCache<Item>* createBag (Bag<Item>*& b, size_t cacheSize, system::ISynchronizer* synchro)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagPartition.hpp:142:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:113:90: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class IBloom : public Container<Item>, public Bag<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:189:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (blooma, 0, nchar*sizeof(unsigned char));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:204:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().free (blooma);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:238:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
{ throw system::ExceptionNotImplemented (); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:242:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
{ throw system::ExceptionNotImplemented (); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:495:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::ExceptionNotImplemented();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:847:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (cano6, 0, 0x1000 * sizeof(unsigned short int));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:850:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (hpos, 0, 0x40000 * sizeof(unsigned char));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:874:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().free (cano6);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:875:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().free (hpos);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:1263:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("bad Bloom kind %d in createBloom", kind);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:42:70: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item, size_t prec=1> class BloomGroupOld : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:53:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_blooma, 0, _size*sizeof(Result));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:91:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "wb+");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:91:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "wb+");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:121:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "rb+");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:121:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "rb+");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:132:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_blooma, 0, _size*sizeof(Result));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:178:67: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item, size_t prec=1> class BloomGroup : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:200:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void memset (u_int64_t v) { system::impl::System::memory().memset (value, v, prec*sizeof(u_int64_t)); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:221:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_blooma, 0, _size*sizeof(Result));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:243:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "wb+");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:243:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "wb+");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:262:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "rb+");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:262:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "rb+");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:273:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_blooma, 0, _size*sizeof(Result));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:345:80: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item, size_t prec=1> class BloomGroupCacheCoherent : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:358:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_blooma, 0, _size*sizeof(Result));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:375:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
~BloomGroupCacheCoherent () { system::impl::System::memory().free (_blooma); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:386:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "wb+");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:386:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "wb+");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:408:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "rb+");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:408:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "rb+");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BloomGroup.hpp:422:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_blooma, 0, _size*sizeof(Result));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:231:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class BooPHF : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:275:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (isBuilt==true) { throw system::Exception ("MFHP: built already done"); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/CollectionCache.hpp:55:87: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class CollectionCache : public CollectionAbstract<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/CollectionCache.hpp:60:64: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CollectionCache (Collection<Item>& ref, size_t cacheSize, system::ISynchronizer* synchro)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/CollectionCache.hpp:90:93: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class CollectionCacheSorted : public CollectionAbstract<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/CollectionCache.hpp:95:95: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CollectionCacheSorted (Collection<Item>& ref, size_t cacheSize, size_t sharedCacheSize, system::ISynchronizer* synchro, system::ISynchronizer* outsynchro, Item* sharedBuffer, size_t * idxShared) //
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/CollectionCache.hpp:95:127: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CollectionCacheSorted (Collection<Item>& ref, size_t cacheSize, size_t sharedCacheSize, system::ISynchronizer* synchro, system::ISynchronizer* outsynchro, Item* sharedBuffer, size_t * idxShared) //
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/ContainerSet.hpp:51:78: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class ContainerSet : public Container<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Hash16.hpp:79:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IMemory& _memory;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Hash16.hpp:88:93: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Hash16 (size_t sizeMB) : datah(0), mask(0), tai(0), nb_elem(0), max_nb_elem(0), _memory(system::impl::System::memory())
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Hash16.hpp:96:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (tai_Hash16 > 32) { throw system::Exception ("Hash16: max size for this hash is 2^32, but ask for %d", tai_Hash16); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Hash16.hpp:117:121: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Hash16 (u_int64_t nb_entries, u_int64_t * nb_created) : datah(0), mask(0), tai(0), nb_elem(0), max_nb_elem(0), _memory(system::impl::System::memory())
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Hash16.hpp:125:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (tai_Hash16 > 32) { throw system::Exception ("Hash16: max size for this hash is 2^32, but ask for %d", tai_Hash16); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IterableHelpers.hpp:95:53: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IterableAdaptor : public Iterable<T2>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:64:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (_filename, "rb");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:74:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (filename, "rb");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:99:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (it._filename, "rb");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:147:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* _file;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:162:102: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class IterableFile : public tools::collections::Iterable<Item>, public virtual system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:175:14: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (!system::impl::System::file().doesExist(filename))
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:177:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
auto _file2 = system::impl::System::file().newFile (filename, "wb");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:195:90: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DEBUG_ITERATORFILE(std::cout << "IteratorFile::getNbItems called (file size: "<< system::impl::System::file().getSize(_filename) << "), returning " << system::impl::System::file().getSize(_filename) / sizeof(Item) << std::endl;)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:195:160: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
DEBUG_ITERATORFILE(std::cout << "IteratorFile::getNbItems called (file size: "<< system::impl::System::file().getSize(_filename) << "), returning " << system::impl::System::file().getSize(_filename) / sizeof(Item) << std::endl;)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:196:16: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return system::impl::System::file().getSize(_filename) / sizeof(Item); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:216:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (_filename, "rb");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:226:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* _file;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:354:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (_filename, "rb");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:363:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (filename, "rb");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:388:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (it._filename, "rb");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:446:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* _file;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:482:104: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class IterableGzFile : public tools::collections::Iterable<Item>, public virtual system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:499:48: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int64_t estimateNbItems () { return 3* (system::impl::System::file().getSize(_filename) / sizeof(Item)); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:508:117: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class IterableCountCompressedFile : public tools::collections::Iterable<Item>, public virtual system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:525:48: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int64_t estimateNbItems () { return 2* (system::impl::System::file().getSize(_filename) / sizeof(Item)); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:57:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class MapMPHF : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/OAHash.hpp:70:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (hash_size == 0) { throw system::Exception ("empty OAHash allocated"); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/OAHash.hpp:210:55: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (_ref.hash_size > (1ULL<<32)) { throw system::Exception ("OAHash::sort too many items..."); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/OAHash.hpp:272:46: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (exceptionOnBadKey) { throw system::Exception ("OAHash: max rehashes reached: %lld (notify a developer)", hash_size); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:430:2: [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 (_qualseq, _sequence->getQuality().c_str()); // copy the qual sequence of this read in _qualseq
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:453:2: [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(_bufferQuals + _bufferQuals_idx, _qualseq);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:2426:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
} catch (system::Exception& e) {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:42:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.hpp:43:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:78:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class ICommand : virtual public system::ISmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:137:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IDispatcher : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:237:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
virtual system::ISynchronizer* newSynchro () = 0;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:262:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* synchro = newSynchro();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:291:96: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item, typename Functor> class IteratorCommand : public ICommand, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:300:61: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
IteratorCommand (Iterator<Item>* it, Functor*& fct, system::ISynchronizer& synchro, size_t groupSize, bool deleteSynchro)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:336:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer& _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/api/IObserver.hpp:62:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class EventInfo : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/api/Iterator.hpp:117:47: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class Iterator : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/api/Iterator.hpp:240:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IteratorListener : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:26:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:37:53: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class CommandStartSynchro : public ICommand, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:41:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CommandStartSynchro (ICommand* ref, system::ISynchronizer* synchro) : _ref(0), _synchro(synchro) { setRef(ref); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:60:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:64:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class SynchronizerNull : public system::ISynchronizer, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:64:63: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class SynchronizerNull : public system::ISynchronizer, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:104:1: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* SerialDispatcher::newSynchro ()
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:119:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (_nbUnits==0) { _nbUnits = system::impl::System::info().getNbCores(); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:134:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IThreadGroup* threadGroup = system::impl::ThreadGroup::create ();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:134:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IThreadGroup* threadGroup = system::impl::ThreadGroup::create ();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:161:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::ThreadGroup::destroy (threadGroup);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:177:1: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* Dispatcher::newSynchro ()
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:179:12: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return system::impl::System::thread().newSynchronizer();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:190:1: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IThread* Dispatcher::newThread (ICommand* command)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:192:12: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return system::impl::System::thread().newThread (mainloop, command);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:222:12: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (system::Exception& e)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.hpp:73:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* newSynchro ();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.hpp:120:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* newSynchro ();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/designpattern/impl/Command.hpp:123:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IThread* newThread (ICommand* command);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/Integer.hpp:479:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Failure because of unhandled kmer size %d", kmerSize);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:144:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
u_int64_t toInt () const { throw system::Exception ("LargeInt<%d> no support of toInt", precision); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Enums.hpp:50:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
else { throw system::Exception ("bad bank convert kind '%s'", s.c_str()); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Enums.hpp:63:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("bad bank convert kind %d", kind);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Enums.hpp:93:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
else { throw system::Exception ("bad Bloom kind '%s'", s.c_str()); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Enums.hpp:108:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("bad Bloom kind %d", kind);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Enums.hpp:135:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
else { throw system::Exception ("bad debloom kind '%s'", s.c_str()); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Enums.hpp:149:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("bad debloom kind %d", kind);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Enums.hpp:173:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
else { throw system::Exception ("bad debloom impl '%s'", s.c_str()); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Enums.hpp:186:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("bad debloom impl %d", kind);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Enums.hpp:208:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
else { throw system::Exception ("bad branching kind '%s'", s.c_str()); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Enums.hpp:220:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("bad branching kind %d", kind);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Enums.hpp:255:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
else { throw system::Exception ("bad kmer solidity kind '%s'", s.c_str()); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Enums.hpp:272:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("bad kmer solidity kind %d", kind);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Enums.hpp:297:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
else { throw system::Exception ("bad traversal kind '%s'", s.c_str()); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Enums.hpp:310:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("bad traversal kind %d", kind);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp:60:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IHistogram : virtual public system::ISmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/IOptionsParser.hpp:80:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IOptionsParser : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/IProperty.hpp:54:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IProperty : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/IProperty.hpp:119:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IPropertiesVisitor : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/IProperty.hpp:154:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IProperties : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Range.hpp:46:74: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class T> class Range : public collections::Iterable<T>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Vector.hpp:47:44: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template<typename T> class Vector : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp:26:19: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define DEBUG(a) printf a
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:55:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class Algorithm : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:170:16: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (system::Exception& e) { std::cerr << "EXCEPTION: " << e.getMessage() << std::endl; }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp:28:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:51:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class Histogram : public IHistogram, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:155:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class HistogramNull : public IHistogram, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:207:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class HistogramCache : public IHistogram, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:214:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
HistogramCache (IHistogram* ref, system::ISynchronizer* synchro=0)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:220:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::LocalSynchronizer ls (_synchro);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:285:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:54:16: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
static system::SmartObject singleton;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:61:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "name", "%s", system::impl::System::info().getHostName().c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:62:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "nb_cores", "%d", system::impl::System::info().getNbCores());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:63:64: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "memory", "%.1f", (double)system::impl::System::info().getMemoryPhysicalTotal() / (double)system::GBYTE);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:63:128: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "memory", "%.1f", (double)system::impl::System::info().getMemoryPhysicalTotal() / (double)system::GBYTE);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:64:64: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "disk_current_dir", "%.1f", (double)system::impl::System::file().getAvailableSpace(system::impl::System::file().getCurrentDirectory()) / (double)system::MBYTE);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:64:111: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "disk_current_dir", "%.1f", (double)system::impl::System::file().getAvailableSpace(system::impl::System::file().getCurrentDirectory()) / (double)system::MBYTE);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:64:173: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "disk_current_dir", "%.1f", (double)system::impl::System::file().getAvailableSpace(system::impl::System::file().getCurrentDirectory()) / (double)system::MBYTE);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:65:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "max_file_nb", "%lld", system::impl::System::file().getMaxFilesNumber());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/HostInfo.hpp:66:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "pid", "%d", system::impl::System::thread().getProcess());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp:55:16: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
static system::SmartObject singleton;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp:62:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "version", "%s", system::impl::System::info().getVersion().c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp:64:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "build_date", "%s", system::impl::System::info().getBuildDate().c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp:65:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "build_system", "%s", system::impl::System::info().getBuildSystem().c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp:66:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "build_compiler", "%s", system::impl::System::info().getBuildCompiler().c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp:82:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::info().getVersion().c_str(),
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp:83:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::info().getBuildDate().c_str(),
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp:84:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::info().getBuildSystem().c_str(),
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp:85:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::info().getBuildCompiler().c_str(),
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp:32:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp:33:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Pool.hpp:108:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Internal memory allocator is full!");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Pool.hpp:365:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Pool reserve() failed for %lld (+ %lld extra for %d cores) bytes",
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Pool.hpp:379:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Pool allocation failed for %lld bytes (%s). Current usage is %lld and capacity is %lld",
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Pool.hpp:387:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Pool allocation failed for %lld bytes (%s), mainbuffer is null?. Current usage is %lld and capacity is %lld",
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Pool.hpp:417:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
setSynchro (system::impl::System::thread().newSynchronizer());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Pool.hpp:426:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* getSynchro() { return _synchro; }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Pool.hpp:435:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Pool.hpp:436:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void setSynchro (system::ISynchronizer* synchro) { SP_SETATTR(synchro); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:31:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:359:5: [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 (buffer, tmp);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:154:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ITime::Value heure_debut;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:155:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ITime::Value heure_actuelle;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:182:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISystemInfo::CpuInfo* _cpuinfo;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:183:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void setCpuInfo (system::ISystemInfo::CpuInfo* cpuinfo) { SP_SETATTR(cpuinfo); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:239:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
ProgressSynchro (dp::IteratorListener* ref, system::ISynchronizer* synchro)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:247:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void init () { system::LocalSynchronizer l(_synchro); ProgressProxy::init(); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:250:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void finish () { system::LocalSynchronizer l(_synchro); ProgressProxy::finish (); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:253:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void inc (u_int64_t ntasks_done) { system::LocalSynchronizer l(_synchro); ProgressProxy::inc (ntasks_done); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:256:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void set (u_int64_t ntasks_done) { system::LocalSynchronizer l(_synchro); ProgressProxy::set (ntasks_done); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:259:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void reset (u_int64_t ntasks) { system::LocalSynchronizer l(_synchro); ProgressProxy::reset(ntasks); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:262:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void setMessage (const std::string& msg) { system::LocalSynchronizer l(_synchro); ProgressProxy::setMessage (msg); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:266:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:267:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void setSynchro (system::ISynchronizer* synchro) { SP_SETATTR(synchro); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:31:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:189:9: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf (buffer, sizeof(buffer), format, ap);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:960:9: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf (buffer, sizeof(buffer), format, ap);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Stringify.hpp:99:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw gatb::core::system::Exception("Stringify::format could not allocate memory");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp:27:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp:28:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp:42:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeInfo::TimeInfo () : _time(system::impl::System::time())
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp:55:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeInfo::TimeInfo (system::ITime& aTime) : _time(aTime)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.hpp:72:25: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class TimeInfo : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.hpp:84:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeInfo (system::ITime& aTime);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.hpp:129:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ITime& _time;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/TimeInfo.hpp:132:14: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
gatb::core::system::ISynchronizer* _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Tool.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Tool.cpp:31:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Tool.hpp:79:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class Tool : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp:29:19: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define DEBUG(a) printf a
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/api/ICell.hpp:46:30: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class ICell : public virtual system::ISmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Cell.hpp:43:43: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class Cell : public virtual ICell, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp:56:105: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class CollectionFile : public collections::impl::CollectionAbstract<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp:76:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
gatb::core::system::impl::System::file().remove (_name);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp:77:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
gatb::core::system::impl::System::file().remove (_propertiesName);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp:142:107: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class CollectionGzFile : public collections::impl::CollectionAbstract<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp:158:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void remove () { gatb::core::system::impl::System::file().remove (_name); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp:167:110: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class CollectionCountFile : public collections::impl::CollectionAbstract<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp:182:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void remove () { gatb::core::system::impl::System::file().remove (_name); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:57:77: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class BagHDF5 : public collections::Bag<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:67:65: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
BagHDF5 (hid_t datasetId, hid_t typeId, u_int64_t& nbItems, system::ISynchronizer* synchro)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:85:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::LocalSynchronizer localsynchro (_synchro);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:94:46: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Dset_extent), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:101:46: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Sselect_hyperslab), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:105:46: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Dwrite), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:115:46: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Sclose), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:128:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:136:87: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class IterableHDF5 : public collections::Iterable<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:141:74: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
IterableHDF5 (hid_t datasetId, hid_t typeId, u_int64_t& nbItems, system::ISynchronizer* synchro)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:180:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:191:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::LocalSynchronizer localsynchro (_synchro);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:198:46: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Sselect_hyperslab), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:202:46: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Dread), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:207:46: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Sclose), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:341:105: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class CollectionHDF5 : public collections::impl::CollectionAbstract<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:346:64: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CollectionHDF5 (hid_t fileId, const std::string& filename, system::ISynchronizer* synchro)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:351:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::LocalSynchronizer localsynchro (synchro);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:65:64: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> struct CollectionDataHDF5Patch : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:70:73: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CollectionDataHDF5Patch (hid_t fileId, const std::string& filename, system::ISynchronizer* synchro, int compress)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:97:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::LocalSynchronizer localsynchro (_synchro);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:120:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::LocalSynchronizer localsynchro (_synchro);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:137:46: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Aread), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:144:46: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Dvlen_reclaim), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:192:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Pset_chunk), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:217:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::LocalSynchronizer localsynchro (_synchro);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:227:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:244:82: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class BagHDF5Patch : public collections::Bag<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:270:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::LocalSynchronizer localsynchro (_common->_synchro);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:282:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Dset_extent), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:289:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Sselect_hyperslab), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:293:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Dwrite), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:326:93: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class IterableHDF5Patch : public collections::Iterable<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:379:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::LocalSynchronizer localsynchro (_common->_synchro);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:387:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Sselect_hyperslab), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:391:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Dread), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:396:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Sclose), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:534:110: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class CollectionHDF5Patch : public collections::impl::CollectionAbstract<Item>, public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:539:65: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CollectionHDF5Patch (hid_t fileId, const std::string& name, system::ISynchronizer* synchro, int compressLevel)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:542:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::LocalSynchronizer localsynchro (synchro);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:325:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_files[fileId] = system::impl::System::file().newFile (_path, ss.str(), mode);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:326:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_synchros[fileId] = system::impl::System::thread().newSynchronizer();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:335:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().mkdir(_path, 0755);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:342:16: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_files[ii] = system::impl::System::file().newFile (_path, ss.str(), mode);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:343:19: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_synchros[ii] = system::impl::System::thread().newSynchronizer();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:457:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().remove(ss.str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:459:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().rmdir(_path);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:203:88: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
virtual void addProperty (const std::string& key, const std::string value) { throw system::ExceptionNotImplemented (); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:210:83: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
virtual std::string getProperty (const std::string& key) { return "?"; throw system::ExceptionNotImplemented (); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:213:88: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
virtual void setProperty (const std::string& key, const std::string value) { throw system::ExceptionNotImplemented (); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:285:14: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
std::vector<system::IFile* > _files;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:286:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
std::vector <system::ISynchronizer*> _synchros;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:385:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:408:64: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
PartitionCache (Partition<Type>& ref, size_t nbItemsCache, system::ISynchronizer* synchro=0);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:435:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:436:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
std::vector <system::ISynchronizer*> _synchros;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:447:92: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
PartitionCacheSorted (Partition<Type>& ref, size_t nbItemsCache, u_int32_t max_memory, system::ISynchronizer* synchro=0);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:474:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:478:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
std::vector <system::ISynchronizer*> _synchros;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:479:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
std::vector <system::ISynchronizer*> _outsynchros;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:601:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class StorageFactory : public system::SmartPointer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:653:85: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CollectionNode<Type>* createCollection (ICell* parent, const std::string& name, system::ISynchronizer* synchro);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:58:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (!system::impl::System::file().isFolderEndingWith(prefix,"_gatb"))
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:62:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if(!system::impl::System::file().doesExistDirectory(folder)){
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:63:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int ok = system::impl::System::file().mkdir(folder, 0755);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:65:124: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
std::cout << "Error: can't create output directory (" << folder<< ")\n" << " debug, doesexist:" << system::impl::System::file().doesExistDirectory(folder);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:100:17: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().rmdir(folder); // hack to remove the trashme folers. I'd have liked to make that call in remove() but for some reason remove() isn't called
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:220:14: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (!system::impl::System::file().isFolderEndingWith(storage_prefix,"_gatb"))
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:238:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
for (auto filename : system::impl::System::file().listdir(file_folder))
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:256:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
for (auto filename : system::impl::System::file().listdir(file_folder))
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:263:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().remove(file_folder + "/" + filename);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:280:92: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
static CollectionNode<Type>* createCollection (ICell* parent, const std::string& name, system::ISynchronizer* synchro)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:288:14: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (!system::impl::System::file().isFolderEndingWith(storage_prefix,"_gatb"))
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:292:7: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if(!system::impl::System::file().doesExistDirectory(folder)){
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:293:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int ok = system::impl::System::file().mkdir(folder, 0755);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:295:116: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
std::cout << "Error: can't create output directory (" << folder<< ")\n" << " debug, doesexist:" << system::impl::System::file().doesExistDirectory(folder);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:351:92: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
static CollectionNode<Type>* createCollection (ICell* parent, const std::string& name, system::ISynchronizer* synchro)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:406:92: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
static CollectionNode<Type>* createCollection (ICell* parent, const std::string& name, system::ISynchronizer* synchro)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:123:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (nb==0) { throw system::Exception ("Partition '%s' has 0 items", name.c_str()); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:141:92: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
static CollectionNode<Type>* createCollection (ICell* parent, const std::string& name, system::ISynchronizer* synchro)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:163:16: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
static system::ISynchronizer* singleton()
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:170:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
GlobalSynchro () { synchro = system::impl::System::thread().newSynchronizer(); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:172:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* synchro;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:199:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (deleteIfExist) { system::impl::System::file().remove (getActualName()); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:202:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
bool exists = system::impl::System::file().doesExist(getActualName());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:229:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().remove (getActualName());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:340:58: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Aread), status %d key", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:347:58: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (status < 0) { throw gatb::core::system::Exception ("HDF5 error (H5Dvlen_reclaim), status %d", status); }
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench1.cpp:43:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench1.cpp:44:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench1.cpp:357:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_bagfile.cpp:50:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_bagfile.cpp:51:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_bloom.cpp:59:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_bloom.cpp:60:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_bloom.cpp:272:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_graph.cpp:54:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_graph.cpp:55:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_minim.cpp:52:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_minim.cpp:53:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_mphf.cpp:51:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_mphf.cpp:52:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:38:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:39:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:340:75: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CPPUNIT_ASSERT_THROW (BankFasta::Iterator it(bankKO), gatb::core::system::Exception);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:40:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:41:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestSequence.cpp:32:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestSequence.cpp:33:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bcalm/TestBcalm.cpp:46:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bcalm/TestBcalm.cpp:47:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:67:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:68:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:1272:13: [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(bigseq,sequence);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp:68:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp:69:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestSimplifications.cpp:68:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestSimplifications.cpp:69:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestSimplificationsUnitigs.cpp:68:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestSimplificationsUnitigs.cpp:69:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestDSK.cpp:48:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestDSK.cpp:49:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestDebloom.cpp:38:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestDebloom.cpp:39:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestKmer.cpp:42:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestKmer.cpp:43:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestKmer.cpp:370:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestKmerBank.cpp:33:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestKmerBank.cpp:34:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestMPHF.cpp:40:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestMPHF.cpp:41:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp:32:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp:33:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp:212:77: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CPPUNIT_ASSERT_THROW (p2 = mem.malloc (KBYTE+1), gatb::core::system::Exception);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp:577:79: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CPPUNIT_ASSERT_THROW (TimeSystem s (ITime::UNDEFINED), gatb::core::system::Exception);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp:734:25: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw core::system::Exception ("something wrong");
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp:736:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (core::system::Exception& e)
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp:767:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (core::system::Exception& e)
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/collections/TestBag.cpp:44:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/collections/TestBag.cpp:45:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/collections/TestCollection.cpp:50:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/collections/TestCollection.cpp:51:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/collections/TestMap.cpp:47:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/collections/TestMap.cpp:48:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/collections/TestMap.cpp:91:62: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CPPUNIT_ASSERT_THROW (hash.increment (badKey), core::system::Exception);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/misc/TestMisc.cpp:39:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/misc/TestMisc.cpp:40:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp:49:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp:50:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/tools/BankDownload.cpp:71:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int res1 = system (ss1.str().c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/tools/BankDownload.cpp:105:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int res2 = system (ss2.str().c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/tools/BankDownload.cpp:113:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int res3 = system (ss3.str().c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/tools/BankDownload.cpp:156:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system (Stringify::format ("mv %s %s/", finalBankFile.c_str(), options->getStr(STR_URI_OUTPUT_DIR).c_str()).c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/tools/BankDownload.cpp:184:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/gatb-core-1.4.2+dfsg/gatb-core/tools/ClearCache.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/tools/KmerChecksum.cpp:28:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/gatb-core-1.4.2+dfsg/gatb-core/tools/dbgh5.cpp:127:6: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
::system (cmd.str().c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/tools/leon.cpp:52:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankRandom.cpp:91:5: [3] (random) srand:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
srand (time(NULL));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:101:22: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
if ( (dir = getenv ("TMPDIR")) != 0) { return dir; }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:102:22: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
else if ( (dir = getenv ("TMP")) != 0) { return dir; }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:103:22: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
else if ( (dir = getenv ("TEMPDIR")) != 0) { return dir; }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:167:9: [3] (buffer) realpath:
This function does not protect against buffer overflows, and some
implementations can overflow internally (CWE-120/CWE-785!). Ensure that the
destination buffer is at least of size MAXPATHLEN, andto protect against
implementation problems, the input argument should also be checked to
ensure it is no larger than MAXPATHLEN.
if (realpath (file.c_str(), buf) != 0)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.hpp:71:54: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
std::string getHomeDirectory () const { return getenv("HOME") ? getenv("HOME") : "."; }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.hpp:71:71: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
std::string getHomeDirectory () const { return getenv("HOME") ? getenv("HOME") : "."; }
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_bloom.cpp:80:22: [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.
#define srandomdev() srand((unsigned) time(NULL))
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_bloom.cpp:85:11: [3] (random) random:
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.
low = random();
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_bloom.cpp:86:12: [3] (random) random:
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.
high = random();
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_bloom.cpp:129:23: [3] (random) random:
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.
kmer_type start = random();
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:94:26: [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.
void setUp () { srand (time(NULL)); }
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:80:26: [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.
void setUp () { srand (time(NULL)); }
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestSequence.cpp:58:26: [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.
void setUp () { srand (time(NULL)); }
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/main.cpp:76:9: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
if (getenv ("CPPUNIT_VERBOSE")) {
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp:87:26: [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.
void setUp () { srand (time(NULL)); }
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/collections/TestContainer.cpp:59:26: [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.
void setUp () { srand (time(NULL)); }
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/collections/TestIterable.cpp:48:26: [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.
void setUp () { srand (time(NULL)); }
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/collections/TestMap.cpp:71:26: [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.
void setUp () { srand (time(NULL)); }
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/misc/TestMisc.cpp:74:26: [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.
void setUp () { srand (time(NULL)); }
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank10.cpp:51:34: [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).
IBank* inputBank = Bank::open (options->getStr(STR_URI_INPUT));
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank12.cpp:47:22: [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 (options->getStr(STR_URI_SEQ_IDS).c_str(), "r");
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank12.cpp:50:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[128];
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank12.cpp:51:78: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
while (fgets (buffer, sizeof(buffer), file)) { indexes.insert (atoi(buffer)); }
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank12.cpp:62:34: [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).
IBank* inputBank = Bank::open (options->getStr(STR_URI_INPUT));
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank13.cpp:43:31: [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).
IBank* inBank = Bank::open (options->getStr(STR_URI_INPUT));
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank14.cpp:33:34: [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).
IBank* inputBank = Bank::open (options->getStr(STR_URI_INPUT));
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank15.cpp:27:25: [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).
IBank* bank = Bank::open (filename);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank16.cpp:37:29: [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).
IBank* bank = Bank::open (filename);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank18.cpp:41:30: [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).
IBank* bank1 = Bank::open (options->getStr(STR_BANK1)); LOCAL (bank1);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank18.cpp:42:30: [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).
IBank* bank2 = Bank::open (options->getStr(STR_BANK2)); LOCAL (bank2);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank19.cpp:33:34: [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).
IBank* inputBank = Bank::open (options->getStr(STR_URI_INPUT));
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank2.cpp:29:34: [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).
IBank* inputBank = Bank::open (argv[1]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank20.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).
dump (Bank::open (options->getStr(STR_URI_INPUT)));
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank21.cpp:47:32: [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).
IBank* fasBank = Bank::open (argv[1]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank21.cpp:53:33: [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).
IBank* leonBank = Bank::open (argv[2]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank22.cpp:25:24: [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).
IBank* inBank = Bank::open (argv[1]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank22.cpp:38:14: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int limit = atoi(argv[3]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank23.cpp:27:25: [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).
IBank* bank = Bank::open (filename);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank24.cpp:53:30: [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).
IBank* inputBank = Bank::open (argv[1]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank25.cpp:44:32: [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).
IBank* fasBank = Bank::open (argv[1]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank25.cpp:49:33: [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).
IBank* leonBank = Bank::open (argv[2]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank26.cpp:32:34: [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).
IBank* inputBank = Bank::open (argv[1]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank27.cpp:40:34: [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).
IBank* inputBank = Bank::open (options->getStr(STR_URI_INPUT));
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank28.cpp:39:34: [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).
IBank* inputBank = Bank::open (options->getStr(STR_URI_INPUT));
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank3.cpp:45:30: [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).
IBank* inputBank = Bank::open (argv[1]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank4.cpp:34:34: [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).
IBank* inputBank = Bank::open (argv[1]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank5.cpp:29:34: [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).
IBank* inputBank = Bank::open (argv[1]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank6.cpp:39:40: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
size_t dataLineSize = argc >= 3 ? atoi(argv[2]) : 60;
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank6.cpp:48:17: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int m = atoi (argv[3]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank6.cpp:54:43: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
u_int64_t nbSequences = (argc >= 5 ? atol (argv[4]) : ~0);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank7.cpp:42:34: [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).
IBank* inputBank = Bank::open (argv[1]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank7.cpp:46:21: [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).
threshold = atoi (argv[2]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank8.cpp:39:34: [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).
IBank* inputBank = Bank::open (argv[1]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank8.cpp:55:27: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (argc >= 4 && atoi(argv[3])==1)
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank9.cpp:49:34: [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).
IBank* inputBank = Bank::open (argv[1]);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/bank/bank9.cpp:56:34: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int modulo = argc >= 4 ? atoi (argv[3]) : 1;
data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn22.cpp:59:34: [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).
IBank* ibank = Bank::open (graph.getInfo().getStr("bank_uri"));
data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn3.cpp:27:44: [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).
Graph graph = Graph::create (Bank::open(argv[1]), "-abundance-min %d", 5);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer11.cpp:51:27: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
size_t kmerSize = atol (storage->root().getProperty("kmer_size").c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer11.cpp:61:28: [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* outputFile = fopen (outputUri.c_str(), "w");
data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer17.cpp:122:23: [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).
IBank* bank = Bank::open (bankFilename);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer4.cpp:44:29: [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).
IBank* bank = Bank::open (options->getStr(STR_URI_INPUT));
data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer5.cpp:63:29: [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).
IBank* bank = Bank::open (bankFilename);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer5.cpp:131:28: [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* output = fopen (outputFilename.c_str(), "w");
data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer7.cpp:53:29: [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).
IBank* bank = Bank::open (options->getStr(STR_URI_INPUT));
data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer8.cpp:104:29: [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).
IBank* bank = Bank::open (options->getStr(STR_URI_INPUT));
data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer9.cpp:30:29: [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).
IBank* bank = Bank::open (options->getStr(STR_URI_INPUT));
data/gatb-core-1.4.2+dfsg/gatb-core/examples/protos/MicroSNP.cpp:25:23: [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).
FILE * snps = fopen ("snps","w");
data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading1.cpp:24:34: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
size_t nbCores = (argc >=2 ? atoi(argv[1]) : 0);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading2.cpp:19:34: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
size_t nbCores = (argc >=2 ? atoi(argv[1]) : 0);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading3.cpp:37:34: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
size_t nbCores = (argc >=2 ? atoi(argv[1]) : 0);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading4.cpp:20:34: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
size_t nbCores = (argc >=2 ? atoi(argv[1]) : 0);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading5.cpp:19:34: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
size_t nbCores = (argc >=2 ? atoi(argv[1]) : 0);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading6.cpp:32:34: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
size_t nbCores = (argc >=3 ? atoi(argv[2]) : 0);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading7.cpp:30:34: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
size_t nbCores = (argc >=2 ? atoi(argv[1]) : 0);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/tools/multithreading8.cpp:32:34: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
size_t nbCores = (argc >=4 ? atoi(argv[3]) : 0);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/Bank.hpp:87:19: [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).
static IBank* open (const std::string& uri) { return singleton()._open_ (uri); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/Bank.hpp:91:79: [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).
static size_t getCompositionNb (const std::string& uri) { IBank* bank = open (uri); LOCAL (bank); return bank->getCompositionNb(); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:56:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[256];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:81:47: [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).
BankComposite::addBank (Bank::open(bankUri));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:109:39: [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).
BankComposite::addBank (Bank::open(*it));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:128:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* file = fopen (uri.c_str(), "r");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:131:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[256];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:198:24: [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).
result = Bank::open(bankUri);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:330:36: [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).
banks.push_back (Bank::open (names[i]));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:184:40: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (binary_read_file == 0) { open (true); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:209:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buffer+cpt_buffer,&readlen,sizeof(int));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:268:18: [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 BankBinary::open (bool write)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:270:24: [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).
binary_read_file = fopen (_filename.c_str(), write?"wb":"rb");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:348:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* file = fopen (uri.c_str(), "rb");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:401:28: [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).
binary_read_file = fopen (_ref._filename.c_str(), "rb");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:467:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy (&len, _bufferData->getBuffer() + cpt_buffer, sizeof(int)); // read len
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:502:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* file = fopen (_ref._filename.c_str(), "rb");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.cpp:527:17: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy (&readlen, loop, sizeof(int));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankBinary.hpp:184:10: [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).
void open (bool write);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp:235:25: [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).
_insertHandle = fopen (_filenames[_filenames.size()-1].c_str(), "w");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp:272:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[4*1024];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp:457:10: [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 (s->string + s->length, bf->buffer + bf->buffer_start, i - bf->buffer_start);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp:790:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[256];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:501:42: [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).
uint32_t abundance = atoi(comment.c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:758:23: [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).
IBank *in = Bank::open (prefix + ".glue");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.cpp:766:29: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
nb_glue_sequences = atol(bcalmGroup.getProperty ("nb_sequences_in_glue").c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.hpp:61:29: [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).
_insertHandle = fopen (filename.c_str(), "w");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/logging.cpp:22:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmp[128];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/unionFind.hpp:157:18: [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).
dumpfile.open (file);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:780:77: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
_state = (GraphTemplate<Node, Edge, GraphDataVariant_t>::StateMask) atol (getGroup().getProperty ("state").c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:781:37: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
_kmerSize = atol (getGroup().getProperty ("kmer_size").c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:875:88: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
_state = (typename GraphTemplate<Node, Edge, GraphDataVariant>::StateMask) atol (getGroup().getProperty ("state").c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:876:41: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
_kmerSize = atol (getGroup().getProperty ("kmer_size").c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:879:29: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
_kmerSize = atol (getGroup("dsk").getProperty ("kmer_size").c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Graph.cpp:906:35: [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).
bank::IBank* bank = Bank::open (params->getStr(STR_URI_INPUT));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:296:18: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
nb_unitigs = atol (BaseGraph::getGroup().getProperty ("nb_unitigs").c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:325:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
uint64_t unitig = atoi(tok.substr(tok.find_last_of(':')+1).c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:655:6: [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).
gfi.open(gfa_filename.c_str(), std::ifstream::in);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:680:15: [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).
kmerSize = atoi(line_tokens[2].c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:694:25: [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).
uint32_t unitig_id = atoi(tokens[1].c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:716:34: [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).
uint64_t unitig_id = atoi(tokens[1].c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:763:6: [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).
gfi.open(gfa_filename.c_str(), std::ifstream::in);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:769:39: [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).
uint64_t from_unitig_id = atoi(tokens[1].c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:770:37: [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).
uint64_t to_unitig_id = atoi(tokens[3].c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:896:82: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
BaseGraph::_state = (typename GraphUnitigsTemplate<span>::StateMask) atol (BaseGraph::getGroup().getProperty ("state").c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:898:33: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
BaseGraph::_kmerSize = atol (BaseGraph::getGroup().getProperty ("kmer_size").c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:901:40: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
BaseGraph::_kmerSize = atol (BaseGraph::getGroup("dsk").getProperty ("kmer_size").c_str());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:936:35: [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).
bank::IBank* bank = Bank::open (params->getStr(STR_URI_INPUT));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp:2083:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char res[n];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:401:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[128];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:1305:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[128];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp:1628:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[128];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:113:25: [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).
FILE * histo2Dfile = fopen (_histo2Dfilename.c_str(),"w");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/CountProcessorHistogram.hpp:132:25: [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).
FILE * histo1Dfile = fopen (_histo1Dfilename.c_str(),"w");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp:29:23: [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 const unsigned char comp_NT[4];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp:30:14: [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 const char bin2NT[4];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp:31:14: [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 const char binrev[4];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp:32:23: [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 const unsigned char revcomp_4NT[256];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp:38:16: [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.
const unsigned char comp_NT[4] = { 2,3,0,1 };
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp:39:7: [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.
const char bin2NT[4] = {'A','C','T','G'};
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp:40:7: [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.
const char binrev[4] = {2,3,0,1};
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/ModelData.cpp:43:16: [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.
const unsigned char revcomp_4NT[256] = {
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:496:42: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (_bank == 0) { setBank (Bank::open (getInput()->getStr(STR_URI_INPUT))); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/Exception.hpp:85:10: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[256];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/api/IMemory.hpp:103:19: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
virtual void* memcpy (void* dest, const void* src, size_t n) = 0;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:67:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char path[1000];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:165:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf [4*1024];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:200:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* fp = fopen (path.c_str(), "rb");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:63:42: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
_handle = _isStdout ? stdout : fopen (path, mode);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp:140:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4*1024];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp:161:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4*1024];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp:136:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4*1024];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp:157:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4*1024];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/MemoryCommon.hpp:348:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
void* memcpy (void* dest, const void* src, size_t n) { return ::memcpy (dest, src, n); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/MemoryCommon.hpp:348:72: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
void* memcpy (void* dest, const void* src, size_t n) { return ::memcpy (dest, src, n); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/MemoryCommon.hpp:391:12: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
void* memcpy (void* dest, const void* src, size_t n) { return _ope.memcpy (dest, src, n); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/MemoryCommon.hpp:391:76: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
void* memcpy (void* dest, const void* src, size_t n) { return _ope.memcpy (dest, src, n); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:131:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* file = fopen ("/proc/cpuinfo", "r");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:134:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[256];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:149:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char hostname[1024];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:191:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* file = fopen("/proc/self/status", "r");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:194:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[128];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:204:26: [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).
result = atoi(loop);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:277:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char hostname[1024];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:380:5: [2] (buffer) TCHAR:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
TCHAR infoBuf[1024];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/TimeCommon.hpp:64:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[256];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:211:44: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
system::impl::System::memory().memcpy (_sharedBuffer + *_idxShared, this->_items, this->_idx*sizeof(Item));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:271:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(_bufferOut+_idx,&abundance, 1 ); _idx+= 1;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:272:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(_bufferOut+_idx,&elem, _size_item ); _idx+= _size_item;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BagPartition.hpp:82:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char filename[128]; snprintf (filename, sizeof(filename), _uriFormat.c_str(), idx);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:309:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* file = fopen(filename,"wb");
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:1282:49: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
return createBloom<T> (kind, (u_int64_t)atol (sizeStr.c_str()), (size_t)atol (nbHashStr.c_str()), atol (kmerSizeStr.c_str()));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:1282:81: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
return createBloom<T> (kind, (u_int64_t)atol (sizeStr.c_str()), (size_t)atol (nbHashStr.c_str()), atol (kmerSizeStr.c_str()));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:1282:107: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
return createBloom<T> (kind, (u_int64_t)atol (sizeStr.c_str()), (size_t)atol (nbHashStr.c_str()), atol (kmerSizeStr.c_str()));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:69:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(reinterpret_cast<char*>(&tmp), from, 8);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:464:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy (_buffer,_buffer + _idx,_cpt_buffer ); _idx = 0;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:30:1: [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 bin2NTrev[4] = {'T','G','A','C'};
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:1307:2: [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 outbuffer[32768];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:397:22: [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).
setInputBank (Bank::open(_inputFilename));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:600:2: [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 outbuffer[32768];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:2063:24: [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).
originalBank = Bank::open(originalFilename);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:2066:19: [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).
newBank = Bank::open(_outputFile->getPath());
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:124:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char buffer[256];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:685:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char seq[sizeKmer+1];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/LargeInt.hpp:686:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char bin2NT[4] = {'A','C','T','G'};
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/NativeInt128.hpp:134:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char seq[65];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/NativeInt128.hpp:135:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char bin2NT[4] = {'A','C','T','G'};
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:110:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char seq[33];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:111:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char bin2NT[4] = {'A','C','T','G'};
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:132:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char seq[33];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/math/NativeInt64.hpp:133:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char bin2NT[4] = {'A','C','T','G'};
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/IProperty.hpp:89:48: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
long getInt () { return atol (value.c_str()); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Vector.hpp:132:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy (_buffer, buffer, _size*sizeof(char));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp:150:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer [128];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:349:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmp[128];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:120:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[512];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:186:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[PROP_BUFFER_SIZE];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:437:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[64];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:457:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[64];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:479:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[256];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:956:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[PROP_BUFFER_SIZE];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:1005:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[1024];
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp:105:17: [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).
myfile2.open (_propertiesName);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:268:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy (_data, it._data, _blockSize*sizeof(Item));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp:461:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy (_data, it._data, _blockSize*sizeof(Item));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:133:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[bufferSize]; // data buffer
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:576:2: [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(_buffers[file_id] + _buffers_idx[file_id] , superk,nb_bytes);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:141:24: [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).
myfile.open (filename);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:187:55: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (nbPartStr.empty()==false) { result = atoi (nbPartStr.c_str()); }
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench1.cpp:310:23: [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).
size_t kmerSize = atoi(argv[1]);
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_bloom.cpp:241:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[250];
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_bloom.cpp:258:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(temp,"expected theoretical with %i hash",ideal_nb_hash);
data/gatb-core-1.4.2+dfsg/gatb-core/test/benchmark/bench_bloom.cpp:261:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(temp,"expected theoretical with %lli hash",nhash);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:117:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[32];
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:186:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[32];
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:224:29: [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).
IBank* bank = Bank::open(filename);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:688:29: [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).
IBank* bank = Bank::open (DBPATH(bankuri));
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:951:29: [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).
IBank* bank = Bank::open (albumFilename);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:1062:30: [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).
IBank* bank1 = Bank::open (DBPATH("sample1.fa"));
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:160:32: [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).
IBank* fasBank = Bank::open (fastqFile); //BankFasta
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:161:27: [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).
IBank* leonBank = Bank::open (leonFile); //BankLeon
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:220:27: [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).
IBank* leonBank = Bank::open (leonFile); //BankLeon
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:265:26: [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).
IBank* fasBank = Bank::open (fasPath);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:273:27: [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).
IBank* leonBank = Bank::open (leonPath);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:328:33: [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).
IBank* leonBank = Bank::open (leonFile); //BankLeon freshly created
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:329:30: [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).
IBank* leonBankRef = Bank::open (leonFileRef); //BankLeon reference
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:424:36: [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).
IBank* leonRefBank = Bank::open (leonRefFile);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestLeon.cpp:425:27: [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).
IBank* leonBank = Bank::open (leonFile);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestDSK.cpp:694:29: [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).
IBank* bank = Bank::open(filepath);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestKmer.cpp:334:32: [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).
banks.push_back (Bank::open (DBPATH("reads1.fa")));
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp:450:26: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
System::memory().memcpy (ptr2, ptr1, nb);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp:487:26: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
System::memory().memcpy (ptr2, ptr1, nb);
data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h:446:5: [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(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) );
data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h:460:5: [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(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) );
data/gatb-core-1.4.2+dfsg/gatb-core/tools/ClearCache.cpp:77:52: [2] (integer) atol:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
u_int64_t toErase = 1024 * 1024 * (argc >= 2 ? atol (argv[1]) : 0);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/debruijn/debruijn26.cpp:22:23: [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).
size_t kmerSize = strlen (seq) - 1;
data/gatb-core-1.4.2+dfsg/gatb-core/examples/kmer/kmer2.cpp:29:23: [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).
size_t kmerSize = strlen(seq);
data/gatb-core-1.4.2+dfsg/gatb-core/examples/storage/storage10.cpp:51:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read (reinterpret_cast<char*>(buffer), nbItems*sizeof(float));
data/gatb-core-1.4.2+dfsg/gatb-core/examples/storage/storage8.cpp:60:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read (reinterpret_cast<char*>(buffer), nbItems*sizeof(float));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:137:23: [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).
int len = strlen(buffer);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:144:17: [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 (strlen(buffer) > 0)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp:89:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
buffered_strings_t () : read(new variable_string_t), dummy(new variable_string_t), header(new variable_string_t), quality(new variable_string_t) {}
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp:92:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
delete read;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp:98:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
variable_string_t *read, *dummy, *header, *quality;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp:176:46: [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 (strstr (fname, "gz") == (fname + strlen (fname) - 2))
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bank/impl/BankFasta.cpp:532:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
buffered_gets (bf, bs->read, NULL, true, true);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/bcalm_algo.cpp:325:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)freq_order, sizeof(uint32_t) * rg);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/bcalm2/bglue_algo.hpp:114:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read(std::string &seq, std::string &comment)
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:109:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_kmerSize, sizeof(_kmerSize));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:110:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_minim_size, sizeof(_minim_size));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:111:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_repartitionType, sizeof(_repartitionType));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:112:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_minimizerType, sizeof(_minimizerType));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:113:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_max_disk_space, sizeof(_max_disk_space));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:114:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_max_memory, sizeof(_max_memory));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:115:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_nbCores, sizeof(_nbCores));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:116:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_nb_partitions_in_parallel, sizeof(_nb_partitions_in_parallel));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:117:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_abundanceUserNb, sizeof(_abundanceUserNb));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:121:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_nbCores_per_partition, sizeof(_nbCores_per_partition));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:122:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_estimateSeqNb, sizeof(_estimateSeqNb));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:123:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_estimateSeqTotalSize, sizeof(_estimateSeqTotalSize));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:124:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_estimateSeqMaxSize, sizeof(_estimateSeqMaxSize));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:125:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_available_space, sizeof(_available_space));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:126:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_volume, sizeof(_volume));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:127:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_kmersNb, sizeof(_kmersNb));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:128:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_nb_passes, sizeof(_nb_passes));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:129:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_nb_partitions, sizeof(_nb_partitions));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:130:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_nb_bits_per_kmer, sizeof(_nb_bits_per_kmer));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:131:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_nb_banks, sizeof(_nb_banks));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/Configuration.cpp:132:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_nb_cached_items_per_core_per_part, sizeof(_nb_cached_items_per_core_per_part));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:233:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_nbpart, sizeof(_nbpart));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:234:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_nb_minims, sizeof(_nb_minims));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:235:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_nbPass, sizeof(_nbPass));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:244:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)_repart_table.data(), sizeof(Value) * _nb_minims);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:246:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&hasMinimizerFrequencies, sizeof(bool));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:249:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&magic, sizeof(magic));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:256:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is2.read ((char*)_freq_order, sizeof(uint32_t)*_nb_minims);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/kmer/impl/PartiInfo.cpp:258:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is2.read ((char*)&magic, sizeof(magic));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:83:40: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int get () { return (isOpen() ? fgetc (getHandle()) : 0); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:100:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
result = strlen (tmp);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:103:89: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (result > 0) { for (char c = tmp[result-1]; c !='\n' && c!=EOF; c = fgetc (getHandle())) {} }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp:168:83: [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 ::setxattr (filename.c_str(), (string("user.") + key).c_str(), buffer, strlen(buffer), XATTR_CREATE);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp:164:83: [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 ::setxattr (filename.c_str(), (string("user.") + key).c_str(), buffer, strlen(buffer), 0, XATTR_CREATE);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:152:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
result.assign (hostname, strlen(hostname));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:201:26: [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).
result = strlen(line);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:280:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
result.assign (hostname, strlen(hostname));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:385:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
result.assign (infoBuf, strlen(infoBuf));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/collections/impl/BooPHF.hpp:173:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&m_seed), sizeof(m_seed));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/DnaCoder.cpp:1286:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
_inputStream->read(_inbuffer,_blockSize );
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:73:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read (reinterpret_cast<char*> (&data),sizeof(data));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:1069:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
tempFile.read(buffer, bufsize);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:1378:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
isInfo.read (reinterpret_cast<char*> (&infoByte),sizeof(infoByte));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:1458:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
isk.read (reinterpret_cast<char*> (&_kmerSize),sizeof(_kmerSize));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:1529:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
isH.read (reinterpret_cast<char *>(tempS), firstHeaderSize);
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:1542:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read (reinterpret_cast<char *>(_headerBlockSizes.data()), _headerBlockSizes.size()*sizeof(u_int64_t));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/compression/Leon.cpp:1563:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read (reinterpret_cast<char *>(_dnaBlockSizes.data()), _dnaBlockSizes.size()*sizeof(u_int64_t));
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/api/Data.hpp:82:60: [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).
Data (char* buffer) : encoding(ASCII) { setRef(buffer,strlen(buffer)); }
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:486:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
char* value = key + strlen (key) + 1;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:491:27: [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).
value[strlen(value)-1] = 0;
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/Property.cpp:595:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
reader.read ();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp:71:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void XmlReader::read ()
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/misc/impl/XmlReader.hpp:181:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void read ();
data/gatb-core-1.4.2+dfsg/gatb-core/src/gatb/tools/storage/impl/StorageTools.hpp:152:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read (reinterpret_cast<char*>(bloom->getArray()), bloom->getSize()*sizeof(char));
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:737:32: [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).
actualTotalSize += strlen (table[i]);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:738:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (actualMaxSize < strlen(table[i])) { actualMaxSize = strlen(table[i]); }
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:738:70: [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 (actualMaxSize < strlen(table[i])) { actualMaxSize = strlen(table[i]); }
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/bank/TestBank.cpp:751:53: [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).
CPPUNIT_ASSERT ((*it)->getDataSize() == strlen(table[idx]) );
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:183:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t seqLen = strlen (seq);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:218:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t seqLen = strlen (seq);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:531:40: [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).
CPPUNIT_ASSERT (path.rank() == strlen (seq) - kmerSize);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:729:77: [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).
CPPUNIT_ASSERT (graph.getInfo().getInt ("kmers_nb_solid") == (int) (strlen(seq) - kmerSize + 1));
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:738:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t kmerSize = strlen (sequences[0]);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:790:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t kmerSize = strlen (sequences[0]);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:848:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t kmerSize = strlen (sequences[0])-1;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:1269:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
char *bigseq= (char *)calloc(strlen(sequence)*1001,1);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:1274:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t kmerSize = strlen (sequence);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp:176:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t seqLen = strlen (seq);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/debruijn/TestDebruijnUnitigs.cpp:773:77: [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).
CPPUNIT_ASSERT (graph.getInfo().getInt ("kmers_nb_solid") == (int) (strlen(seq) - kmerSize + 1));
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestDebloom.cpp:109:82: [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).
CPPUNIT_ASSERT (sortingCount.getSolidCounts()->getNbItems() == (int64_t)(strlen(seqs[0]) - kmerSize + 1) );
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestKmer.cpp:161:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
data.set ((char*)seq, strlen(seq));
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestKmer.cpp:564:31: [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).
data.set ((char*)seq, strlen(seq));
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestMPHF.cpp:118:66: [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).
if (sortingCount.getSolidCounts()->getNbItems() != (int)(strlen(seqs[0]) - kmerSize + 1))
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestMPHF.cpp:119:132: [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).
std::cout << "problem with sortingcount nb items: " << sortingCount.getSolidCounts()->getNbItems() << " != " << (int)(strlen(seqs[0]) - kmerSize + 1) << std::endl;
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/kmer/TestMPHF.cpp:122:78: [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).
CPPUNIT_ASSERT (sortingCount.getSolidCounts()->getNbItems() == (int)(strlen(seqs[0]) - kmerSize + 1) );
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp:678:13: [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 (rand() % 10 + 1);
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp:894:50: [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).
CPPUNIT_ASSERT (writer->getSize() == strlen (info));
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/system/TestSystem.cpp:916:47: [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).
CPPUNIT_ASSERT (reader->tell() == strlen (info));
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp:378:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_nbpart2, sizeof(_nbpart));
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp:386:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_mm2, sizeof(_mm));
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp:388:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_nb_minims2, sizeof(_nb_minims));
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp:389:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char*)&_nbPass2, sizeof(_nbPass));
data/gatb-core-1.4.2+dfsg/gatb-core/test/unit/src/tools/storage/TestStorage.cpp:445:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read ((char *)buffer2, size);
data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h:639:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&_size), sizeof(_size));
data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h:640:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&_nchar), sizeof(_nchar));
data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h:642:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char *>(_bitArray), (std::streamsize)(sizeof(uint64_t) * _nchar));
data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h:645:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char *>(&sizer), sizeof(size_t));
data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h:647:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size()));
data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h:963:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&_gamma), sizeof(_gamma));
data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h:964:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&_nb_levels), sizeof(_nb_levels));
data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h:965:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&_lastbitsetrank), sizeof(_lastbitsetrank));
data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h:966:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&_nelem), sizeof(_nelem));
data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h:998:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char *>(&final_hash_size), sizeof(size_t));
data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h:1005:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char *>(&key), sizeof(elem_t));
data/gatb-core-1.4.2+dfsg/gatb-core/thirdparty/BooPHF/BooPHF.h:1006:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char *>(&value), sizeof(uint64_t));
ANALYSIS SUMMARY:
Hits = 944
Lines analyzed = 96296 in approximately 2.82 seconds (34203 lines/second)
Physical Source Lines of Code (SLOC) = 49496
Hits@level = [0] 136 [1] 108 [2] 212 [3] 20 [4] 600 [5] 4
Hits@level+ = [0+] 1080 [1+] 944 [2+] 836 [3+] 624 [4+] 604 [5+] 4
Hits/KSLOC@level+ = [0+] 21.8199 [1+] 19.0722 [2+] 16.8903 [3+] 12.6071 [4+] 12.203 [5+] 0.0808146
Dot directories skipped = 4 (--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.