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/unanimity-3.3.0+dfsg/include/pacbio/UnanimityConfig.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/UnanimityVersion.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/AffineAlignment.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/AlignConfig.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/BandedAligner.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/BandedChainAlignment.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/ChainScorer.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/ChainSeeds.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/ChainSeedsConfig.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/FilterSeeds.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/FindSeeds.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/FindSeedsConfig.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/HomopolymerHasher.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/LinearAlignment.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/LocalAlignment.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/PairwiseAlignment.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/SeedScorer.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/SparseAlignment.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/internal/BCAlignBlocks.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/align/internal/BCAlignImpl.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/ccs/ConsensusSettings.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/ccs/SparseAlignment.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Whitelist.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/chimera/ChimeraLabel.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/chimera/ChimeraLabeler.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/chimera/ChimeraResultWriter.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/consensus/AbstractMatrix.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/consensus/Coverage.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/consensus/EasyReadScorer.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/consensus/Evaluator.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/consensus/Integrator.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/consensus/IntervalMask.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/consensus/MatrixViewConvention.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/consensus/ModelConfig.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/consensus/ModelSelection.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/consensus/Mutation.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/consensus/Polish.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/consensus/PolishResult.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/consensus/Template.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/consensus/internal/ModelInternalInitializer.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/data/ChemistryMapping.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/data/ChemistryTriple.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/data/Interval.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/data/IntervalTree.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/data/PlainOption.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/data/Read.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/data/ReadId.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/data/Sequence.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/data/State.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/data/StrandType.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/data/SubreadResultCounter.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/data/internal/BaseEncoding.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/data/internal/ConversionFunctions.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/denovo/PoaConsensus.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/denovo/PoaGraph.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/denovo/RangeFinder.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/denovo/SparsePoa.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/exception/CCSExceptions.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/exception/InvalidEvaluatorException.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/exception/ModelError.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/exception/StateError.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Consensus.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Input.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Intervals.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/NoCallStyle.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Output.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/ReferenceWindow.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Settings.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Sorting.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/SortingStrategy.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Utils.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Variant.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/WindowResult.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Consensus.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/ConsensusMode.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/ConsensusModelFactory.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Filters.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/GenomicConsensus.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/IConsensusModel.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/IPoaModel.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Input.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Intervals.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/NoCallStyle.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Output.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/ReferenceWindow.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Settings.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Sorting.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/SortingStrategy.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Utils.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Variant.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/WindowResult.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/WorkChunk.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Workflow.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/ArrowModel.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/io/FastaWriter.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/io/FastqWriter.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/io/FileProducer.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/io/GffWriter.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/io/VcfWriter.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/plurality/Plurality.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/plurality/PluralityModel.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/poa/Poa.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/poa/PoaModel.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/quiver/Quiver.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/plurality/Plurality.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/poa/Poa.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/io/Utility.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/parallel/WorkQueue.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/util/ExecUtils.h
Examining data/unanimity-3.3.0+dfsg/include/pacbio/util/Timer.h
Examining data/unanimity-3.3.0+dfsg/src/ChemistryMapping.cpp
Examining data/unanimity-3.3.0+dfsg/src/ChemistryTriple.cpp
Examining data/unanimity-3.3.0+dfsg/src/ConsensusSettings.cpp
Examining data/unanimity-3.3.0+dfsg/src/Constants.h
Examining data/unanimity-3.3.0+dfsg/src/Coverage.cpp
Examining data/unanimity-3.3.0+dfsg/src/EasyReadScorer.cpp
Examining data/unanimity-3.3.0+dfsg/src/Evaluator.cpp
Examining data/unanimity-3.3.0+dfsg/src/EvaluatorImpl.cpp
Examining data/unanimity-3.3.0+dfsg/src/EvaluatorImpl.h
Examining data/unanimity-3.3.0+dfsg/src/Integrator.cpp
Examining data/unanimity-3.3.0+dfsg/src/Interval.cpp
Examining data/unanimity-3.3.0+dfsg/src/IntervalMask.cpp
Examining data/unanimity-3.3.0+dfsg/src/JsonHelpers.h
Examining data/unanimity-3.3.0+dfsg/src/LocalAlignment.cpp
Examining data/unanimity-3.3.0+dfsg/src/ModelConfig.cpp
Examining data/unanimity-3.3.0+dfsg/src/ModelFactory.cpp
Examining data/unanimity-3.3.0+dfsg/src/ModelFactory.h
Examining data/unanimity-3.3.0+dfsg/src/ModelFormFactory.cpp
Examining data/unanimity-3.3.0+dfsg/src/ModelFormFactory.h
Examining data/unanimity-3.3.0+dfsg/src/ModelNaming.h
Examining data/unanimity-3.3.0+dfsg/src/ModelSelection.cpp
Examining data/unanimity-3.3.0+dfsg/src/Mutation.cpp
Examining data/unanimity-3.3.0+dfsg/src/MutationTracker.h
Examining data/unanimity-3.3.0+dfsg/src/Polish.cpp
Examining data/unanimity-3.3.0+dfsg/src/PolishResult.cpp
Examining data/unanimity-3.3.0+dfsg/src/Read.cpp
Examining data/unanimity-3.3.0+dfsg/src/ReadId.cpp
Examining data/unanimity-3.3.0+dfsg/src/Recursor.cpp
Examining data/unanimity-3.3.0+dfsg/src/Recursor.h
Examining data/unanimity-3.3.0+dfsg/src/Sequence.cpp
Examining data/unanimity-3.3.0+dfsg/src/Simulator.h
Examining data/unanimity-3.3.0+dfsg/src/SparsePoa.cpp
Examining data/unanimity-3.3.0+dfsg/src/SubreadResultCounter.cpp
Examining data/unanimity-3.3.0+dfsg/src/Template.cpp
Examining data/unanimity-3.3.0+dfsg/src/Timer.cpp
Examining data/unanimity-3.3.0+dfsg/src/UnanimityInternalConfig.h
Examining data/unanimity-3.3.0+dfsg/src/Utility.cpp
Examining data/unanimity-3.3.0+dfsg/src/align/AffineAlignment.cpp
Examining data/unanimity-3.3.0+dfsg/src/align/AlignConfig.cpp
Examining data/unanimity-3.3.0+dfsg/src/align/BandedChainAlignment.cpp
Examining data/unanimity-3.3.0+dfsg/src/align/LinearAlignment.cpp
Examining data/unanimity-3.3.0+dfsg/src/align/PairwiseAlignment.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Consensus.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/ConsensusModelFactory.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Filters.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/GenomicConsensus.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/IPoaModel.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Input.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Intervals.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Output.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Settings.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/SettingsOptions.h
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/SettingsToolContract.h
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Sorting.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Workflow.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/arrow/ArrowModel.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/io/FastaWriter.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/io/FastqWriter.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/io/GffWriter.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/io/VcfWriter.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/plurality/PluralityModel.cpp
Examining data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/poa/PoaModel.cpp
Examining data/unanimity-3.3.0+dfsg/src/main/ChimeraLabeler.cpp
Examining data/unanimity-3.3.0+dfsg/src/main/arrow.cpp
Examining data/unanimity-3.3.0+dfsg/src/main/ccs.cpp
Examining data/unanimity-3.3.0+dfsg/src/main/ccs_sim.cpp
Examining data/unanimity-3.3.0+dfsg/src/main/gcpp.cpp
Examining data/unanimity-3.3.0+dfsg/src/main/genomic_sim.cpp
Examining data/unanimity-3.3.0+dfsg/src/matrix/BasicDenseMatrix.cpp
Examining data/unanimity-3.3.0+dfsg/src/matrix/BasicDenseMatrix.h
Examining data/unanimity-3.3.0+dfsg/src/matrix/ScaledMatrix.cpp
Examining data/unanimity-3.3.0+dfsg/src/matrix/ScaledMatrix.h
Examining data/unanimity-3.3.0+dfsg/src/matrix/SparseMatrix.cpp
Examining data/unanimity-3.3.0+dfsg/src/matrix/SparseMatrix.h
Examining data/unanimity-3.3.0+dfsg/src/matrix/SparseVector.h
Examining data/unanimity-3.3.0+dfsg/src/models/CounterWeight.h
Examining data/unanimity-3.3.0+dfsg/src/models/HelperFunctions.h
Examining data/unanimity-3.3.0+dfsg/src/models/MarginalModelForm.cpp
Examining data/unanimity-3.3.0+dfsg/src/models/P6C4NoCov_Model.cpp
Examining data/unanimity-3.3.0+dfsg/src/models/PwSnrAModelForm.cpp
Examining data/unanimity-3.3.0+dfsg/src/models/PwSnrModelForm.cpp
Examining data/unanimity-3.3.0+dfsg/src/models/S_P1C1Beta_Model.cpp
Examining data/unanimity-3.3.0+dfsg/src/models/S_P1C1v1_Model.cpp
Examining data/unanimity-3.3.0+dfsg/src/models/S_P1C1v2_Model.cpp
Examining data/unanimity-3.3.0+dfsg/src/models/S_P2C2v5_Model.cpp
Examining data/unanimity-3.3.0+dfsg/src/models/SnrModelForm.cpp
Examining data/unanimity-3.3.0+dfsg/src/poa/BoostGraph.h
Examining data/unanimity-3.3.0+dfsg/src/poa/PoaAlignmentMatrix.cpp
Examining data/unanimity-3.3.0+dfsg/src/poa/PoaAlignmentMatrix.h
Examining data/unanimity-3.3.0+dfsg/src/poa/PoaConsensus.cpp
Examining data/unanimity-3.3.0+dfsg/src/poa/PoaGraph.cpp
Examining data/unanimity-3.3.0+dfsg/src/poa/PoaGraphImpl.cpp
Examining data/unanimity-3.3.0+dfsg/src/poa/PoaGraphImpl.h
Examining data/unanimity-3.3.0+dfsg/src/poa/PoaGraphTraversals.cpp
Examining data/unanimity-3.3.0+dfsg/src/poa/RangeFinder.cpp
Examining data/unanimity-3.3.0+dfsg/src/poa/VectorL.h
Examining data/unanimity-3.3.0+dfsg/src/variantCaller/VariantCallerSettings.cpp
Examining data/unanimity-3.3.0+dfsg/src/variantCaller/VariantCallerSettings.h
Examining data/unanimity-3.3.0+dfsg/src/variantCaller/variantCaller.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/ChimeraTest.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/Mutations.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/Mutations.h
Examining data/unanimity-3.3.0+dfsg/tests/unit/RandomDNA.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/RandomDNA.h
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestAlignment.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestAmbiguousBases.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestBandedChainAlign.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestChemistry.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestConsensus.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestCoverage.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestGenomicConsensus.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestGenomicConsensus_Experimental.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestInterval.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestIntervalMask.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestLoadModels.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestMutationEnumerator.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestMutationTracker.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestPlurality.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestPoaConsensus.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestPolish.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestSequence.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestSparseAlign.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestSparsePoa.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestSparseVector.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestTemplate.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestUtility.cpp
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestUtility.h
Examining data/unanimity-3.3.0+dfsg/tests/unit/TestWhitelist.cpp
Examining data/unanimity-3.3.0+dfsg/third-party/cpp-optparse/OptionParser.cpp
Examining data/unanimity-3.3.0+dfsg/third-party/cpp-optparse/OptionParser.h
Examining data/unanimity-3.3.0+dfsg/third-party/cpp-optparse/test.cpp
Examining data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.c
Examining data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.h
Examining data/unanimity-3.3.0+dfsg/third-party/cssw/ssw_cpp.cpp
Examining data/unanimity-3.3.0+dfsg/third-party/cssw/ssw_cpp.h
Examining data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc
Examining data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock/gmock.h
Examining data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock_main.cc
Examining data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gtest/gtest.h
FINAL RESULTS:
data/unanimity-3.3.0+dfsg/tests/unit/TestPoaConsensus.cpp:45:19: [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.
int ret = system(cmd.c_str());
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:1623:10: [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.
# define vsnprintf _vsnprintf
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:4119:5: [4] (format) vprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vprintf(fmt, args);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:4138:3: [4] (format) vprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vprintf(fmt, args);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:4145:3: [4] (format) vprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vprintf(fmt, args);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gtest/gtest.h:2868:20: [4] (buffer) StrNCpy:
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).
inline const char* StrNCpy(char* dest, const char* src, size_t n) {
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gtest/gtest.h:2940:26: [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.
# define GTEST_SNPRINTF_ _snprintf
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gtest/gtest.h:2942:26: [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.
# define GTEST_SNPRINTF_ snprintf
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gtest/gtest.h:8322:5: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf(\
data/unanimity-3.3.0+dfsg/src/ModelFactory.cpp:44:27: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
const char* pth = getenv("SMRT_CHEMISTRY_BUNDLE_DIR");
data/unanimity-3.3.0+dfsg/third-party/cpp-optparse/OptionParser.cpp:109:21: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
const char* s = getenv("COLUMNS");
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:712:37: [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.
void ShuffleRange(internal::Random* random, int begin, int end,
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:733:39: [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.
inline void Shuffle(internal::Random* random, std::vector<E>* v) {
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:734:16: [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.
ShuffleRange(random, 0, static_cast<int>(v->size()), v);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:1202:21: [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.
internal::Random* random() { return &random_; }
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:3947:47: [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.
void TestCase::ShuffleTests(internal::Random* random) {
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:3948:11: [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.
Shuffle(random, &test_indices_);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:5777:7: [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.
random()->Reseed(random_seed_);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:6087:16: [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.
ShuffleRange(random(), 0, last_death_test_case_ + 1, &test_case_indices_);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:6090:16: [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.
ShuffleRange(random(), last_death_test_case_ + 1,
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:6095:34: [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.
test_cases_[i]->ShuffleTests(random());
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gtest/gtest.h:2906:27: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
const char* const env = getenv(name);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gtest/gtest.h:2909:10: [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.
return getenv(name);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gtest/gtest.h:18306:39: [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.
void ShuffleTests(internal::Random* random);
data/unanimity-3.3.0+dfsg/include/pacbio/util/ExecUtils.h:17:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char env[32];
data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Workflow.cpp:154:23: [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).
logStream.open(logFile);
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:337:23: [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).
logStream.open(logFile);
data/unanimity-3.3.0+dfsg/src/variantCaller/variantCaller.cpp:31:23: [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).
logStream.open(logFile);
data/unanimity-3.3.0+dfsg/tests/unit/TestPoaConsensus.cpp:605:9: [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 fname[100];
data/unanimity-3.3.0+dfsg/tests/unit/TestPoaConsensus.cpp:606:9: [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(fname, "/tmp/gr%03d.dot", run);
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw_cpp.cpp:275:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(score_matrix_, score_matrix, sizeof(int8_t) * score_matrix_size_ * score_matrix_size_);
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw_cpp.cpp:277:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(translation_matrix_, translation_matrix, sizeof(int8_t) * translation_matrix_size);
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw_cpp.cpp:454:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(score_matrix_, score_matrix, sizeof(int8_t) * score_matrix_size_ * score_matrix_size_);
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw_cpp.cpp:456:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(translation_matrix_, translation_matrix, sizeof(int8_t) * translation_matrix_size);
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw_cpp.cpp:466:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(translation_matrix_, kBaseTranslation, sizeof(int8_t) * SizeOfArray(kBaseTranslation));
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:2328:7: [2] (buffer) MultiByteToWideChar:
Requires maximum length in CHARACTERS, not bytes (CWE-120).
MultiByteToWideChar(CP_ACP, 0, ansi, length,
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:2331:3: [2] (buffer) MultiByteToWideChar:
Requires maximum length in CHARACTERS, not bytes (CWE-120).
MultiByteToWideChar(CP_ACP, 0, ansi, length,
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:2841:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char error_text[kBufSize] = { '\0' };
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:2925:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[5]; // Big enough for the largest valid code point.
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:6808:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[256];
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:7224:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char executable_path[_MAX_PATH + 1]; // NOLINT
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:7503:22: [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).
const int cwd_fd = open(".", O_RDONLY);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:7941:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:7944:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:8321:18: [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).
const int fd = open("/proc/self/as", O_RDONLY);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:8651:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buffer, regex, len);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:8728:5: [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 temp_dir_path[MAX_PATH + 1] = { '\0' }; // NOLINT
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:8729:5: [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 temp_file_path[MAX_PATH + 1] = { '\0' }; // NOLINT
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:8766:29: [2] (tmpfile) mkstemp:
Potential for temporary file vulnerability in some circumstances. Some
older Unix-like systems create temp files with permission to write by all
by default, so be sure to set the umask to override this. Also, some older
Unix systems might fail to use O_EXCL when opening the file, so make sure
that O_EXCL is used by the library (CWE-377).
const int captured_fd = mkstemp(name_template);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:9074:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char text[5] = "";
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gtest/gtest.h:2880:10: [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).
return fopen(path, mode);
data/unanimity-3.3.0+dfsg/include/pacbio/align/AlignConfig.h:20:32: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
AlignParams(int match, int mismatch, int insert, int delete_);
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:170:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads) {
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:171:37: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
longest = std::max(longest, read.Seq.length());
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:172:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((read.Flags & BAM::ADAPTER_BEFORE) && (read.Flags & BAM::ADAPTER_AFTER) &&
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:172:52: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((read.Flags & BAM::ADAPTER_BEFORE) && (read.Flags & BAM::ADAPTER_AFTER) &&
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:173:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.ReadAccuracy >= settings.MinReadScore)
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:174:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
lengths.emplace_back(read.Seq.length());
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:188:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads) {
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:192:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.SignalToNoise.Minimum() < settings.MinSNR) {
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:195:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
} else if (read.ReadAccuracy < settings.MinReadScore) {
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:198:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
} else if (read.Seq.length() < maxLen) {
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:199:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
results.emplace_back(&read);
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:210:48: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto lexForm = [median](const TRead* read) {
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:234:60: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
boost::optional<MappedRead> ExtractMappedRead(const TRead& read, const PoaAlignmentSummary& summary,
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:249:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.Flags & BAM::ADAPTER_BEFORE && (poaLength - tplEnd) <= kStickyEnds)
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:251:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.Flags & BAM::ADAPTER_AFTER && tplStart <= kStickyEnds) tplStart = 0;
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:253:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.Flags & BAM::ADAPTER_BEFORE && tplStart <= kStickyEnds) tplStart = 0;
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:254:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.Flags & BAM::ADAPTER_AFTER && (poaLength - tplEnd) <= kStickyEnds)
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:260:44: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
PBLOG_DEBUG << "Skipping read " << read.Id << ", too short (<" << settings.MinLength << ')';
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:264:44: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
PBLOG_DEBUG << "Skipping read " << read.Id << ", too long (>" << settings.MaxLength << ')';
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:268:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const SNR& snr = read.SignalToNoise;
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:269:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const std::string& chem = read.Chemistry;
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:272:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Read(read.Id, read.Seq.substr(readStart, readEnd - readStart),
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:272:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Read(read.Id, read.Seq.substr(readStart, readEnd - readStart),
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:273:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::vector<uint8_t>(read.IPD.begin() + readStart, read.IPD.begin() + readEnd),
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:273:65: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::vector<uint8_t>(read.IPD.begin() + readStart, read.IPD.begin() + readEnd),
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:274:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::vector<uint8_t>(read.PulseWidth.begin() + readStart,
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:275:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.PulseWidth.begin() + readEnd),
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:321:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto read : reads) {
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:361:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : chunk.Reads) {
data/unanimity-3.3.0+dfsg/include/pacbio/ccs/Consensus.h:362:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.SignalToNoise.Minimum() < settings.MinSNR) readsBelowMinSNR++;
data/unanimity-3.3.0+dfsg/include/pacbio/consensus/Integrator.h:75:73: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual PacBio::Data::State AddRead(const PacBio::Data::MappedRead& read);
data/unanimity-3.3.0+dfsg/include/pacbio/consensus/Integrator.h:139:65: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const PacBio::Data::MappedRead& read);
data/unanimity-3.3.0+dfsg/include/pacbio/consensus/Integrator.h:141:83: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::unique_ptr<AbstractTemplate> GetTemplate(const PacBio::Data::MappedRead& read);
data/unanimity-3.3.0+dfsg/include/pacbio/data/Read.h:69:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Read(const Read& read) = default;
data/unanimity-3.3.0+dfsg/include/pacbio/data/Read.h:70:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Read(Read&& read) = default;
data/unanimity-3.3.0+dfsg/include/pacbio/data/Read.h:86:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
MappedRead(const Read& read, StrandType strand, size_t templateStart, size_t templateEnd,
data/unanimity-3.3.0+dfsg/include/pacbio/data/Read.h:88:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
MappedRead(const MappedRead& read) = default;
data/unanimity-3.3.0+dfsg/include/pacbio/data/Read.h:89:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
MappedRead(MappedRead&& read) = default;
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Sorting.h:36:54: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
auto lengthInWindow = [&window](const BamRecord& read) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Sorting.h:37:57: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto start = std::max(static_cast<size_t>(read.ReferenceStart()), window.Start());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Sorting.h:38:55: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto end = std::min(static_cast<size_t>(read.ReferenceEnd()), window.End());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Utils.h:47:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (auto& read : *reads)
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Utils.h:48:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.Clip(PacBio::BAM::ClipType::CLIP_TO_REFERENCE, winStart, winEnd);
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Utils.h:73:58: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto spansReferenceRange = [](const BamRecord& read, const ReferenceWindow& window) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Utils.h:74:49: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto tStart = static_cast<size_t>(read.ReferenceStart());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Utils.h:75:47: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto tEnd = static_cast<size_t>(read.ReferenceEnd());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Utils.h:81:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Utils.h:82:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.AlignedStrand() == Strand::FORWARD && spansReferenceRange(read, window))
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Utils.h:82:76: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.AlignedStrand() == Strand::FORWARD && spansReferenceRange(read, window))
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Utils.h:83:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.push_back(read.Sequence(Orientation::NATIVE, false)); // excise soft clips?
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Utils.h:106:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/Utils.h:111:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
annotation.append(read.FullName());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:102:62: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto spansReferenceRange = [](const BamRecord& read, const ReferenceWindow& window) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:103:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto tStart = static_cast<size_t>(read.ReferenceStart());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:104:51: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto tEnd = static_cast<size_t>(read.ReferenceEnd());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:110:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:111:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.AlignedStrand() == Strand::FORWARD && spansReferenceRange(read, window))
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:111:80: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.AlignedStrand() == Strand::FORWARD && spansReferenceRange(read, window))
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:112:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.push_back(read.Sequence(Orientation::NATIVE, false)); // excise soft clips?
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:155:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (auto& read : *mappedReads) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:156:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.TemplateStart = queryPositions[read.TemplateStart];
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:156:49: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.TemplateStart = queryPositions[read.TemplateStart];
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:157:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.TemplateEnd = queryPositions[read.TemplateEnd];
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:157:47: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.TemplateEnd = queryPositions[read.TemplateEnd];
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:381:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:382:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.ReferenceName() == window.name) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:383:56: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto start = static_cast<size_t>(read.ReferenceStart());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:384:54: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto end = static_cast<size_t>(read.ReferenceEnd());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:671:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:676:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
annotation.append(read.FullName());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:687:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (auto& read : *reads)
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:688:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.Clip(PacBio::BAM::ClipType::CLIP_TO_REFERENCE, winStart, winEnd);
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:731:88: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::count_if(reads.begin(), reads.end(), [&interval](const BamRecord& read) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:732:64: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto readStart = static_cast<size_t>(read.ReferenceStart());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/arrow/Arrow.h:733:62: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto readEnd = static_cast<size_t>(read.ReferenceEnd());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Utils.h:50:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (auto& read : *reads)
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Utils.h:51:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.Clip(PacBio::BAM::ClipType::CLIP_TO_REFERENCE, winStart, winEnd);
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Utils.h:76:58: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto spansReferenceRange = [](const BamRecord& read, const ReferenceWindow& window) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Utils.h:77:49: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto tStart = static_cast<size_t>(read.ReferenceStart());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Utils.h:78:47: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto tEnd = static_cast<size_t>(read.ReferenceEnd());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Utils.h:84:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Utils.h:85:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.AlignedStrand() == Strand::FORWARD && spansReferenceRange(read, window))
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Utils.h:85:76: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.AlignedStrand() == Strand::FORWARD && spansReferenceRange(read, window))
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Utils.h:86:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.push_back(read.Sequence(Orientation::NATIVE, false)); // excise soft clips?
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Utils.h:109:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/Utils.h:114:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
annotation.append(read.FullName());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:105:62: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto spansReferenceRange = [](const BamRecord& read, const ReferenceWindow& window) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:106:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto tStart = static_cast<size_t>(read.ReferenceStart());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:107:51: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto tEnd = static_cast<size_t>(read.ReferenceEnd());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:113:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:114:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.AlignedStrand() == Strand::FORWARD && spansReferenceRange(read, window))
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:114:80: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.AlignedStrand() == Strand::FORWARD && spansReferenceRange(read, window))
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:115:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.push_back(read.Sequence(Orientation::NATIVE, false)); // excise soft clips?
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:158:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (auto& read : *mappedReads) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:159:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.TemplateStart = queryPositions[read.TemplateStart];
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:159:49: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.TemplateStart = queryPositions[read.TemplateStart];
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:160:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.TemplateEnd = queryPositions[read.TemplateEnd];
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:160:47: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.TemplateEnd = queryPositions[read.TemplateEnd];
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:384:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:385:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.ReferenceName() == window.name) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:386:56: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto start = static_cast<size_t>(read.ReferenceStart());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:387:54: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto end = static_cast<size_t>(read.ReferenceEnd());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:674:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:679:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
annotation.append(read.FullName());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:690:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (auto& read : *reads)
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:691:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.Clip(PacBio::BAM::ClipType::CLIP_TO_REFERENCE, winStart, winEnd);
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:734:88: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::count_if(reads.begin(), reads.end(), [&interval](const BamRecord& read) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:735:64: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto readStart = static_cast<size_t>(read.ReferenceStart());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/arrow/Arrow.h:736:62: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto readEnd = static_cast<size_t>(read.ReferenceEnd());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/plurality/Plurality.h:97:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.Clip(ClipType::CLIP_TO_REFERENCE, refStart, refEnd);
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/plurality/Plurality.h:99:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto alnRead = read.Sequence(Orientation::GENOMIC, true);
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/plurality/Plurality.h:100:50: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto alnRef = AlignedReference(read.CigarData(), input.ReferenceInWindow(window));
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/plurality/Plurality.h:110:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto s = read.AlignedStart() - refStart;
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/plurality/Plurality.h:111:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto e = read.AlignedEnd() - refStart;
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/poa/Poa.h:132:87: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
reads.begin(), reads.end(), [&interval](const PacBio::BAM::BamRecord& read) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/poa/Poa.h:133:64: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto readStart = static_cast<size_t>(read.ReferenceStart());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/experimental/poa/Poa.h:134:62: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto readEnd = static_cast<size_t>(read.ReferenceEnd());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/plurality/Plurality.h:97:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.Clip(ClipType::CLIP_TO_REFERENCE, refStart, refEnd);
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/plurality/Plurality.h:99:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto alnRead = read.Sequence(Orientation::GENOMIC, true);
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/plurality/Plurality.h:100:50: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto alnRef = AlignedReference(read.CigarData(), input.ReferenceInWindow(window));
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/plurality/Plurality.h:110:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto s = read.AlignedStart() - refStart;
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/plurality/Plurality.h:111:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto e = read.AlignedEnd() - refStart;
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/poa/Poa.h:131:87: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
reads.begin(), reads.end(), [&interval](const PacBio::BAM::BamRecord& read) {
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/poa/Poa.h:132:64: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto readStart = static_cast<size_t>(read.ReferenceStart());
data/unanimity-3.3.0+dfsg/include/pacbio/genomicconsensus/poa/Poa.h:133:62: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto readEnd = static_cast<size_t>(read.ReferenceEnd());
data/unanimity-3.3.0+dfsg/src/Coverage.cpp:24:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (int read = 0; read < nReads; read++) {
data/unanimity-3.3.0+dfsg/src/Coverage.cpp:25:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int tStart_ = tStart[read];
data/unanimity-3.3.0+dfsg/src/Coverage.cpp:26:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int tEnd_ = tEnd[read];
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:38:57: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Data::MappedRead& read)
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:43:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.TemplateEnd <= read.TemplateStart) throw std::invalid_argument("template span < 2!");
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:43:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.TemplateEnd <= read.TemplateStart) throw std::invalid_argument("template span < 2!");
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:45:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.Length() < 2) throw std::invalid_argument("read span < 2!");
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:47:51: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
evals_.emplace_back(Evaluator(std::move(tpl), read, cfg_.MinZScore, cfg_.ScoreDiff));
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:243:59: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
State Integrator::AddRead(const PacBio::Data::MappedRead& read)
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:246:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
return AddRead(GetTemplate(read), read);
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:246:43: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
return AddRead(GetTemplate(read), read);
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:300:91: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::unique_ptr<AbstractTemplate> Integrator::GetTemplate(const PacBio::Data::MappedRead& read)
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:302:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const size_t len = read.TemplateEnd - read.TemplateStart;
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:302:43: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const size_t len = read.TemplateEnd - read.TemplateStart;
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:304:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.Strand == StrandType::FORWARD) {
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:305:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const size_t start = read.TemplateStart;
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:306:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const size_t end = read.TemplateEnd;
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:308:92: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
return std::make_unique<Template>(fwdTpl_.substr(start, len), ModelFactory::Create(read),
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:309:55: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
start, end, read.PinStart, read.PinEnd);
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:309:70: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
start, end, read.PinStart, read.PinEnd);
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:310:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
} else if (read.Strand == StrandType::REVERSE) {
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:311:47: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const size_t start = revTpl_.size() - read.TemplateEnd;
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:312:45: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const size_t end = revTpl_.size() - read.TemplateStart;
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:314:92: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
return std::make_unique<Template>(revTpl_.substr(start, len), ModelFactory::Create(read),
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:315:55: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
start, end, read.PinEnd, read.PinStart);
data/unanimity-3.3.0+dfsg/src/Integrator.cpp:315:68: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
start, end, read.PinEnd, read.PinStart);
data/unanimity-3.3.0+dfsg/src/ModelFactory.cpp:73:77: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::unique_ptr<ModelConfig> ModelFactory::Create(const PacBio::Data::Read& read)
data/unanimity-3.3.0+dfsg/src/ModelFactory.cpp:75:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
return Create(read.Model, read.SignalToNoise);
data/unanimity-3.3.0+dfsg/src/ModelFactory.cpp:75:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
return Create(read.Model, read.SignalToNoise);
data/unanimity-3.3.0+dfsg/src/ModelFactory.h:52:74: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static std::unique_ptr<ModelConfig> Create(const PacBio::Data::Read& read);
data/unanimity-3.3.0+dfsg/src/Read.cpp:46:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
MappedRead::MappedRead(const Read& read, StrandType strand, size_t templateStart,
data/unanimity-3.3.0+dfsg/src/Read.cpp:48:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
: Read(read)
data/unanimity-3.3.0+dfsg/src/align/AlignConfig.cpp:8:41: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
AlignParams::AlignParams(int match, int mismatch, int insert, int delete_)
data/unanimity-3.3.0+dfsg/src/align/AlignConfig.cpp:9:30: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
: Match(match), Mismatch(mismatch), Insert(insert), Delete(delete_)
data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/IPoaModel.cpp:23:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads) {
data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/IPoaModel.cpp:28:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
annotation.append(read.FullName());
data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/IPoaModel.cpp:39:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (auto& read : *reads)
data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/IPoaModel.cpp:40:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.Clip(PacBio::BAM::ClipType::CLIP_TO_REFERENCE, winStart, winEnd);
data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/IPoaModel.cpp:111:84: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
reads.begin(), reads.end(), [&subWindow](const PacBio::BAM::BamRecord& read) {
data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/IPoaModel.cpp:112:60: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto readStart = static_cast<size_t>(read.ReferenceStart());
data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/IPoaModel.cpp:113:58: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto readEnd = static_cast<size_t>(read.ReferenceEnd());
data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Sorting.cpp:20:54: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
auto lengthInWindow = [&window](const BamRecord& read) {
data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Sorting.cpp:21:57: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto start = std::max(static_cast<size_t>(read.ReferenceStart()), window.Start());
data/unanimity-3.3.0+dfsg/src/genomicconsensus/experimental/Sorting.cpp:22:55: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto end = std::min(static_cast<size_t>(read.ReferenceEnd()), window.End());
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:510:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : *query) {
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:511:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const string movieName = read.MovieName();
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:517:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((!holeNumber) || (holeNumber.value() != read.HoleNumber())) {
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:522:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
holeNumber = read.HoleNumber();
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:525:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.HasBarcodes() && read.HasBarcodeQuality()) {
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:525:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.HasBarcodes() && read.HasBarcodeQuality()) {
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:527:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
uint8_t quality = read.BarcodeQuality();
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:528:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
tie(first, second) = read.Barcodes();
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:546:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (barcodes && (!read.HasBarcodes() || !read.HasBarcodeQuality() ||
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:546:50: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (barcodes && (!read.HasBarcodes() || !read.HasBarcodeQuality() ||
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:547:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.BarcodeForward() != get<0>(*barcodes) ||
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:548:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.BarcodeReverse() != get<1>(*barcodes) ||
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:549:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.BarcodeQuality() != get<2>(*barcodes))) {
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:555:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.HasIPD())
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:556:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ipd = read.IPD().Encode();
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:558:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ipd = vector<uint8_t>(read.Sequence().length(), 0);
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:561:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.HasPulseWidth())
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:562:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
pw = read.PulseWidth().Encode();
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:564:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
pw = vector<uint8_t>(read.Sequence().length(), 0);
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:566:41: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
string chem(modelSpec.empty() ? read.ReadGroup().SequencingChemistry() : modelSpec);
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:569:37: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Interval(read.QueryStart(), read.QueryEnd())),
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:569:56: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Interval(read.QueryStart(), read.QueryEnd())),
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:570:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.Sequence(), move(ipd), move(pw), read.LocalContextFlags(),
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:570:59: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.Sequence(), move(ipd), move(pw), read.LocalContextFlags(),
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:571:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.ReadAccuracy(), SNR(read.SignalToNoise()), move(chem)});
data/unanimity-3.3.0+dfsg/src/main/ccs.cpp:571:46: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.ReadAccuracy(), SNR(read.SignalToNoise()), move(chem)});
data/unanimity-3.3.0+dfsg/src/main/ccs_sim.cpp:31:94: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const std::string& tpl, const std::string& read)
data/unanimity-3.3.0+dfsg/src/main/ccs_sim.cpp:50:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (tpl[posOnTpl] == read[posOnRead]) {
data/unanimity-3.3.0+dfsg/src/main/genomic_sim.cpp:35:94: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const std::string& tpl, const std::string& read)
data/unanimity-3.3.0+dfsg/src/main/genomic_sim.cpp:54:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (tpl[posOnTpl] == read[posOnRead]) {
data/unanimity-3.3.0+dfsg/src/models/MarginalModelForm.cpp:66:62: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static std::vector<uint8_t> EncodeRead(const MappedRead& read);
data/unanimity-3.3.0+dfsg/src/models/MarginalModelForm.cpp:161:69: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::vector<uint8_t> MarginalRecursor::EncodeRead(const MappedRead& read)
data/unanimity-3.3.0+dfsg/src/models/MarginalModelForm.cpp:164:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.reserve(read.Length());
data/unanimity-3.3.0+dfsg/src/models/MarginalModelForm.cpp:166:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const char bp : read.Seq) {
data/unanimity-3.3.0+dfsg/src/models/P6C4NoCov_Model.cpp:59:69: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static inline std::vector<uint8_t> EncodeRead(const MappedRead& read);
data/unanimity-3.3.0+dfsg/src/models/P6C4NoCov_Model.cpp:218:70: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::vector<uint8_t> P6C4NoCovRecursor::EncodeRead(const MappedRead& read)
data/unanimity-3.3.0+dfsg/src/models/P6C4NoCov_Model.cpp:221:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.reserve(read.Length());
data/unanimity-3.3.0+dfsg/src/models/P6C4NoCov_Model.cpp:223:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const char bp : read.Seq) {
data/unanimity-3.3.0+dfsg/src/models/PwSnrAModelForm.cpp:69:62: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static std::vector<uint8_t> EncodeRead(const MappedRead& read);
data/unanimity-3.3.0+dfsg/src/models/PwSnrAModelForm.cpp:196:67: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::vector<uint8_t> PwSnrARecursor::EncodeRead(const MappedRead& read)
data/unanimity-3.3.0+dfsg/src/models/PwSnrAModelForm.cpp:199:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.reserve(read.Length());
data/unanimity-3.3.0+dfsg/src/models/PwSnrAModelForm.cpp:201:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (size_t i = 0; i < read.Length(); ++i) {
data/unanimity-3.3.0+dfsg/src/models/PwSnrAModelForm.cpp:202:40: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.emplace_back(EncodeBase(read.Seq[i], read.PulseWidth[i]));
data/unanimity-3.3.0+dfsg/src/models/PwSnrAModelForm.cpp:202:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.emplace_back(EncodeBase(read.Seq[i], read.PulseWidth[i]));
data/unanimity-3.3.0+dfsg/src/models/PwSnrModelForm.cpp:69:62: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static std::vector<uint8_t> EncodeRead(const MappedRead& read);
data/unanimity-3.3.0+dfsg/src/models/PwSnrModelForm.cpp:197:66: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::vector<uint8_t> PwSnrRecursor::EncodeRead(const MappedRead& read)
data/unanimity-3.3.0+dfsg/src/models/PwSnrModelForm.cpp:200:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.reserve(read.Length());
data/unanimity-3.3.0+dfsg/src/models/PwSnrModelForm.cpp:202:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (size_t i = 0; i < read.Length(); ++i) {
data/unanimity-3.3.0+dfsg/src/models/PwSnrModelForm.cpp:203:40: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.emplace_back(EncodeBase(read.Seq[i], read.PulseWidth[i]));
data/unanimity-3.3.0+dfsg/src/models/PwSnrModelForm.cpp:203:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.emplace_back(EncodeBase(read.Seq[i], read.PulseWidth[i]));
data/unanimity-3.3.0+dfsg/src/models/S_P1C1Beta_Model.cpp:53:69: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static inline std::vector<uint8_t> EncodeRead(const MappedRead& read);
data/unanimity-3.3.0+dfsg/src/models/S_P1C1Beta_Model.cpp:177:72: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::vector<uint8_t> S_P1C1Beta_Recursor::EncodeRead(const MappedRead& read)
data/unanimity-3.3.0+dfsg/src/models/S_P1C1Beta_Model.cpp:180:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.reserve(read.Length());
data/unanimity-3.3.0+dfsg/src/models/S_P1C1Beta_Model.cpp:182:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const char bp : read.Seq) {
data/unanimity-3.3.0+dfsg/src/models/S_P1C1v1_Model.cpp:56:69: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static inline std::vector<uint8_t> EncodeRead(const MappedRead& read);
data/unanimity-3.3.0+dfsg/src/models/S_P1C1v1_Model.cpp:334:70: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::vector<uint8_t> S_P1C1v1_Recursor::EncodeRead(const MappedRead& read)
data/unanimity-3.3.0+dfsg/src/models/S_P1C1v1_Model.cpp:337:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.reserve(read.Length());
data/unanimity-3.3.0+dfsg/src/models/S_P1C1v1_Model.cpp:339:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (size_t i = 0; i < read.Length(); ++i) {
data/unanimity-3.3.0+dfsg/src/models/S_P1C1v1_Model.cpp:340:40: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.emplace_back(EncodeBase(read.Seq[i], read.PulseWidth[i]));
data/unanimity-3.3.0+dfsg/src/models/S_P1C1v1_Model.cpp:340:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.emplace_back(EncodeBase(read.Seq[i], read.PulseWidth[i]));
data/unanimity-3.3.0+dfsg/src/models/S_P1C1v2_Model.cpp:56:69: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static inline std::vector<uint8_t> EncodeRead(const MappedRead& read);
data/unanimity-3.3.0+dfsg/src/models/S_P1C1v2_Model.cpp:329:70: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::vector<uint8_t> S_P1C1v2_Recursor::EncodeRead(const MappedRead& read)
data/unanimity-3.3.0+dfsg/src/models/S_P1C1v2_Model.cpp:332:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.reserve(read.Length());
data/unanimity-3.3.0+dfsg/src/models/S_P1C1v2_Model.cpp:334:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (size_t i = 0; i < read.Length(); ++i) {
data/unanimity-3.3.0+dfsg/src/models/S_P1C1v2_Model.cpp:335:40: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.emplace_back(EncodeBase(read.Seq[i], read.PulseWidth[i]));
data/unanimity-3.3.0+dfsg/src/models/S_P1C1v2_Model.cpp:335:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.emplace_back(EncodeBase(read.Seq[i], read.PulseWidth[i]));
data/unanimity-3.3.0+dfsg/src/models/S_P2C2v5_Model.cpp:58:69: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static inline std::vector<uint8_t> EncodeRead(const MappedRead& read);
data/unanimity-3.3.0+dfsg/src/models/S_P2C2v5_Model.cpp:316:70: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::vector<uint8_t> S_P2C2v5_Recursor::EncodeRead(const MappedRead& read)
data/unanimity-3.3.0+dfsg/src/models/S_P2C2v5_Model.cpp:319:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.reserve(read.Length());
data/unanimity-3.3.0+dfsg/src/models/S_P2C2v5_Model.cpp:321:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (size_t i = 0; i < read.Length(); ++i) {
data/unanimity-3.3.0+dfsg/src/models/S_P2C2v5_Model.cpp:322:40: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.emplace_back(EncodeBase(read.Seq[i], read.PulseWidth[i]));
data/unanimity-3.3.0+dfsg/src/models/S_P2C2v5_Model.cpp:322:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.emplace_back(EncodeBase(read.Seq[i], read.PulseWidth[i]));
data/unanimity-3.3.0+dfsg/src/models/SnrModelForm.cpp:63:62: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static std::vector<uint8_t> EncodeRead(const MappedRead& read);
data/unanimity-3.3.0+dfsg/src/models/SnrModelForm.cpp:192:64: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::vector<uint8_t> SnrRecursor::EncodeRead(const MappedRead& read)
data/unanimity-3.3.0+dfsg/src/models/SnrModelForm.cpp:195:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
result.reserve(read.Length());
data/unanimity-3.3.0+dfsg/src/models/SnrModelForm.cpp:197:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const char bp : read.Seq) {
data/unanimity-3.3.0+dfsg/src/poa/PoaConsensus.cpp:46:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const std::string& read : reads) {
data/unanimity-3.3.0+dfsg/src/poa/PoaConsensus.cpp:47:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read.length() == 0) {
data/unanimity-3.3.0+dfsg/src/poa/PoaConsensus.cpp:50:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
pg.AddRead(read, config);
data/unanimity-3.3.0+dfsg/tests/unit/TestAlignment.cpp:645:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
a = AlignLinear(ref, read, &score);
data/unanimity-3.3.0+dfsg/tests/unit/TestAlignment.cpp:646:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
peerAlignment = Align(ref, read, &peerScore, config);
data/unanimity-3.3.0+dfsg/tests/unit/TestGenomicConsensus.cpp:362:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : query) {
data/unanimity-3.3.0+dfsg/tests/unit/TestGenomicConsensus.cpp:364:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
reads_.emplace_back(read);
data/unanimity-3.3.0+dfsg/tests/unit/TestGenomicConsensus_Experimental.cpp:87:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : query)
data/unanimity-3.3.0+dfsg/tests/unit/TestGenomicConsensus_Experimental.cpp:88:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
reads.push_back(read);
data/unanimity-3.3.0+dfsg/tests/unit/TestGenomicConsensus_Experimental.cpp:290:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads)
data/unanimity-3.3.0+dfsg/tests/unit/TestGenomicConsensus_Experimental.cpp:292:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto readLength = read.AlignedEnd() - read.AlignedStart();
data/unanimity-3.3.0+dfsg/tests/unit/TestGenomicConsensus_Experimental.cpp:292:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto readLength = read.AlignedEnd() - read.AlignedStart();
data/unanimity-3.3.0+dfsg/tests/unit/TestGenomicConsensus_Experimental.cpp:293:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto refLength = read.ReferenceEnd() - read.ReferenceStart();
data/unanimity-3.3.0+dfsg/tests/unit/TestGenomicConsensus_Experimental.cpp:293:54: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto refLength = read.ReferenceEnd() - read.ReferenceStart();
data/unanimity-3.3.0+dfsg/tests/unit/TestGenomicConsensus_Experimental.cpp:308:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads)
data/unanimity-3.3.0+dfsg/tests/unit/TestGenomicConsensus_Experimental.cpp:310:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto snr = read.SignalToNoise();
data/unanimity-3.3.0+dfsg/tests/unit/TestGenomicConsensus_Experimental.cpp:326:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (const auto& read : reads)
data/unanimity-3.3.0+dfsg/tests/unit/TestGenomicConsensus_Experimental.cpp:327:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
EXPECT_GE(read.ReadAccuracy(), minReadScore);
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:205:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
string read;
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:209:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::tie(read, strand) = Mutate(app, nmut, &gen);
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:210:50: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const vector<uint8_t> pws = RandomPW(read.length(), &gen);
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:213:66: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto arr1 = addRead(ai1, MappedRead(MkRead(read, snr, mdl, pws), strand, 0,
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:219:42: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << " " << read.length() << ", " << read << std::endl;
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:219:67: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << " " << read.length() << ", " << read << std::endl;
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:222:66: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const auto arr2 = addRead(ai2, MappedRead(MkRead(read, snr, mdl, pws), strand, 0,
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:228:42: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << " " << read.length() << ", " << read << std::endl;
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:228:67: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << " " << read.length() << ", " << read << std::endl;
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:254:42: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << " " << read.length() << ", " << read << " - " << result.str()
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:254:67: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << " " << read.length() << ", " << read << " - " << result.str()
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:265:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << " " << read.length() << ", " << read << std::endl;
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:265:63: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << " " << read.length() << ", " << read << std::endl;
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:307:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
string read;
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:311:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::tie(read, strand) = Mutate(app, nmut, &gen);
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:312:46: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const vector<uint8_t> pws = RandomPW(read.length(), &gen);
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:316:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
MappedRead(MkRead(read, snr, mdl, pws), strand, 0, tpl.length(), true, true));
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:321:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << " " << read.length() << ", " << read << std::endl;
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:321:59: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << " " << read.length() << ", " << read << std::endl;
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:326:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
MappedRead(MkRead(read, snr, mdl, pws), strand, 0, app.length(), true, true));
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:331:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << " " << read.length() << ", " << read << std::endl;
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:331:59: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << " " << read.length() << ", " << read << std::endl;
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:353:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << " " << read.length() << ", " << read << " - " << result.str()
data/unanimity-3.3.0+dfsg/tests/unit/TestIntegrator.cpp:353:59: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::cerr << " " << read.length() << ", " << read << " - " << result.str()
data/unanimity-3.3.0+dfsg/tests/unit/TestPlurality.cpp:44:22: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
EXPECT_TRUE(std::equal(expected.cbegin(), expected.cend(), basecalls.begin()));
data/unanimity-3.3.0+dfsg/tests/unit/TestPolish.cpp:55:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
MappedRead(MkRead(read, snr, mdl), StrandType::FORWARD, 0, tpl.length(), true, true));
data/unanimity-3.3.0+dfsg/tests/unit/TestPolish.cpp:56:52: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ai.AddRead(MappedRead(MkRead(ReverseComplement(read), snr, mdl), StrandType::REVERSE, 0,
data/unanimity-3.3.0+dfsg/tests/unit/TestPolish.cpp:59:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
MappedRead(MkRead(read, snr, mdl), StrandType::FORWARD, 0, tpl.length(), true, true));
data/unanimity-3.3.0+dfsg/tests/unit/TestPolish.cpp:73:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
EXPECT_EQ(read, string(ai));
data/unanimity-3.3.0+dfsg/tests/unit/TestSparsePoa.cpp:55:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (auto& read : reads) {
data/unanimity-3.3.0+dfsg/tests/unit/TestSparsePoa.cpp:56:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
SparsePoa::ReadKey id = sp.OrientAndAddRead(read);
data/unanimity-3.3.0+dfsg/tests/unit/TestSparsePoa.cpp:98:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (auto& read : reads) {
data/unanimity-3.3.0+dfsg/tests/unit/TestSparsePoa.cpp:99:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
SparsePoa::ReadKey id = sp.OrientAndAddRead(read);
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.c:70:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int32_t read; //alignment ending position on read, 0-based
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.c:81:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const int8_t* read;
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.c:564:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const int8_t* read,
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.c:635:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
temp2 = h_b[d] + mat[ref[j] * n + read[i]];
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.c:764:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
s_profile* ssw_init (const int8_t* read, const int32_t readLen, const int8_t* mat, const int32_t n, const int8_t score_size) {
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.c:777:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
p->profile_byte = qP_byte (read, mat, readLen, n, bias);
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.c:779:69: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (score_size == 1 || score_size == 2) p->profile_word = qP_word (read, mat, readLen, n);
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.c:780:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
p->read = read;
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.c:839:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
r->read_end1 = bests[0].read;
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.c:851:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read_reverse = seq_reverse(prof->read, r->read_end1);
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.c:862:51: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
r->read_begin1 = r->read_end1 - bests_reverse[0].read;
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.c:929:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const int8_t* read,
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.c:946:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (*ref != *read) {
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.c:957:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
++ read;
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.h:77:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
s_profile* ssw_init (const int8_t* read, const int32_t readLen, const int8_t* mat, const int32_t n, const int8_t score_size);
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw.h:152:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const int8_t* read,
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw_cpp.cpp:331:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int query_len = strlen(query);
data/unanimity-3.3.0+dfsg/third-party/cssw/ssw_cpp.cpp:366:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int query_len = strlen(query);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:2326:22: [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).
const int length = strlen(ansi);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:2986:34: [1] (buffer) wcslen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
num_chars = static_cast<int>(wcslen(str));
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:4740:32: [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).
segment = next_segment + strlen("]]>");
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:4905:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
result.reserve(strlen(str) + 1);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:6148:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const size_t prefix_len = strlen(prefix);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:8385:33: [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).
const size_t full_regex_len = strlen(regex) + 10;
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:8639:22: [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).
const size_t len = strlen(regex);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:9328:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
PrintCharsAsStringTo(s, strlen(s), os);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gmock-gtest-all.cc:9345:29: [1] (buffer) wcslen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
PrintCharsAsStringTo(s, wcslen(s), os);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gtest/gtest.h:2869:10: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
return strncpy(dest, src, n);
data/unanimity-3.3.0+dfsg/third-party/gmock-1.7.0/gtest/gtest.h:2891:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
return static_cast<int>(read(fd, buf, count));
ANALYSIS SUMMARY:
Hits = 377
Lines analyzed = 86916 in approximately 2.05 seconds (42344 lines/second)
Physical Source Lines of Code (SLOC) = 58698
Hits@level = [0] 60 [1] 326 [2] 27 [3] 15 [4] 9 [5] 0
Hits@level+ = [0+] 437 [1+] 377 [2+] 51 [3+] 24 [4+] 9 [5+] 0
Hits/KSLOC@level+ = [0+] 7.44489 [1+] 6.42271 [2+] 0.868854 [3+] 0.408873 [4+] 0.153327 [5+] 0
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.