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/libmaus2-2.0.766+dfsg/src/libmaus2/LibMausWindows.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/StaticInitialization.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/ArrayFile.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/ArrayFileContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/ArrayFileSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/ArrayInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/ArrayInputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/ArrayInputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/Buffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/BufferedOutput.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/CharArrayInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/CharArrayInputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/CharArrayOutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/CharArrayOutputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/CircularBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/CircularWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/CompactDecoder4.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/CompactEncoder4.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/ConcatInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/ConcatInputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/CountOutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/CountOutputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/DebugLineOutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/DebugLineOutputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/FStreamInputOutputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/FileFragment.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/FileRemoval.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/FileRemoval.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/GenericPeeker.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/GetLength.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/IFStreamInputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/IStreamWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputOutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputOutputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputOutputStreamFactoryContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputOutputStreamInstance.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputOutputStreamInstance.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputOutputStreamPointerWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputOutputStreamWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputStreamFactoryContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputStreamInstance.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputStreamInstance.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputStreamInstanceAtOffset.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputStreamObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputStreamObjectAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputStreamObjectTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputStreamPointerWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/InputStreamWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/LineSplittingPosixFdOutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/LineSplittingPosixFdOutputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryBackedOutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryBackedOutputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryFile.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryFileAdapter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryFileContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryInputOutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryInputOutputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryInputOutputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryInputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryInputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryOutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryOutputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryOutputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/NamedTemporaryFile.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/NamedTemporaryFileAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/NamedTemporaryFileTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/OFStreamOutputStreamFactory.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/OFStreamOutputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/OutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/OutputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/OutputStreamFactoryContainer.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/OutputStreamFactoryContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/OutputStreamInstance.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/OutputStreamInstance.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/OutputStreamInstanceArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/OutputStreamPointerWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/OutputStreamWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PairFileDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInput.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInput.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInputOutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInputOutputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInputOutputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInputWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdOutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdOutputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdOutputStreamFactory.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdOutputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PutOutputIterator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/ReorderConcatGenericInput.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SecrecyCache.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SecrecyInputStreamFactory.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SecrecyInputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SecrecyOutputStreamFactory.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SecrecyOutputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SerialisedPeeker.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SingleFileFragmentMerge.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SizeMonitorThread.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SkipConcatInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SkipConcatInputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SplitWriter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/StreamLock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SynchronousFastReaderBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SynchronousGenericInput.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SynchronousGenericOutput.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/TempFileArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/URLObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/WriteCompactArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/alignment/BamLineInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/alignment/FMIIntervalComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/alignment/FactorMatchInfo.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/alignment/FactorMatchInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/alignment/FactorMatchInfoPosComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/alignment/KmerInfo.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/alignment/KmerInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/alignment/KmerTuple.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/alignment/SimpleLocalAligner.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/arch/CacheLineSize.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/arch/CacheLineSize.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/arch/I386Features.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/arch/I386Features.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/arch/PageSize.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/arch/PageSize.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/autoarray/AutoArray.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/autoarray/AutoArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/autoarray/AutoArray2d.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/autoarray/AutoArrayAllocType.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/autoarray/AutoArrayMultiMap.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/avl/AVLSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/AdapterFilter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/AdapterOffsetStrand.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/AlignmentValidity.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/AlignmentValidity.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAccessor.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignment.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignment.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderBase.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderInfo.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentEncoderBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentExpungeCallback.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentFilter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentFixedSizeData.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentFreeList.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentHashComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentInputCallbackBam.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentInputCallbackSnappy.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentInputPositionCallbackNull.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentInputPositionUpdateCallback.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentListNode.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentNameComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentNameHIComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentNameLexicographicComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentPairFreeList.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentPairListNode.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentPosComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentPrinter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentReadGroupFilter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentReg2Bin.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentSnappyInput.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentSortingCircularHashEntryOverflow.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentTagComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAuxFilterVector.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAuxSortingBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAuxSortingBufferEntry.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamBlockWriterBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamBlockWriterBaseFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamCat.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamCatHeader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamDefaultAdapters.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamDefaultAdapters.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamEntryContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamFlagBase.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamFlagBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamFormatAuxiliary.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamHeader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamHeaderLowMem.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamHeaderParserState.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamHeaderParserStateBase.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamHeaderParserStateBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamHeaderReadGroupInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamHeaderUpdate.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndex.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexBin.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexBinChunk.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexBinChunk.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexGenerator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexLinear.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexLinearChunk.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexLinearChunk.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexMetaInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexRef.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamMergeCoordinate.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamMergeQueryName.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamMergeTemplate.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamMultiAlignmentDecoderFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamNumExtractor.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamNumericalIndexBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamNumericalIndexDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamNumericalIndexGenerator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamParallelRewrite.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamPeeker.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamRange.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamRange.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamRangeDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamRangeParser.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamRawDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamSeqEncodeTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamStreamingMarkDuplicates.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamStreamingMarkDuplicatesSupport.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamStreamingMarkDuplicatesSupport.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamToFastqOutputFileSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamWriter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BgzfDeflateOutputCallbackBamIndex.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BgzfDeflateOutputCallbackBamNumericalIndex.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ChecksumsFactory.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ChecksumsFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ChecksumsInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ChecksumsInterfaceAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ChecksumsInterfaceTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Chromosome.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ChromosomeVectorMerge.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/CigarDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/CigarOperation.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/CigarRunLengthDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/CigarStringParser.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/CigarStringParser.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/CigarStringReader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/CircularHashCollatingBamDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/CollatingBamDecoderAlignmentInputCallback.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/CompactReadEndsBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/CompactReadEndsComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/CramRange.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/DecoderBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/DupMarkBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/DupSetCallback.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/DupSetCallbackSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/DupSetCallbackSharedVector.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/DupSetCallbackStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/DupSetCallbackVector.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/DuplicationMetrics.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/DuplicationMetrics.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/EncoderBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/GeneFlatFile.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/GeneFlatFile.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/GeneFlatFileEntry.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/GeneFlatFileEntry.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/HeaderLine.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/MdNmRecalculation.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/MdStringComputationContext.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/MergeQueueElement.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/OptName.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/OptNameReader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/OpticalComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/PileQualityVectorElement.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/PileQualityVectorElement.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/PileVectorElement.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/PileVectorElement.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ProgramHeaderLineSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEnds.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEnds.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsBaseLongHashAttributeComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsBasePointerComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsBaseShortHashAttributeComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsBlockDecoderBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsBlockDecoderBaseCollection.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsBlockDecoderBaseCollectionInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsBlockDecoderBaseCollectionInfoBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsBlockIndexSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsContainer.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsContainerBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsFreeList.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsHeapPairComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsListNode.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsStreamDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsStreamDecoderBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsStreamDecoderFileBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadGroup.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadGroup.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/RgInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamDecoderWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfoAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfoBase.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfoBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfoTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamPrintableTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamZPrintableTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.h Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ScramDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ScramEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ScramInputContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SeqChksumPrimeNumbers.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SeqChksumUpdateContext.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SnappyAlignmentMergeInput.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SortedFragDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/StrCmpNum.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/StrCmpNum.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/StrCmpNumRecode.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AddDuplicationMetricsInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AddPendingCompressBufferWriteInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AddWritePendingBgzfBlockInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentBlockCompressPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentBlockCompressPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentBufferAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentBufferHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentBufferReinsertInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentBufferReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentBufferTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentRewriteBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentRewriteBufferAddPendingInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentRewriteBufferAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentRewriteBufferCoordinateComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentRewriteBufferPosComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentRewriteBufferReinsertForFillingInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentRewritePosMergeSortPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentRewritePosSortBaseSortPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentRewritePosSortContext.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentRewritePosSortContextBaseBlockSortedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentRewritePosSortContextMergePackageFinished.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BamBlockIndexingBlockFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BamBlockIndexingWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BamBlockIndexingWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BamBlockIndexingWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BamBlockNumericalIndexingBlockFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BamBlockNumericalIndexingWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BamBlockNumericalIndexingWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BamBlockNumericalIndexingWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BaseMergeSortWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BaseSortWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BaseSortWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BgzfInflateZStreamBaseGetInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BgzfInflateZStreamBaseReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BgzfLinearMemCompressWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BgzfLinearMemCompressWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BgzfLinearMemCompressWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BgzfOutputBlockWrittenInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BlockCompressPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BlockMergeControl.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BlockMergeControlTypeBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BlockSortControl.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BlockSortControlBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ChecksumsInterfaceGetInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ChecksumsInterfacePutInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CompressBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CompressBufferAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CompressBufferHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CompressionPendingElement.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ControlInputInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramEncodingSupportData.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramEncodingWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramEncodingWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramEncodingWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramInterface.h Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramOutputBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramOutputBlockChecksumComputedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramOutputBlockChecksumPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramOutputBlockChecksumPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramOutputBlockChecksumPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramOutputBlockIdComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramOutputBlockSizeComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramOutputBlockWritePackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramOutputBlockWritePackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramOutputBlockWritePackageFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramOutputBlockWritePackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramPassPointerObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramPassPointerObjectAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramPassPointerObjectComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/CramPassPointerObjectTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/DecompressBlockWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/DecompressBlockWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/DecompressBlockWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/DecompressBlocksWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/DecompressBlocksWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/DecompressBlocksWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/DecompressedBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/DecompressedBlockAddPendingInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/DecompressedBlockAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/DecompressedBlockHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/DecompressedBlockReorderHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/DecompressedBlockReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/DecompressedBlockTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/DecompressedPendingObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/DecompressedPendingObjectHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FastQInputDesc.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FastQInputDescBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FastqInputPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FastqInputPackageAddPendingInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FastqInputPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FastqInputPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FastqParsePackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FastqParsePackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FastqParsePackageFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FastqParsePackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FastqToBamControl.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FastqToBamControlInputBlockHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FastqToBamControlSubReadPending.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FastqToBamControlSubReadPendingHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FileChecksumBlockFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FileChecksumBlockWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FileChecksumBlockWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FileChecksumBlockWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragReadEndsContainerFlushFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragReadEndsContainerFlushWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragReadEndsContainerFlushWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragReadEndsContainerFlushWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragReadEndsMergeWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragReadEndsMergeWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragReadEndsMergeWorkPackageFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragReadEndsMergeWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferBaseSortPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferBaseSortWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferBaseSortWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferFragment.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferMergeSortPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferMergeSortWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferMergeSortWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferMergeSortWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferNameComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferPointerTypeSwitch.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferPointerTypeSwitchHelper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferPosComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferQueryNameComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferReorderWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferReorderWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferReorderWorkPackageFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferReorderWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteFragmentCompleteInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteReadEndsWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteReadEndsWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteReadEndsWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteUpdateInterval.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferSortContext.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferSortContextBaseBlockSortedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferSortContextMergePackageFinished.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferSortFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBamParseObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBamParseWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBamParseWorkPackageBlockParsedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBamParseWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBamParseWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBgzfDecompressionWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBgzfDecompressionWorkPackageDecompressedBlockReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBgzfDecompressionWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBgzfDecompressionWorkPackageMemInputBlockReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBgzfDecompressionWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBgzfDecompressionWorkSubBlockDecompressionFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBlockAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBlockFillResult.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBlockSubBlockInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBlockTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlBlockCompressionFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlBlockCompressionWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlBlockCompressionWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlBlockCompressionWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlBlockWritePackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlBlockWritePackageBlockWrittenInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlBlockWritePackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlBlockWritePackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlBlocksWritePackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlBlocksWritePackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlBlocksWritePackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlCompressionPending.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlCompressionPendingHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlGetCompressorInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlMergeBlockFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlMergeHeapEntry.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlMergeRequeue.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlPutCompressorInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlReadAddPendingInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlReadWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlReadWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlReadWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlReorderWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlReorderWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlReorderWorkPackageFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlReorderWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlSetMergeStallSlotInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlStreamInfo.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlStreamInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlSubBlockPending.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputControlSubBlockPendingHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputMergeDecompressedBlockReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputMergeWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputMergeWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputMergeWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputMergeWorkRequest.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputSingleData.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputSingleDataBamParseInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GetBgzfDeflateZStreamBaseInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/InputBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/InputBlockAddPendingInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/InputBlockAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/InputBlockReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/InputBlockTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/InputBlockWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/InputBlockWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/InputBlockWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/MemInputBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/MergeSortWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/PairReadEndsContainerFlushFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/PairReadEndsContainerFlushWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/PairReadEndsContainerFlushWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/PairReadEndsContainerFlushWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/PairReadEndsMergeWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/PairReadEndsMergeWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/PairReadEndsMergeWorkPackageFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/PairReadEndsMergeWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ParseBlockWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ParseBlockWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ParseInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ParseInfoHeaderCompleteCallback.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ParsePackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ParsedBlockAddPendingInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ParsedBlockStallInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/PushBackSpace.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/PutBgzfDeflateZStreamBaseInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ReadEndsContainerAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ReadEndsContainerFreeListInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ReadEndsContainerTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ReadEndsMergeRequest.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/RefIdInterval.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/RefIdInterval.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/RequeReadInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ReturnBgzfOutputBufferInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ReturnCompressionPendingElementInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ReturnRewriteBufferInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/RewriteBlockWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/RewriteBlockWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/RewritePackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SamEncoderObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SamEncodingWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SamEncodingWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SamEncodingWorkPackageWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SamEncodingWorkPackageWrapperReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SamParseDecompressedBlockFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SamParseFragmentParsedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SamParseGetSamInfoInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SamParsePending.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SamParsePendingHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SamParsePutSamInfoInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SamParseWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SamParseWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SamParseWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ScramCramEncoding.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SmallLinearBlockCompressionPendingObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SmallLinearBlockCompressionPendingObjectFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SmallLinearBlockCompressionPendingObjectHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SortControl.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/SortFinishedInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ValidateBlockAddPendingInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ValidateBlockFragmentAddPendingInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ValidateBlockFragmentPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ValidateBlockFragmentWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ValidateBlockFragmentWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ValidateBlockWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ValidateBlockWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ValidatePackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ValidationFragment.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/ValidationFragment.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/WriteBlockWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/WriteBlockWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/WriteBlockWorkPackageReturnInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/WritePendingObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/WritePendingObjectHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitbtree/bitbtree.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/ArrayDecode.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitIO.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitIOInput.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitIOOutput.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitStreamFileDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitVector.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitVectorConcat.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitVectorInput.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitVectorOutput.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitWriter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BufferIterator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/CheckedBitWriter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/Clz.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/CompactArray.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/CompactArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/CompactArrayBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/CompactArrayWriter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/CompactArrayWriterFile.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/CompactDecoderBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/CompactOffsetArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/CompactOffsetOneArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/CompactQueue.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/CompactSparseArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/Ctz.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/FastWriteBitWriter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/MarkerFastWriteBitWriter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/OutputBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/PacDecoderBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/ReverseTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/SignedCompactArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/SwapWordBitBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/getBit.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/getBits.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/putBit.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/putBits.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/readElias.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/swapBitBlocksByReversal.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/btree/btree.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/clustering/HashCreation.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/clustering/HashCreationBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/clustering/KMeans.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/clustering/KmerBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/clustering/ProduceEdgeRequest.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/cumfreq/DynamicCumulativeFrequencies.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/cumfreq/SlowCumFreq.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/AlignmentFile.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/AlignmentFileCat.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/AlignmentFileConstants.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/AlignmentFileDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/AlignmentFileRegion.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/AlignmentFileSymmetryCheck.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/AlignmentSplitWriter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/AlignmentWriter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/AlignmentWriterArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/ApproximateRun.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/ApproximateRun.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/ApproximateRunPartContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/BinIndexDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/CompactRunPartContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/DalignerIndexDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/FilterUnique.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GetTransitiveStrict.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphCheck.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphDecoderContext.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphDecoderContextAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphDecoderContextTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/LASToBamConverterBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/LasFileRange.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/LasIntervals.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/LasMerge2.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/LasRangeDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/LasSort2.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/LasSort2Cascade.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/Overlap.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/Overlap.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapAdapter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapData.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapDataInterface.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapDataInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapHeader.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapHeader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapIndexer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapIndexerBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapInfo.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapInfoIndexer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapMeta.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapMeta.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapMetaIteratorGet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapParser.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapProperCheck.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/Path.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/Path.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/ReadIntervals.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/ReadIntervalsVector.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/RefMapEntry.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/RefMapEntryVector.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/SimpleOverlapParser.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/SimpleOverlapVectorParser.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/SortOrderCheck.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/SortingOverlapBlockInput.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/SortingOverlapOutputBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/SortingOverlapOutputBufferMerger.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/SubIntervalResult.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/Tandem.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/Tandem.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/TandemVector.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/TandemVector.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/TandemVectorPartContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/TraceBlock.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/TraceBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/TraceBlockVectorCache.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/TracePoint.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/TracePoint.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/TrueOverlap.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/TrueOverlapStats.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/FastaInfo.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/FastaInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/GetByteCounter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/IQVDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/IndexBase.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/IndexBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/InputBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/InqualContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/OutputBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/PartTrackContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/Read.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/Read.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/ReadContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/ReadLRUContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/SatsContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/StringTrackWriter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/Track.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/TrackAnno.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/TrackAnnoInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/TrackExtra.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/stringgraph/ContainmentInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/stringgraph/Edge.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/stringgraph/OverlapNode.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/stringgraph/StringGraph.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/stringgraph/TraversalElement.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/deleter/Deleter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/demangle/Demangle.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/demangle/Demangle.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/CRC32.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/CRC32.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/CRC32C.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/CRC32C.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/CRC32C_Core.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/CRC32C_Core.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/CRC32_Core.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/CRC32_Core.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/DigestBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/DigestFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/DigestFactoryContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/DigestFactoryInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/DigestInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/Digests.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/MurmurHash3_x64_128.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/Null.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/SHA1.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/SHA1.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/SHA2_224.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/SHA2_224.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/SHA2_256.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/SHA2_256.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/SHA2_384.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/SHA2_384.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/SHA2_512.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/SHA2_512.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/SHA3_256.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/SHA3_256.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/md5.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/md5.h Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/md5.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/md5_interface.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/eta/LinearETA.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/exception/LibMausException.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/exception/LibMausException.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/BgzfFastAIndexEntry.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/BgzfFastAIndexEntryIdComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/BgzfFastAIndexEntryNameComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CharBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CharTermTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactFastDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactFastDecoderBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactFastEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactFastQBlockGenerator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactFastQContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactFastQContainerDictionary.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactFastQContainerDictionaryCreator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactFastQContext.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactFastQDecoderBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactFastQHeader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactFastQMultiBlockReader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactFastQSingleBlockReader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactFastReplace.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactFastTerminator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactReadContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/ComputeFastXIntervals.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/ConcatWriter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CoordinateCache.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CoordinateCacheBiDir.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/DNAIndexMetaData.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/DNAIndexMetaData.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/DNAIndexMetaDataBigBand.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/DNAIndexMetaDataBigBand.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/DNAIndexMetaDataBigBandBiDir.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/DNAIndexMetaDataBigBandBiDir.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/DNAIndexMetaDataSequence.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/DNAIndexMetaDataSequence.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FASTQEntry.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastABPConstants.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastABPGenerator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastABgzfDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastABgzfDecoderBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastABgzfIndex.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastABgzfIndex.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastABgzfIndexEntry.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastABgzfIndexEntry.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastADefinedBasesTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAIndex.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAIndex.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAIndexEntry.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAIndexEntry.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAIndexGenerator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastALineParser.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastALineParserLineInfo.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastALineParserLineInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAMapTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAMatchTable.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAMatchTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAReader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAReaderSplit.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAStreamSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAStreamWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAToCompact4BigBand.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAToCompact4BigBand.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAToCompact4BigBandBiDir.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastATwoBitTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastFirstToLastReverseAdapter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastIDBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastInterval.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastQBgzfWriter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastQElement.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastQReader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastQReaderSplit.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaBPDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaBPSequenceDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaPeeker.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastqPeeker.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FirstWhiteSpaceSlashStrip.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FqWeightQuantiser.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/GCContent.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/GzipFileFastQReader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/GzipStreamFastQReader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/KmerCount.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/KmerFreqInWindowStats.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/KmerRepeatDetector.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/LineBufferFastAReader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/MultiWordDNABitBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/NameInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/NameInfoBase.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/NameInfoBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/Pattern.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/PatternBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/Phred.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/Phred.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/QReorder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/ReadContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/RefPathLookup.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/RefPathToken.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/RefPathToken.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/RefPathTokenVector.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/RefPathTokenVector.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/RefPathTokenVectorSequence.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/SingleWordDNABitBuffer.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/SingleWordDNABitBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/SlashStrip.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/SpaceTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/StreamFastAReader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/StreamFastQReader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/StreamFastReaderBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/SubSamplingFastReader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/acgtnMap.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/isFastQ.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/isFastQ.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fm/BiIndex.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fm/BidirectionalDnaIndexTemplate.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fm/BidirectionalIndexInterval.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fm/BidirectionalIndexInterval.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fm/BidirectionalIndexIntervalSymbol.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fm/BidirectionalIndexIntervalSymbol.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fm/DictionaryInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fm/DictionaryInfoImpCompactHuffmanWaveletTree.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fm/FA4CompactSampledSuffixArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fm/FM.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fm/KmerCache.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fm/MausFmToBwaConversion.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fm/MausFmToBwaConversion.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fm/SampledISA.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/fm/SampledSA.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/FlaggedInterval.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaDecoderBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaDifferenceDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaDifferenceEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaDifferenceMerge.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaDifferenceOutputBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaEncoderBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaFlaggedIntervalDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaFlaggedIntervalEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaFlaggedPartitionDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaFlaggedPartitionEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaGapDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaGapEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaGenericBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaGenericClz.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaGenericDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaGenericEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaIntervalDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaIntervalEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaPDDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaPDEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaPDIndexDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaPDIndexDecoderBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaPartitionDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaPartitionEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaRLDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/GammaRLEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/Interval.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SimpleGammaDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SimpleGammaDecoderData.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SimpleGammaEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SimpleGammaEncoderArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SimpleGammaEncoderData.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SparseGammaGapBlockEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SparseGammaGapConcatDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SparseGammaGapDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SparseGammaGapEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SparseGammaGapFile.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SparseGammaGapFileIndexDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SparseGammaGapFileIndexDecoderEntry.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SparseGammaGapFileIndexDecoderEntry.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SparseGammaGapFileIndexMultiDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SparseGammaGapFileLevelSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SparseGammaGapFileSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SparseGammaGapMerge.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SparseGammaGapMultiFile.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SparseGammaGapMultiFileLevelSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gamma/SparseGammaGapMultiFileSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/geometry/IntervalTree.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/geometry/RangeSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/graph/IdentityTargetProjector.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/graph/ReachableVertices.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/graph/StronglyConnectedComponents.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/graph/TopologicalSorting.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/BAMGTFMap.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/CDS.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/CDS.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/Exon.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/Exon.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/ExonIdOffsetComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/ExonInfo.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/ExonInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/ExonInterval.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/ExonInterval.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/ExonSubInfo.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/ExonSubInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GTFData.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/Gene.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GeneChrComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GeneRangeSets.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/IntervalList.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/IntervalListSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/RangeSets.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/Tag.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/Transcript.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/TranscriptRangeSets.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/hashing/CircularHash.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/hashing/ConstantStringHash.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/hashing/Crc32.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/hashing/Crc32.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/hashing/MurmurHash3.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/hashing/MurmurHash3.h Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/hashing/hash.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/BitInputBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/CanonicalEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/CompressTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/DecodeTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/EncodeTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/FileStreamBaseType.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/GapDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/GapDecoderIndexBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/GapEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/HuffmanBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/HuffmanEncoderFile.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/HuffmanInputFile.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/HuffmanSorting.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/HuffmanTree.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/HuffmanTree.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/HuffmanTreeInnerNode.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/HuffmanTreeLeaf.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/HuffmanTreeLeafComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/HuffmanTreeNode.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexDecoderDataArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexEntry.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoaderBase.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoaderBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexWriter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/InputAdapter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/KvInitResult.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/KvInitResult.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFPhiPair.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFPhiPairDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFPhiPairEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFPhiPairLCP.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFPhiPairLCPDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFPhiPairLCPEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFRankLCP.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFRankLCPDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFRankLCPEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFRankPos.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFRankPosDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFRankPosEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFSetBit.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFSetBitDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFSetBitEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFSupportBitDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFSupportDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFSupportEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFSymRankPos.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFSymRankPosDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFSymRankPosEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFValue.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFValueDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFValueEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/OutputAdapter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/PairAddSecond.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/RLDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/RLDecoderIndexBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/RLEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/RLInitType.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/RLRun.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/SymBit.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/SymBitDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/SymBitEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/SymBitRun.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/SymCount.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/SymCountDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/SymCountEncoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/SymCountRun.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/hufEncodeString.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/huffman.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/index/ExternalMemoryIndexDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/index/ExternalMemoryIndexDecoderFindLargestSmallerResult.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/index/ExternalMemoryIndexGenerator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/index/ExternalMemoryIndexRecord.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcp/ComputeSuccinctLCPResult.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcp/LCP.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcp/PLCPBitDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcp/SuccinctLCP.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcp/WaveletLCP.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcp/WaveletLCPResult.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/Aligner.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/AlignerFactory.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/AlignerFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/AlignmentOneAgainstManyAVX2.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/AlignmentOneAgainstManyAVX2.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/AlignmentOneAgainstManyFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/AlignmentOneAgainstManyGeneric.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/AlignmentOneAgainstManyInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/AlignmentPrint.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/AlignmentStatistics.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/AlignmentStatistics.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/AlignmentTraceContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/BandedAligner.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/BandedAlignerFactory.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/BandedAlignerFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/BandedEditDistance.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/BandedLocalEditDistance.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/BaseConstants.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/BitVector.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/BitVectorResultCallbackInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/Chain.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/Chain.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainAddQueueElement.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainAddQueueElement.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainAddQueueElementHeapComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainAlignment.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainLeftMostComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainNode.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainNode.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainNodeInfo.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainNodeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainNodeInfoSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainRemoveQueueElement.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainRemoveQueueElement.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainRemoveQueueElementComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainSplayTreeNode.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainSplayTreeNode.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainSplayTreeNodeComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/CheckSelf.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/DistNodeType.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/EditDistance.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/EditDistancePriorityType.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/EditDistanceResult.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/EditDistanceResult.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/EditDistanceTraceContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/GenericAlignmentPrint.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/GenericEditDistance.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/LCS.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/LCSDynamic.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/LCSRef.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/LocalAlignmentPrint.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/LocalAlignmentTraceContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/LocalBaseConstants.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/LocalBaseConstants.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/LocalEditDistance.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/LocalEditDistanceResult.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/LocalEditDistanceResult.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/LocalEditDistanceTraceContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/LocalPenaltyConstants.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/MetaEditDistance.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/MetaLocalEditDistance.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNP.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPAlignResult.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPAlignResult.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPCor.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPCorL.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPCorLocalAligner.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPLocalAligner.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPTraceContainer.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPTraceContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPTraceElement.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPTraceElement.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NP.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NPL.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NPLLinMem.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NPLNoTrace.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NPLinMem.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NPNoTrace.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/OverlapOrientation.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/PenaltyConstants.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/PosMapping.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SMEMProcessor.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ScoreBandedAligner.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreTemplate.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreTemplate.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreY256_16.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreY256_16.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreY256_16_def.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreY256_16_undef.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentTemplate.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentTemplate.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentX128_16.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentX128_16.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentX128_16_def.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentX128_16_undef.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentX128_8.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentX128_8.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentX128_8_def.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentX128_8_undef.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_16.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_16.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_16_def.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_16_undef.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_8.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_8.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_8_def.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_8_undef.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentConstants128.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentConstants128.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentConstants256.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentConstants256.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentScoreConstants256.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentTemplate.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentTemplate.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentX128_16.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentX128_16.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentX128_16_def.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentX128_16_undef.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentX128_8.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentX128_8.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentX128_8_def.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentX128_8_undef.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentY256_16.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentY256_16.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentY256_16_def.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentY256_16_undef.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentY256_8.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentY256_8.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentY256_8_def.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86GlobalAlignmentY256_8_undef.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SuffixArrayLCS.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SuffixPrefix.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SuffixPrefixAlignmentPrint.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SuffixPrefixResult.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/TraceContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/TwoSidedNPL.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lf/DArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lf/HuffmanLF.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lf/ImpCacheLineRankLF.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lf/ImpCacheLineRankLFNonZero.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lf/ImpCompactHuffmanWaveletLF.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lf/ImpHuffmanWaveletLF.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lf/ImpWTLF.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lf/LF.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lf/LFBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lf/LFZero.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lf/MultiRankCacheLF.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lf/MultiRankLF.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lf/QuickLF.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lf/RLIndexLF.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lru/FileBunchLRU.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lru/LRU.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lru/SparseLRU.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lru/SparseLRUFileBunch.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfConstants.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflate.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateBlockIdComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateBlockIdInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateHeaderFunctions.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateHeaderFunctions.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateInputBufferBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateOutputBufferBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateOutputBufferBaseAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateOutputBufferBaseTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateOutputCallback.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateOutputCallbackMD5.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateParallel.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateParallelContext.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateParallelThread.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateZStreamBase.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateZStreamBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateZStreamBaseAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateZStreamBaseFlushInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateZStreamBaseTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflate.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateBaseAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateBaseTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateBlockIdComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateBlockIdInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateDecompressPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateDeflateParallel.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateDeflateParallelInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateDeflateParallelThread.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateDeflateParallelWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateFile.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateHeaderBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateParallel.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateParallelContext.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateParallelStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateParallelThread.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateParallelWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateReadPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateThreadPoolReader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateZStreamBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateZStreamBaseAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateZStreamBaseTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInputContext.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfParallelRecodeDeflateBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfRecode.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfRecodeParallel.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfStreamWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfThreadOpBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfVirtualOffset.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BufferedGzipStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BufferedGzipStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BufferedGzipStreamWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/CompressorObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/CompressorObjectFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/CompressorObjectFreeListAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/CompressorObjectFreeListAllocatorFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/DecompressorObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/DecompressorObjectFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/DeflateDefaults.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/GzipHeader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/GzipOutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/GzipOutputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/GzipSingleStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/GzipStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/GzipStreamWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Inflate.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/IsGzip.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/IstreamSource.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/LineSplittingGzipOutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/LineSplittingGzipOutputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Lz4Base.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Lz4Base.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Lz4Compress.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Lz4Compress.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Lz4CompressStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Lz4CompressStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Lz4CompressWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Lz4Decoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Lz4DecoderBuffer.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Lz4DecoderBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Lz4Index.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/PlainOrGzipStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/PlainOrGzipStreamBufferWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SimpleCompressedConcatInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SimpleCompressedConcatInputStreamFragment.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SimpleCompressedInputBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SimpleCompressedInputBlockConcat.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SimpleCompressedInputBlockConcatBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SimpleCompressedInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SimpleCompressedOutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SimpleCompressedStreamInterval.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SimpleCompressedStreamNamedInterval.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyCompress.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyCompress.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyCompressorObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyCompressorObjectFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyCompressorObjectFactoryWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyCompressorObjectFreeListAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyDecompressorObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyDecompressorObjectFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyFileInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyFileOutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyInputStreamArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyInputStreamArrayFile.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyOffsetFileInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyOutputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyStringInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/StdOstreamSink.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/StreamWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/StreamWrapperBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/XzDecoder.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/XzDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/XzInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/XzInputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/ZlibCompressorObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/ZlibCompressorObjectFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/ZlibCompressorObjectFactoryWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/ZlibCompressorObjectFreeListAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/ZlibDecompressorObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/ZlibDecompressorObjectFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/ZlibInterface.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/ZlibInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/lz4.c Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/lz4.h Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/Bernoulli.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/BernoulliNumber.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/ClusteredBernoulli.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/ConstantSumCombinatorics.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/Convolution.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/DecimalNumberParser.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/Distribution.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/DoubleCode.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/Faulhaber.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/GeneralisedBernoulli.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/GeneralisedClusterBernoulli.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/GmpFloat.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/GmpFloat.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/GmpInteger.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/GmpInteger.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/HistogramBuckets.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/IPower.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/IntegerInterval.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/LGammaCache.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/Log.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/LogNormalDistribution.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/Matrix.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/MetaLog.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/NormalDistribution.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/Rational.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/RationalPolynomialSupport.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/RepetetiveKmerFreqEstimate.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/UnsignedInteger.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/binom.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/bitsPerNum.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/gcd.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/iabs.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/ilog.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/ipow.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/isqrt.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/lowbits.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/numbits.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/primes16.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/math/primes16.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlInitObject.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlInitObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlInputStream.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlInputStreamBuffer.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlInputStreamBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlObject.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlObjectReader.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlObjectReader.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlObjectThreadCallable.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlObjectThreadCallable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlOutputBlock.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlOutputBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlResponseAcceptor.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlResponseAcceptor.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/FileUrl.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/FtpCurlResponseAcceptor.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/FtpCurlResponseAcceptor.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/GetHostName.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/GetHostName.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/HttpCurlResponseAcceptor.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/HttpCurlResponseAcceptor.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/UrlBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/UrlInputStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/UrlInputStreamBufferWrapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/network/UrlInputStreamFactory.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/LockedBool.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/LockedCounter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/LockedFreeList.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/LockedGrowingFreeList.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/LockedHeap.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/LockedQueue.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/NumCpus.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/OMPNumThreadsScope.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/SimpleThreadPool.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/SimpleThreadPoolBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/SimpleThreadPoolInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/SimpleThreadPoolInterfaceEnqueTermInterface.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/SimpleThreadPoolThread.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/SimpleThreadPoolThreadId.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/SimpleThreadPoolThreadIdNode.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/SimpleThreadPoolThreadIdTree.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/SimpleThreadPoolWorkPackageFreeList.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/SimpleThreadWorkPackage.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/SimpleThreadWorkPackage.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/SimpleThreadWorkPackageComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/SimpleThreadWorkPackageDispatcher.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/StaticInitialisation.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/StdBasicSpinLock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/StdMutex.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/StdMutex.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/StdSemaphore.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/StdSemaphore.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/StdSpinLock.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/StdSpinLock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/StdSynchronousConditionQueue.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/StdSynchronousHeap.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/StdSynchronousQueue.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/StdTerminatableSynchronousHeap.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/StdTerminatableSynchronousQueue.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/StdThread.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/SynchronousCounter.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/threadpool/ThreadPool.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/threadpool/bgzf/BGZFInputThread.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/threadpool/bgzf/DecompressThread.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/threadpool/input/ThreadPoolInput.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixExecute.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixExecute.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixFunctions.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixFunctions.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/protein/Align.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/protein/Blosum62.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/protein/Blosum62.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/protein/CodonMapper.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/protein/CodonMapper.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/quantisation/ClusterComputation.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/quantisation/KmeansDataType.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/quantisation/Quantiser.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/random/GaussianRandom.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/random/LogNormalRandom.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/random/Poisson.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/random/Random.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/random/UniformUnitRandom.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/BSwapBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/CacheLineRank.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ChooseCache.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/CodeBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DNARank.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DNARankBiDir.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DNARankBiDirRange.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DNARankBiDirRange.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DNARankBiDirRangeSizeComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DNARankGetPosition.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DNARankKmerCache.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DNARankMEM.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DNARankMEM.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DNARankMEMPosComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DNARankSMEMComputation.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DNARankSMEMContext.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DNARankSuffixTreeNodeEnumerator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DNARankSuffixTreeNodeEnumeratorQueueElement.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DecodeCache.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ERank.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ERank2.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ERank22.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ERank222.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ERank222B.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ERank222BAppend.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ERank222BAppendDynamic.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ERank222BBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ERank222BP.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ERank22B.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ERank3.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ERank3C.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ERankBase.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ERankBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/EncodeCache.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/FastRank.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/ImpCacheLineRank.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/Proc01.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/RankTable.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/RankTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/RunLengthBitVector.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/RunLengthBitVectorBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/RunLengthBitVectorGenerator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/RunLengthBitVectorGeneratorBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/RunLengthBitVectorGeneratorGammaBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/RunLengthBitVectorStream.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/log2table.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/log2table.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/popcnt.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rl/RLIndex.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rmq/CartesianTree.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rmq/QuickDynamicRMQ.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/rmq/RMMTree.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/select/ESelect222B.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/select/ESelectBase.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/select/ESelectBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/select/ESelectSimple.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/select/ImpCacheLineSelectSupport.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/serialize/Serialize.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/InPlaceParallelSort.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/InterleavedRadixSort.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/MergeStepBinSearchResult.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/MergingReadBack.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/PairFileSorting.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/ParallelExternalRadixSort.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/ParallelRadixSort.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/ParallelRunLengthRadixSort.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/ParallelRunLengthRadixUnsort.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/ParallelStableSort.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/SemiExternalKeyTupleSort.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/SerialRadixSort64.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/SortingBufferedOutputFile.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/sorting.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/stacktrace/StackLineTranslator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/stacktrace/StackTrace.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/stacktrace/StackTrace.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/stacktrace/StackTraceBufferContainer.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/stacktrace/StackTraceBufferContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/BwtMergeBlockSortRequest.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/BwtMergeBlockSortRequest.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/BwtMergeBlockSortRequestBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/BwtMergeBlockSortResult.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/BwtMergeEnumBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/BwtMergeTempFileNameSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/BwtMergeTempFileNameSetVector.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/BwtMergeZBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/BwtMergeZBlockRequest.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/BwtMergeZBlockRequestVector.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/ByteInputTypes.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/CircularBwt.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/CircularSuffixComparator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/CompactInputTypes.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/GapArrayByte.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/GapArrayByteDecoder.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/GapArrayByteDecoderBuffer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/GapArrayByteOverflowKeyAccessor.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/GapMergePacket.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/Lz4InputTypes.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/PacInputTypes.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/PacTermInputTypes.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/SkewSuffixSort.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/SmallestRotation.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/Utf8InputTypes.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BWTB3MBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BaseBlockSortThread.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BaseBlockSorting.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtComputeSSA.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtComputeSSA.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSort.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSort.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortOptions.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortResult.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortResult.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtSelectSSA.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtSelectSSA.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyBaseBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyConstruction.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeExternalBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeGapRequest.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeGapRequest.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeGapRequestQueryObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeInput.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeInput.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeInternalBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeInternalSmallBlock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/divsufsort.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/divsufsort.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixtree/CompressedSuffixTree.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixtree/CompressedSuffixTree.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/sv/sv.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/timing/RealTimeClock.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/timing/RealTimeClock.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/trie/SimpleTrie.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/trie/SimpleTrie.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/trie/TrieState.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/types/types.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/uint/uint.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/AlphaDigitTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/AlphaTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ArgInfo.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ArgInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ArgInfoParseBase.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ArgParser.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ArgParser.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ArrayIterator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/AutoArrayCharBaseAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/AutoArrayCharBaseTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/AutoArrayUInt8TBaseAllocator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/AutoArrayUInt8TBaseTypeInfo.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Base64.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/BitList.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/BitList.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/BitsPerNum.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/BorderArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/CompactNumberArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Concat.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Concat.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ConcatRequest.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ConcatRequest.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ConsoleColor.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ConsoleColor.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ContainerDescription.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ContainerDescriptionList.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ContainerElementFreeList.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ContainerGetObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/CountGetObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/CountPutIterator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/CountPutObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Destructable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/DigitTable.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/DirectoryStructure.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/DynamicLoading.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/DynamicLoading.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Enumerator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/FileEnumerator.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/FileTempFileContainer.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/FiniteSizeHeap.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/FreeList.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/GenericIntervalTree.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/GenericIntervalTree.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/GenericSerialisation.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/GetFileSize.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/GetFileSize.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/GetObject.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/GrowingFreeList.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Histogram.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Histogram.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/HistogramSet.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/HistogramSet.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ImpCompactNumberArray.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/IncreasingList.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/IncreasingList.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/IntervalTree.cpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/IntervalTree.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/KMP.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/LELoad.hpp Examining data/libmaus2-2.0.766+dfsg/src/libmaus2/util/LineAccessor.hpp Examining 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data/libmaus2-2.0.766+dfsg/src/test/testbamrewrite.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testbamtofastq.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testbamwriter.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testbandedlcs.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testbitbtree.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testbtree.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testbwtconstruction.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testbwtconstructionfasta.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testbwtmergeinternal.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testbytecnt.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testbytetocompact.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testcachealignedalloc.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testcirchash.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testcollatespeed.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testcompact.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testcompactfastrandom.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testconvpowercache.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testcst.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testdazzleralignmentrewrite.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testdazzlerdb.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testdazzlerindex.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testdecimalnumberparser.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testdiag.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testdifenc.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testdl.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testdnarank.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testdnasuffixtrav.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testeditdistance.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testexternalmemoryindex.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testexternalsort.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testfaextract.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testfaindex.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testfastablockrecode.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testfastaexplode.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testfastaparse.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testfastarecode.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testfastarewrite.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testfastashred.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testfastasingleline.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testfastqstream.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testfastqtobam.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testfqbgzf.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testftp.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testgammapd.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testgaparraybyte.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testgeneflatfile.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testgunzip.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testhashcollisions.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testhist.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testintervaltree.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testkcnt.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testkmp.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testlassort.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testlibarchive.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testlibcurl.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testlinebuffer.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testlognormal.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testlowbits.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testlowmembamheaderparser.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testlru.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testlz.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testmapperm.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testmatrix.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testmd5.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testmurmur3.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testnnplocalaligner.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testnpl.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testnumcpus.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testoverlap.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testpacdecode.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testpanic.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testparallelbamblocksort.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testparallelbamrewrite.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testparallelbamsorting.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testparallelbamvalidation.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testqreorder.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testrlhist.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testrmmtree.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsamdecoder.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsamrecoding.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testscramtosam.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testserialisedsorting.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsha.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsimplebloomcollisions.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsimplecompressblock.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsimplecountinghash.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsimplehash.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsimplethreadpool.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsimplethreadpoolbamdecode.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsimpletrie.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsnappy.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsnappyconcat.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsort.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsplaytree.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/teststringgraph.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/teststronglyconnectedcomponents.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsymcnt.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsyncfastreaderbase.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testsyncreorderset.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testtopologicalsorting.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testurlinputstream.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testutf8split.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testvalidatebamindex.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testxz.cpp Examining data/libmaus2-2.0.766+dfsg/src/test/testzlibconcat.cpp FINAL RESULTS: data/libmaus2-2.0.766+dfsg/src/libmaus2/stacktrace/StackTrace.cpp:54:7: [5] (race) readlink: This accepts filename arguments; if an attacker can move those files or change the link content, a race condition results. Also, it does not terminate with ASCII NUL. (CWE-362, CWE-20). Reconsider approach. if ( readlink("/proc/self/exe", &buf[0], PATH_MAX) < 0 ) data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ArgInfo.cpp:86:7: [5] (race) readlink: This accepts filename arguments; if an attacker can move those files or change the link content, a race condition results. Also, it does not terminate with ASCII NUL. (CWE-362, CWE-20). Reconsider approach. if ( readlink("/proc/self/exe", &buf[0], PATH_MAX) < 0 ) data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ArgParser.cpp:45:7: [5] (race) readlink: This accepts filename arguments; if an attacker can move those files or change the link content, a race condition results. Also, it does not terminate with ASCII NUL. (CWE-362, CWE-20). Reconsider approach. if ( readlink("/proc/self/exe", &buf[0], PATH_MAX) < 0 ) data/libmaus2-2.0.766+dfsg/src/libmaus2/bitbtree/bitbtree.hpp:1885:9: [4] (race) access: This usually indicates a security flaw. If an attacker can change anything along the path between the call to access() and the file's actual use (e.g., by moving files), the attacker can exploit the race condition (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid()) and try to open the file directly. bool access(uint64_t node, uint64_t i) const data/libmaus2-2.0.766+dfsg/src/libmaus2/bitbtree/bitbtree.hpp:1899:15: [4] (race) access: This usually indicates a security flaw. If an attacker can change anything along the path between the call to access() and the file's actual use (e.g., by moving files), the attacker can exploit the race condition (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid()) and try to open the file directly. return access(innernode.data[j].ptr,i); data/libmaus2-2.0.766+dfsg/src/libmaus2/bitbtree/bitbtree.hpp:2071:12: [4] (race) access: This usually indicates a security flaw. If an attacker can change anything along the path between the call to access() and the file's actual use (e.g., by moving files), the attacker can exploit the race condition (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid()) and try to open the file directly. return access(root,i); data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/ChainNodeInfoSet.hpp:486:19: [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 const r = system(comstr.str().c_str()); data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixExecute.cpp:476:5: [4] (shell) execvp: This causes a new program to execute and is difficult to use safely (CWE-78). try using a library call that implements the same functionality if available. execvp(argptrs[0], argptrs); data/libmaus2-2.0.766+dfsg/src/libmaus2/stacktrace/StackTraceBufferContainer.cpp:313:3: [4] (shell) execv: This causes a new program to execute and is difficult to use safely (CWE-78). try using a library call that implements the same functionality if available. execv(Ptemp.p[0],Ptemp.p); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp:5268:6: [4] (shell) system: This causes a new program to execute and is difficult to use safely (CWE-78). try using a library call that implements the same functionality if available. system(comstr.str().c_str()); data/libmaus2-2.0.766+dfsg/src/libmaus2/wavelet/DynamicHuffmanWaveletTree.hpp:232:8: [4] (race) access: This usually indicates a security flaw. If an attacker can change anything along the path between the call to access() and the file's actual use (e.g., by moving files), the attacker can exploit the race condition (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid()) and try to open the file directly. int access(uint64_t p) const data/libmaus2-2.0.766+dfsg/src/libmaus2/wavelet/WaveletTree.hpp:2715:12: [4] (race) access: This usually indicates a security flaw. If an attacker can change anything along the path between the call to access() and the file's actual use (e.g., by moving files), the attacker can exploit the race condition (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid()) and try to open the file directly. return access(i); data/libmaus2-2.0.766+dfsg/src/libmaus2/wavelet/WaveletTree.hpp:3192:16: [4] (race) access: This usually indicates a security flaw. If an attacker can change anything along the path between the call to access() and the file's actual use (e.g., by moving files), the attacker can exploit the race condition (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid()) and try to open the file directly. symbol_type access(uint64_t i) const data/libmaus2-2.0.766+dfsg/src/test/testBWTHufDyn.cpp:221:13: [4] (race) access: This usually indicates a security flaw. If an attacker can change anything along the path between the call to access() and the file's actual use (e.g., by moving files), the attacker can exploit the race condition (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid()) and try to open the file directly. p = scf[ B.access(p) + 1 ] + (p ? B.rank(B.access(p),p-1) : 0); data/libmaus2-2.0.766+dfsg/src/test/testBWTHufDyn.cpp:221:45: [4] (race) access: This usually indicates a security flaw. If an attacker can change anything along the path between the call to access() and the file's actual use (e.g., by moving files), the attacker can exploit the race condition (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid()) and try to open the file directly. p = scf[ B.access(p) + 1 ] + (p ? B.rank(B.access(p),p-1) : 0); data/libmaus2-2.0.766+dfsg/src/test/testBWTHufDyn.cpp:225:26: [4] (race) access: This usually indicates a security flaw. If an attacker can change anything along the path between the call to access() and the file's actual use (e.g., by moving files), the attacker can exploit the race condition (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid()) and try to open the file directly. uint64_t const sym = B.access(p); data/libmaus2-2.0.766+dfsg/src/test/testRank.cpp:767:23: [4] (race) access: This usually indicates a security flaw. If an attacker can change anything along the path between the call to access() and the file's actual use (e.g., by moving files), the attacker can exploit the race condition (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid()) and try to open the file directly. assert ( A[i] == W.access(i) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/StaticInitialization.cpp:269:21: [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. char const * mem = getenv("MEMORYFILEMAXBLOCKSIZE"); data/libmaus2-2.0.766+dfsg/src/libmaus2/StaticInitialization.cpp:290:24: [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. char const * cthres = getenv("LIBMAUS2_AIO_POSIXFDINPUT_WARN_THRESHOLD"); data/libmaus2-2.0.766+dfsg/src/libmaus2/StaticInitialization.cpp:319:24: [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. char const * cthres = getenv("LIBMAUS2_AIO_POSIXFDOUTPUTSTREAMBUFFER_WARN_THRESHOLD"); data/libmaus2-2.0.766+dfsg/src/libmaus2/StaticInitialization.cpp:342:24: [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. char const * cthres = getenv("LIBMAUS2_AIO_POSIXFDOUTPUTSTREAMBUFFER_CHECK"); data/libmaus2-2.0.766+dfsg/src/libmaus2/StaticInitialization.cpp:371:24: [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. char const * envstr = getenv("LIBMAUS2_POSIXFDINPUT_BLOCKSIZE_OVERRIDE"); data/libmaus2-2.0.766+dfsg/src/libmaus2/StaticInitialization.cpp:503:24: [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. char const * envstr = getenv("LIBMAUS2_PAIRFILESORTING_DELAYDELETE"); data/libmaus2-2.0.766+dfsg/src/libmaus2/StaticInitialization.cpp:536:24: [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. char const * envstr = getenv("LIBMAUS2_LZ_BGZFINFLATEBASE_CHECKCRC"); data/libmaus2-2.0.766+dfsg/src/libmaus2/StaticInitialization.cpp:571:24: [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. char const * envstr = getenv("LIBMAUS2_DAZZLER_ALIGN_ALIGNMENTFILECONSTANTS_TRACE_XOVR"); data/libmaus2-2.0.766+dfsg/src/libmaus2/autoarray/AutoArray.cpp:24:26: [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. char const * mem = getenv("LIBMAUS2_AUTOARRAY_AUTOARRAYMAXMEM"); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/AdapterFilter.hpp:347:27: [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. switch ( libmaus2::random::Random::rand8() % 4 ) data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitVector.hpp:327:5: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitVector.hpp:330:37: [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. uint64_t const v = ::libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/libmaus2/clustering/KMeans.hpp:190:35: [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. double const p = libmaus2::random::UniformUnitRandom::uniformUnitRandom(); data/libmaus2-2.0.766+dfsg/src/libmaus2/clustering/KMeans.hpp:200:22: [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. i = libmaus2::random::Random::rand64() % ileft.size(); data/libmaus2-2.0.766+dfsg/src/libmaus2/clustering/KMeans.hpp:211:21: [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. i = libmaus2::random::Random::rand64() % ileft.size(); data/libmaus2-2.0.766+dfsg/src/libmaus2/clustering/KMeans.hpp:270:27: [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. R[i] = V[libmaus2::random::Random::rand64() % n]; data/libmaus2-2.0.766+dfsg/src/libmaus2/clustering/KMeans.hpp:426:35: [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. double const p = libmaus2::random::UniformUnitRandom::uniformUnitRandom(); data/libmaus2-2.0.766+dfsg/src/libmaus2/clustering/KMeans.hpp:436:22: [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. i = libmaus2::random::Random::rand64() % ileft.size(); data/libmaus2-2.0.766+dfsg/src/libmaus2/clustering/KMeans.hpp:442:21: [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. i = libmaus2::random::Random::rand64() % ileft.size(); data/libmaus2-2.0.766+dfsg/src/libmaus2/clustering/KMeans.hpp:496:27: [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. R[i] = V[libmaus2::random::Random::rand64() % n]; data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAStreamSet.hpp:153:40: [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. char const * datadir = writedata ? getenv("REF_CACHE") : nullptr; data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAStreamSet.hpp:160:28: [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. char const * refpath = getenv("REF_PATH"); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAToCompact4BigBand.cpp:276:41: [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. pattern.spattern[j] = (libmaus2::random::Random::rand8() & 3); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAToCompact4BigBandBiDir.hpp:194:43: [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. pattern.spattern[i] = (libmaus2::random::Random::rand8() & 3); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/KmerFreqInWindowStats.hpp:63:44: [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. uint64_t const windowleft = libmaus2::random::Random::rand64() % (numwindowleftpos); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/KmerFreqInWindowStats.hpp:64:42: [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. uint64_t const inwindow = libmaus2::random::Random::rand64() % numk; data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/RefPathLookup.hpp:33:28: [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. char const * datadir = getenv("REF_CACHE"); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/RefPathLookup.hpp:41:28: [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. char const * refpath = getenv("REF_PATH"); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/SubSamplingFastReader.hpp:37:53: [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. struct SubSamplingFastReader : public ::libmaus2::random::Random data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:29:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. namespace random data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:248:35: [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. state_enum state = (libmaus2::random::UniformUnitRandom::uniformUnitRandom() < state_start_map.find(state_error_low)->second) ? state_error_low : state_error_high; data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:253:24: [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. if ( libmaus2::random::UniformUnitRandom::uniformUnitRandom() < state_change_map.find(state)->second.find(state_error_low)->second ) data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:272:36: [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. while ( (erate = libmaus2::random::GaussianRandom::random(state_erate_sq.find(states[low])->second,state_erate.find(states[low])->second)) < 0 ) data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:272:60: [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. while ( (erate = libmaus2::random::GaussianRandom::random(state_erate_sq.find(states[low])->second,state_erate.find(states[low])->second)) < 0 ) data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:293:33: [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. double const p = libmaus2::random::UniformUnitRandom::uniformUnitRandom(); data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:294:51: [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. uint64_t const errpos = std::floor(libmaus2::random::UniformUnitRandom::uniformUnitRandom() * (high-low-1) + 0.5) + low; data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:347:37: [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. double const pins = libmaus2::random::UniformUnitRandom::uniformUnitRandom(); data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:387:34: [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. int const v = libmaus2::random::Random::rand8() & 3; data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:420:66: [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. while ( (insbase = libmaus2::fastx::remapChar(libmaus2::random::Random::rand8() & 3)) == origc ) data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:491:35: [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. state_enum state = (libmaus2::random::UniformUnitRandom::uniformUnitRandom() < state_start_map.find(state_error_low)->second) ? state_error_low : state_error_high; data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:496:24: [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. if ( libmaus2::random::UniformUnitRandom::uniformUnitRandom() < state_change_map.find(state)->second.find(state_error_low)->second ) data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:516:36: [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. while ( (erate = libmaus2::random::GaussianRandom::random(state_erate_sq.find(states[low])->second,state_erate.find(states[low])->second)) < 0 ) data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:516:60: [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. while ( (erate = libmaus2::random::GaussianRandom::random(state_erate_sq.find(states[low])->second,state_erate.find(states[low])->second)) < 0 ) data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:539:52: [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. uint64_t nexterrpos = std::floor(libmaus2::random::UniformUnitRandom::uniformUnitRandom() * (errdif-1) + 0.5) + low; data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:545:33: [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. double const p = libmaus2::random::UniformUnitRandom::uniformUnitRandom(); data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:562:41: [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. nexterrpos = std::floor(libmaus2::random::UniformUnitRandom::uniformUnitRandom() * (errdif-1) + 0.5) + low; data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:618:37: [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. double const pins = libmaus2::random::UniformUnitRandom::uniformUnitRandom(); data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:658:34: [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. int const v = libmaus2::random::Random::rand8() & 3; data/libmaus2-2.0.766+dfsg/src/libmaus2/random/DNABaseNoiseSpiker.hpp:691:66: [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. while ( (insbase = libmaus2::fastx::remapChar(libmaus2::random::Random::rand8() & 3)) == origc ) data/libmaus2-2.0.766+dfsg/src/libmaus2/random/GaussianRandom.hpp:30:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. namespace random data/libmaus2-2.0.766+dfsg/src/libmaus2/random/GaussianRandom.hpp:80:18: [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. static double random(double const sigma, double const mu) data/libmaus2-2.0.766+dfsg/src/libmaus2/random/LogNormalRandom.hpp:32:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. namespace random data/libmaus2-2.0.766+dfsg/src/libmaus2/random/LogNormalRandom.hpp:204:18: [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. static double random(double const sigma, double const mu) data/libmaus2-2.0.766+dfsg/src/libmaus2/random/Poisson.hpp:30:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. namespace random data/libmaus2-2.0.766+dfsg/src/libmaus2/random/Random.hpp:29:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. namespace random data/libmaus2-2.0.766+dfsg/src/libmaus2/random/Random.hpp:35:5: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(t); data/libmaus2-2.0.766+dfsg/src/libmaus2/random/UniformUnitRandom.hpp:25:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. namespace random data/libmaus2-2.0.766+dfsg/src/libmaus2/random/UniformUnitRandom.hpp:32:42: [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. return static_cast<double>(libmaus2::random::Random::rand32()) / static_cast<double>((1ull<<32)-1); data/libmaus2-2.0.766+dfsg/src/libmaus2/rank/DNARank.hpp:216:29: [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. RV.push_back(libmaus2::random::Random::rand64() % n); data/libmaus2-2.0.766+dfsg/src/libmaus2/stacktrace/StackTraceBufferContainer.cpp:57:26: [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. char const * checkseg = getenv("LIBMAUS2_TRACE_SEGFAULT"); data/libmaus2-2.0.766+dfsg/src/libmaus2/stacktrace/StackTraceBufferContainer.cpp:70:26: [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. char const * checkseg = getenv("LIBMAUS2_TRACE_SEGFAULT_TRANSLATE"); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ArgInfo.cpp:103:23: [3] (buffer) getenv: Environment variables are untrustable input if they can be set by an attacker. They can have any content and length, and the same variable can be set more than once (CWE-807, CWE-20). Check environment variables carefully before using them. char const * cPATH = getenv("PATH"); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ArgParser.cpp:62:23: [3] (buffer) getenv: Environment variables are untrustable input if they can be set by an attacker. They can have any content and length, and the same variable can be set more than once (CWE-807, CWE-20). Check environment variables carefully before using them. char const * cPATH = getenv("PATH"); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/IncreasingList.cpp:65:22: [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. V[i] = ::libmaus2::random::Random::rand64() % k; data/libmaus2-2.0.766+dfsg/src/libmaus2/util/LookupIntervalTree.cpp:60:15: [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. ::libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/LookupIntervalTree.cpp:64:34: [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. uint64_t const v = ::libmaus2::random::Random::rand64() & ((1ull << (rangebits))-1); data/libmaus2-2.0.766+dfsg/src/test/testBitIO.cpp:91:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testBitIO.cpp:132:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testBitIO.cpp:168:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testBitIO.cpp:214:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testBitIO.cpp:285:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testBitIO.cpp:323:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testBitIO.cpp:377:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testBitIO.cpp:588:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(5); data/libmaus2-2.0.766+dfsg/src/test/testDNABitWords.cpp:35:3: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testDNABitWords.cpp:72:3: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testHuffman.cpp:701:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testRank.cpp:483:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand( time(0) ); data/libmaus2-2.0.766+dfsg/src/test/testRank.cpp:1427:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(32); data/libmaus2-2.0.766+dfsg/src/test/testRank.cpp:1549:26: [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. P [ i ] = ::libmaus2::random::Random::rand64() % CLR.n; data/libmaus2-2.0.766+dfsg/src/test/testRank.cpp:1659:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testRank.cpp:1781:3: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(5); data/libmaus2-2.0.766+dfsg/src/test/testToWaveletTreeBits.cpp:35:35: [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. uint64_t const n = ::libmaus2::random::Random::rand64() % (10*1024*1024) + 1; data/libmaus2-2.0.766+dfsg/src/test/testToWaveletTreeBits.cpp:36:35: [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. uint64_t const b = ::libmaus2::random::Random::rand64() % 8 + 1; data/libmaus2-2.0.766+dfsg/src/test/testToWaveletTreeBits.cpp:47:29: [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. C->set ( i, ::libmaus2::random::Random::rand64() & ((1ull<<b)-1) ); data/libmaus2-2.0.766+dfsg/src/test/testWaveletExternal.cpp:369:25: [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. A.push_back(libmaus2::random::Random::rand8() & 0xFF); data/libmaus2-2.0.766+dfsg/src/test/testWaveletExternal.cpp:483:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:60:47: [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. s[i] = libmaus2::fastx::remapChar(libmaus2::random::Random::rand8() % 4); data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:70:13: [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. libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:325:40: [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. std::string const leftb = libmaus2::random::DNABaseNoiseSpiker::modify(lefta,0.2,0.3,0.5,0.0,0.15,0.02); data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:328:41: [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. std::string const rightb = libmaus2::random::DNABaseNoiseSpiker::modify(righta,0.2,0.3,0.5,0.0,0.15,0.02); data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:375:14: [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. libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:392:37: [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. std::string randread = libmaus2::random::DNABaseNoiseSpiker::modify( data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:449:14: [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. libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:466:37: [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. std::string randread = libmaus2::random::DNABaseNoiseSpiker::modify( data/libmaus2-2.0.766+dfsg/src/test/testavlset.cpp:29:10: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. ::std::srand(10); data/libmaus2-2.0.766+dfsg/src/test/testbamdamage.cpp:15:15: [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. ::libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testbamdamage.cpp:27:36: [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. std::min(red-off, ::libmaus2::random::Random::rand64() % (64*1024) ); data/libmaus2-2.0.766+dfsg/src/test/testbamdamage.cpp:30:36: [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. C [ off + skip ] = ::libmaus2::random::Random::rand8(); data/libmaus2-2.0.766+dfsg/src/test/testbammateerase.cpp:32:3: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testbitbtree.cpp:119:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(5); data/libmaus2-2.0.766+dfsg/src/test/testbtree.cpp:608:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testbytecnt.cpp:162:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. libmaus2::random::Random::setup(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testbytecnt.cpp:169:21: [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. B[i] = (libmaus2::random::Random::rand8() & 1) ? '\n' : 'a'; data/libmaus2-2.0.766+dfsg/src/test/testbytecnt.cpp:173:20: [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. B[i] = libmaus2::random::Random::rand8(); data/libmaus2-2.0.766+dfsg/src/test/testbytetocompact.cpp:50:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testcompact.cpp:45:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testdecimalnumberparser.cpp:35:4: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testdecimalnumberparser.cpp:41:28: [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. uint64_t j = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testdifenc.cpp:12:15: [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. ::libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testdifenc.cpp:20:35: [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. uint64_t const j = ::libmaus2::random::Random::rand64() % gaparsize; data/libmaus2-2.0.766+dfsg/src/test/testdnarank.cpp:60:32: [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. uint64_t const p = libmaus2::random::Random::rand64() % Prank->size(); data/libmaus2-2.0.766+dfsg/src/test/testdnarank.cpp:61:43: [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. uint64_t const s = std::min( (libmaus2::random::Random::rand64() % 512), Prank->size()-p ); data/libmaus2-2.0.766+dfsg/src/test/testdnarank.cpp:88:21: [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. RA[i] = libmaus2::random::Random::rand64() % Prank->size(); data/libmaus2-2.0.766+dfsg/src/test/testeditdistance.cpp:100:27: [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. a[i] = 'a' + (libmaus2::random::Random::rand8() % k); data/libmaus2-2.0.766+dfsg/src/test/testeditdistance.cpp:122:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. libmaus2::random::Random::setup(5); data/libmaus2-2.0.766+dfsg/src/test/testfastaparse.cpp:54:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testfastaparse.cpp:82:25: [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. D.insert(libmaus2::random::Random::rand8()%4,cnt+i); data/libmaus2-2.0.766+dfsg/src/test/testfastaparse.cpp:101:43: [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. unsigned int const errtype = libmaus2::random::Random::rand8() % 3; data/libmaus2-2.0.766+dfsg/src/test/testfastaparse.cpp:106:40: [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. uint64_t const inpos = libmaus2::random::Random::rand64() % (D.size()+1); data/libmaus2-2.0.766+dfsg/src/test/testfastaparse.cpp:107:45: [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. unsigned int const inbase = libmaus2::random::Random::rand8() % 4; data/libmaus2-2.0.766+dfsg/src/test/testfastaparse.cpp:114:41: [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. uint64_t const delpos = libmaus2::random::Random::rand64() % (D.size()); data/libmaus2-2.0.766+dfsg/src/test/testfastaparse.cpp:122:42: [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. uint64_t const subspos = libmaus2::random::Random::rand64() % (D.size()); data/libmaus2-2.0.766+dfsg/src/test/testfastaparse.cpp:123:45: [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. unsigned int const inbase = libmaus2::random::Random::rand8() % 4; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:109:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:169:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:330:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:934:29: [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. A[i] = klow + ( libmaus2::random::Random::rand64() % (khigh-klow) ); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:973:33: [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. uint64_t const k0 = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:974:39: [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. uint64_t const k1 = k0 + (libmaus2::random::Random::rand64() % 1024+1); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:975:33: [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. uint64_t const nl = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:976:33: [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. uint64_t const nr = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:988:33: [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. uint64_t const k0 = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:989:39: [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. uint64_t const k1 = k0 + (libmaus2::random::Random::rand64() % 1024+1); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:991:39: [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. uint64_t const k2 = k1 + (libmaus2::random::Random::rand64() % 1024+1); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:993:33: [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. uint64_t const nl = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:994:33: [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. uint64_t const nr = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1006:33: [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. uint64_t const k0 = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1007:39: [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. uint64_t const k1 = k0 + (libmaus2::random::Random::rand64() % 1024+1); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1008:39: [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. uint64_t const k2 = k1 + (libmaus2::random::Random::rand64() % 1024+1); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1009:33: [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. uint64_t const nl = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1010:33: [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. uint64_t const nr = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1027:33: [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. uint64_t const k0 = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1028:39: [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. uint64_t const k1 = k0 + (libmaus2::random::Random::rand64() % 1024+1); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1029:33: [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. uint64_t const nl = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1030:33: [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. uint64_t const nr = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1042:33: [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. uint64_t const k0 = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1043:39: [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. uint64_t const k1 = k0 + (libmaus2::random::Random::rand64() % 1024+1); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1045:39: [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. uint64_t const k2 = k1 + (libmaus2::random::Random::rand64() % 1024+1); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1047:33: [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. uint64_t const nl = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1048:33: [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. uint64_t const nr = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1060:33: [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. uint64_t const k0 = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1061:39: [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. uint64_t const k1 = k0 + (libmaus2::random::Random::rand64() % 1024+1); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1062:39: [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. uint64_t const k2 = k1 + (libmaus2::random::Random::rand64() % 1024+1); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1063:33: [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. uint64_t const nl = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1064:33: [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. uint64_t const nr = libmaus2::random::Random::rand64() % 1024; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1633:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1640:38: [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. uint64_t const n = 996 + libmaus2::random::Random::rand64() % 128; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1648:34: [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. uint64_t const w = (libmaus2::random::Random::rand64() % mod)+1; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1724:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1731:38: [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. uint64_t const n = 996 + libmaus2::random::Random::rand64() % 128; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1738:34: [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. uint64_t const o = (libmaus2::random::Random::rand64() % mod)+1; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1739:34: [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. uint64_t const w = (libmaus2::random::Random::rand64() % mod)+1; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1809:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1816:38: [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. uint64_t const n = 996 + libmaus2::random::Random::rand64() % 128; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1824:34: [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. uint64_t const w = (libmaus2::random::Random::rand64() % mod)+1; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1904:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1911:38: [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. uint64_t const n = 996 + libmaus2::random::Random::rand64() % 128; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1918:34: [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. uint64_t const o = (libmaus2::random::Random::rand64() % mod)+1; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1919:34: [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. uint64_t const w = (libmaus2::random::Random::rand64() % mod)+1; data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:1995:19: [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. libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testgamma.cpp:2171:3: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testgammapd.cpp:27:14: [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. libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testgammapd.cpp:44:36: [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. uint64_t n = base + (libmaus2::random::Random::rand64() % mod); data/libmaus2-2.0.766+dfsg/src/test/testgammapd.cpp:48:28: [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. V.push_back(libmaus2::random::Random::rand64() % 257); data/libmaus2-2.0.766+dfsg/src/test/testgaparraybyte.cpp:34:16: [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. GG[libmaus2::random::Random::rand64() % gsize] = 257; data/libmaus2-2.0.766+dfsg/src/test/testgaparraybyte.cpp:77:3: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testkmp.cpp:31:14: [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. ::libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testkmp.cpp:40:34: [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. probes.push_back( ::libmaus2::random::Random::rand64() % (BP.size()) ); data/libmaus2-2.0.766+dfsg/src/test/testlognormal.cpp:32:44: [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. std::pair<double,double> est = libmaus2::random::LogNormalRandom::estimateParameters(V); data/libmaus2-2.0.766+dfsg/src/test/testlognormal.cpp:40:40: [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. std::cout << x << "\t" << libmaus2::random::LogNormalRandom::search(x,sigma,mu) << std::endl; data/libmaus2-2.0.766+dfsg/src/test/testlz.cpp:35:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testlz.cpp:66:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testlz.cpp:307:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. libmaus2::random::Random::setup(time(0)); data/libmaus2-2.0.766+dfsg/src/test/testlz.cpp:313:32: [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. uint64_t const p = libmaus2::random::Random::rand64() % ( C.size()-r ); data/libmaus2-2.0.766+dfsg/src/test/testmapperm.cpp:32:13: [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. libmaus2::random::Random::setup(19); data/libmaus2-2.0.766+dfsg/src/test/testmapperm.cpp:35:23: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. switch ( libmaus2::random::Random::rand8() % 4 ) data/libmaus2-2.0.766+dfsg/src/test/testparallelbamblocksort.cpp:160:29: [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. char const * refcache = getenv("REF_CACHE"); data/libmaus2-2.0.766+dfsg/src/test/testqreorder.cpp:93:2: [3] (random) srand: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. srand(5); data/libmaus2-2.0.766+dfsg/src/test/testrmmtree.cpp:30:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testrmmtree.cpp:33:25: [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. V.push_back(libmaus2::random::Random::rand64() % 128); data/libmaus2-2.0.766+dfsg/src/test/testrmmtree.cpp:57:13: [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. libmaus2::random::Random::setup(time(0)+z); data/libmaus2-2.0.766+dfsg/src/test/testrmmtree.cpp:58:39: [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. uint64_t const n = 3912 + libmaus2::random::Random::rand64() % 32; data/libmaus2-2.0.766+dfsg/src/test/testrmmtree.cpp:61:26: [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. V.push_back(libmaus2::random::Random::rand64() % 128); data/libmaus2-2.0.766+dfsg/src/test/testsimplebloomcollisions.cpp:30:34: [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. uint64_t const v = ::libmaus2::random::Random::rand64() & 0xFFFFul; data/libmaus2-2.0.766+dfsg/src/test/testsort.cpp:182:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testsort.cpp:223:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testsort.cpp:336:47: [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. V[i] = libmaus2::huffman::LFInfo(libmaus2::random::Random::rand8() % 4 /* sym */, p-19581*i /* p */,0 /* n */, 0 /* rv */, i%2 /* active */); data/libmaus2-2.0.766+dfsg/src/test/testsort.cpp:430:20: [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. r += (libmaus2::random::Random::rand8() % 4); data/libmaus2-2.0.766+dfsg/src/test/testsort.cpp:557:67: [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. V[i] = libmaus2::huffman::LFSymRankPos(i%13 /* sym*/,libmaus2::random::Random::rand8() % 4 /* rank */, p-19581*i /* p */,0 /* n */, 0 /* rv */, i%2 /* active */); data/libmaus2-2.0.766+dfsg/src/test/testsort.cpp:613:27: [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. C[i].second = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testsort.cpp:671:26: [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. C[i].first = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testsort.cpp:850:24: [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. Vrand[i] = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testsplaytree.cpp:125:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/test/testsplaytree.cpp:129:25: [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. V.push_back(libmaus2::random::Random::rand64()); data/libmaus2-2.0.766+dfsg/src/test/testsymcnt.cpp:33:27: [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. ASC[i].sbit = libmaus2::random::Random::rand64() % 2; data/libmaus2-2.0.766+dfsg/src/test/testsymcnt.cpp:37:32: [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. uint64_t const z = libmaus2::random::Random::rand64() % 64; data/libmaus2-2.0.766+dfsg/src/test/testsymcnt.cpp:46:32: [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. uint64_t const z = libmaus2::random::Random::rand64() % 64; data/libmaus2-2.0.766+dfsg/src/test/testsymcnt.cpp:48:34: [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. uint64_t const sym = libmaus2::random::Random::rand64() % 31; data/libmaus2-2.0.766+dfsg/src/test/testsymcnt.cpp:84:27: [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. ASC[i].sbit = libmaus2::random::Random::rand64() % 2; data/libmaus2-2.0.766+dfsg/src/test/testsymcnt.cpp:88:32: [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. uint64_t const z = libmaus2::random::Random::rand64() % 64; data/libmaus2-2.0.766+dfsg/src/test/testsymcnt.cpp:97:32: [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. uint64_t const z = libmaus2::random::Random::rand64() % 64; data/libmaus2-2.0.766+dfsg/src/test/testsymcnt.cpp:99:34: [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. uint64_t const sym = libmaus2::random::Random::rand64() % 31; data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:86:36: [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. uint64_t const lowa = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:87:36: [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. uint64_t const higha = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:104:36: [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. uint64_t const lowa = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:105:36: [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. uint64_t const higha = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:106:36: [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. uint64_t const lowb = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:107:36: [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. uint64_t const highb = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:135:36: [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. uint64_t const lowa = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:136:36: [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. uint64_t const higha = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:137:36: [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. uint64_t const lowb = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:138:36: [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. uint64_t const highb = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:169:36: [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. uint64_t const lowa = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:170:36: [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. uint64_t const higha = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:171:36: [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. uint64_t const lowb = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:172:36: [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. uint64_t const highb = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:209:36: [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. uint64_t const lowa = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:210:36: [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. uint64_t const higha = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:211:36: [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. uint64_t const lowb = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:212:36: [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. uint64_t const highb = libmaus2::random::Random::rand64(); data/libmaus2-2.0.766+dfsg/src/test/testunsignedinteger.cpp:252:12: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. libmaus2::random::Random::setup(); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/ArrayFile.hpp:92:56: [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). libmaus2::aio::InputStreamInstance::unique_ptr_type open() const data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/CountOutputStreamBuffer.hpp:33:4: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char B[16]; data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryFile.hpp:78:5: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(A->begin() + p, c, n); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryFile.hpp:97:5: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(c,A->begin()+p,r); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryFile.hpp:210:6: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy( data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryFile.hpp:257:6: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy( data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInput.cpp:78:41: [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). fd = libmaus2::posix::PosixFunctions::open(cfilename,rflags); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInput.cpp:144:41: [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). fd = libmaus2::posix::PosixFunctions::open(filename.c_str(),rflags); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInputOutputStreamBuffer.hpp:107:52: [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). while ( (fd = libmaus2::posix::PosixFunctions::open(filename.c_str(),mode,Amode.begin())) < 0 ) data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdOutputStreamBuffer.hpp:150:44: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). fd = libmaus2::posix::PosixFunctions::open(filename.c_str(),flags,Amode.begin()); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignment.hpp:948:9: [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 alt[3]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignment.hpp:1003:8: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char alt[3]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignment.hpp:1035:8: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char alt[3]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignment.hpp:1076:8: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char alt[3]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignment.hpp:1361:9: [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 alt[3]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderBase.hpp:2398:5: [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 c[22]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderBase.hpp:3900:7: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char fbuf[256]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderBase.hpp:4033:10: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char fbuf[256]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderBase.hpp:5430:5: [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 pp[5]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderBase.hpp:5446:5: [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 pp[10]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderBase.hpp:5462:5: [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 pp[22]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndex.hpp:69:5: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char magic[4]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamStreamingMarkDuplicates.hpp:375:7: [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(outptr,tag1,l1); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamStreamingMarkDuplicates.hpp:379:7: [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(outptr,tag2,l2); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfo.hpp:317:5: [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 const tag[3] = { pc[0], pc[1], 0 }; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfo.hpp:411:9: [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 const tag[3] = { pc[0], pc[1], 0 }; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfo.hpp:432:10: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char const tag[3] = { pc[0], pc[1], 0 }; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfo.hpp:438:10: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char const tag[3] = { pc[0], pc[1], 0 }; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfo.hpp:466:9: [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 const tag[3] = { pc[0], pc[1], 0 }; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfo.hpp:483:9: [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 const tag[3] = { pc[0], pc[1], 0 }; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfo.hpp:504:9: [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 const tag[3] = { pc[0], pc[1], 0 }; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfoBase.hpp:36:11: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. static char const qnameValid[256]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfoBase.hpp:37:11: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. static char const rnameFirstValid[256]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfoBase.hpp:38:11: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. static char const rnameOtherValid[256]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfoBase.hpp:39:11: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. static char const seqValid[256]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfoBase.hpp:40:11: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. static char const qualValid[256]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamInfoBase.hpp:91:6: [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(str.begin(),field[0],fieldlen); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamPrintableTable.hpp:37:4: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char A[256]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/SamZPrintableTable.hpp:37:4: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char A[256]; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:54:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(object->filename,rfilename,filenamelen); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:56:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(object->mode,rmode,modelen); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:64:3: [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(object->referencefilename,rreferencefilename,referencefilenamelen); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:95:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy ( object->header,samheader->text->str,samheader->text->length ); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:128:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(object->filename,rfilename,filenamelen); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:136:3: [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(object->referencefilename,rreferencefilename,referencefilenamelen); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:171:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy ( object->header,samheader->text->str,samheader->text->length ); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:205:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(object->filename,rfilename,filenamelen); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:207:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(object->mode,rmode,modelen); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:215:3: [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(object->referencefilename,rreferencefilename,referencefilenamelen); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:246:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy ( object->header,samheader->text->str,samheader->text->length ); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:332:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(object->filename,rfilename,filenamelen); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:340:3: [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(object->referencefilename,rreferencefilename,referencefilenamelen); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:375:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy ( object->header,samheader->text->str,samheader->text->length ); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:554:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(header->text,headertext,headerlen); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:620:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(encoder->filename,rfilename,strlen(rfilename)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:628:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(encoder->mode,rmode,strlen(rmode)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:638:3: [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(encoder->referencefilename,rreferencefilename,strlen(rreferencefilename)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:752:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(&(p->ref),seq,len); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ScramDecoder.hpp:235:5: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(alignment.D.begin(),dec->buffer,dec->blocksize); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentBuffer.hpp:187:7: [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(algns[i]->D.begin(),p,len); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentBuffer.hpp:621:8: [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(pA,p,n); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentBuffer.hpp:655:6: [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(pA,p,n); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentRewriteBuffer.hpp:183:7: [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(pA,p,n); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/AlignmentRewriteBuffer.hpp:221:7: [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(pA,p,n); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/BlockCompressPackageDispatcher.hpp:89:7: [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(compin,P.first,P.second); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:766:7: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char t[4] = { data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:882:15: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). nfiles = atol(nfilestokenvector[2].c_str()); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:905:34: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). uint64_t const fnumreads = atol(tokens[0].c_str()); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:923:19: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). numblocks = atol(numblockstokens[2].c_str()); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:944:19: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). blocksize = atol(sizelinetokens[2].c_str()); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:945:16: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). cutoff = atol(sizelinetokens[5].c_str()); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:946:13: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). all = atol(sizelinetokens[8].c_str()); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:969:36: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). uint64_t const unfiltered = atol(blocklinetokens[0].c_str()); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:970:36: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). uint64_t const filtered = atol(blocklinetokens[1].c_str()); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/Read.hpp:114:7: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char C[4] = {0,0,0,0}; data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/md5.cpp:169:3: [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(xbuf, data, 64); data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/md5.cpp:343:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(pms->buf + offset, p, copy); data/libmaus2-2.0.766+dfsg/src/libmaus2/digest/md5.cpp:357:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(pms->buf, p, left); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastALineParser.hpp:126:6: [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(id.begin(),info.line,info.linelen); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAStreamWrapper.hpp:112:9: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(inptr,info.line,linecopy); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaBPDecoder.hpp:53:5: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char magic[8]; data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/huffman.hpp:87:30: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). uint64_t const numnodes = atol( tokens[1].c_str() ); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/huffman.hpp:111:31: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). uint64_t const nodeid = atol( tokens[0].c_str() ); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/huffman.hpp:119:29: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). uint64_t const left = atol(tokens[2].c_str()); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/huffman.hpp:120:30: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). uint64_t const right = atol(tokens[3].c_str()); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/huffman.hpp:143:31: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). uint64_t const nodeid = atol( tokens[0].c_str() ); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/huffman.hpp:148:26: [2] (integer) atoi: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). int const symbol = atoi(tokens[2].c_str()); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/huffman.hpp:149:34: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). uint64_t const frequency = atol(tokens[3].c_str()); data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreTemplate.cpp:189:7: [2] (buffer) bcopy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. *(--bcopy) = bsub; data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreTemplate.cpp:193:7: [2] (buffer) bcopy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. *(--bcopy) = b[i]; data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreTemplate.cpp:194:10: [2] (buffer) bcopy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. while ( bcopy != querymem ) data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreTemplate.cpp:195:7: [2] (buffer) bcopy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. *(--bcopy) = bsub; data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentTemplate.cpp:172:7: [2] (buffer) bcopy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. *(--bcopy) = bsub; data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentTemplate.cpp:176:7: [2] (buffer) bcopy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. *(--bcopy) = b[i]; data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentTemplate.cpp:177:10: [2] (buffer) bcopy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. while ( bcopy != querymem ) data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/SimdX86BandedGlobalAlignmentTemplate.cpp:178:7: [2] (buffer) bcopy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. *(--bcopy) = bsub; data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfDeflateBase.hpp:81:21: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. static unsigned char const block[28] = { 0x1f, 0x8b, 0x08, 0x04, 0x00, 0x00, 0x00, 0x00, 0x00, 0xff, 0x06, 0x00, 0x42, 0x43, 0x02, 0x00, 0x1b, 0x00, 0x03, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00 }; data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/lz4.c:540:9: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(op, anchor, iend - anchor); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/lz4.c:645:9: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy((void*)(lz4ds->bufferStart), (const void*)(lz4ds->nextBlock - 64 KB), 64 KB); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/lz4.c:651:3: [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((void*)(lz4ds->bufferStart), (const void*)(lz4ds->nextBlock - 64 KB), 64 KB); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/lz4.c:733:13: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(op, ip, length); data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixExecute.cpp:414:4: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(argmemt,V[i].c_str(),V[i].size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixExecute.cpp:419:20: [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). if ( (stderrfd = mkstemp(&stderrfn[0])) < 0 ) data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixExecute.cpp:431:20: [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). if ( (stdoutfd = mkstemp(&stdoutfn[0])) < 0 ) data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixExecute.cpp:443:51: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). if ( (nullfd = libmaus2::posix::PosixFunctions::open("/dev/null",libmaus2::posix::PosixFunctions::get_O_RDONLY())) < 0 ) data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixFunctions.cpp:53:38: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). int libmaus2::posix::PosixFunctions::open(const char *pathname, int flags) data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixFunctions.cpp:55:11: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). return ::open(pathname,flags); data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixFunctions.cpp:58:38: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). int libmaus2::posix::PosixFunctions::open(const char *pathname, int flags) data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixFunctions.cpp:66:38: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). int libmaus2::posix::PosixFunctions::open(const char *pathname, int flags, unsigned char const * inmode) data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixFunctions.cpp:69:11: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). return ::open(pathname,flags,mode); data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixFunctions.cpp:76:38: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). int libmaus2::posix::PosixFunctions::open(const char *pathname, int flags, unsigned char const * /* inmode */) data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixFunctions.hpp:164:15: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). static int open(const char *pathname, int flags); data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixFunctions.hpp:165:15: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). static int open(const char *pathname, int flags, unsigned char const * inmode); data/libmaus2-2.0.766+dfsg/src/libmaus2/protein/CodonMapper.hpp:32:11: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. static char const codonArray[64]; data/libmaus2-2.0.766+dfsg/src/libmaus2/protein/CodonMapper.hpp:33:11: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. static char const stopArray[64]; data/libmaus2-2.0.766+dfsg/src/libmaus2/stacktrace/StackTrace.cpp:51:2: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buf[PATH_MAX+1]; data/libmaus2-2.0.766+dfsg/src/libmaus2/stacktrace/StackTraceBufferContainer.cpp:279:8: [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). rmk = mkstemp(Atemp.p); data/libmaus2-2.0.766+dfsg/src/libmaus2/stacktrace/StackTraceBufferContainer.cpp:296:24: [2] (misc) open: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). int const nullfd = ::open("/dev/null",O_WRONLY); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/AlphaDigitTable.hpp:37:4: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char A[256]; data/libmaus2-2.0.766+dfsg/src/libmaus2/util/AlphaTable.hpp:37:4: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char A[256]; data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ArgInfo.cpp:83:2: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buf[PATH_MAX+1]; data/libmaus2-2.0.766+dfsg/src/libmaus2/util/ArgParser.cpp:42:2: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buf[PATH_MAX+1]; data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Base64.hpp:32:12: [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 const table[64] = { data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Base64.hpp:42:6: [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 tout[4]; data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Base64.hpp:91:15: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. unsigned char c[256]; data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Base64.hpp:116:21: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. static unsigned char const table[256] = { data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Base64.hpp:129:6: [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 tin[4] = { '=','=','=','=' }; data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Base64.hpp:202:15: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. unsigned char tout[3]; data/libmaus2-2.0.766+dfsg/src/libmaus2/util/DigitTable.hpp:37:4: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char A[256]; data/libmaus2-2.0.766+dfsg/src/libmaus2/util/LineBuffer.hpp:173:10: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(tmpbuf.begin(),bufferptrout,numbytes); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/NotDigitOrTermTable.hpp:30:11: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. static char const table[256]; data/libmaus2-2.0.766+dfsg/src/libmaus2/util/SimpleHashMapKeyPrint.hpp:61:6: [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 C[39]; data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Terminal.cpp:34:41: [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). fd = libmaus2::posix::PosixFunctions::open("/dev/tty",libmaus2::posix::PosixFunctions:get_O_RDWR()); data/libmaus2-2.0.766+dfsg/src/libmaus2/wavelet/HuffmanWaveletTree.hpp:111:32: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). uint64_t const numnodes = atol( tokens[1].c_str() ); data/libmaus2-2.0.766+dfsg/src/libmaus2/wavelet/HuffmanWaveletTree.hpp:130:32: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). uint64_t const nodeid = atol( tokens[0].c_str() ); data/libmaus2-2.0.766+dfsg/src/libmaus2/wavelet/HuffmanWaveletTree.hpp:139:30: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). uint64_t const left = atol(tokens[2].c_str()); data/libmaus2-2.0.766+dfsg/src/libmaus2/wavelet/HuffmanWaveletTree.hpp:140:31: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). uint64_t const right = atol(tokens[3].c_str()); data/libmaus2-2.0.766+dfsg/src/test/testRank.cpp:1175:2: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(inbuf.get(),sostr.str().c_str(),totalwords*8); data/libmaus2-2.0.766+dfsg/src/test/testbwtconstruction.cpp:51:62: [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). libmaus2::aio::InputStreamInstance::unique_ptr_type ISI(AF.open()); data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp:38:9: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). return atol(sid.c_str()); data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp:102:30: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). uint64_t const ufrom = atol(sfrom.c_str()); data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp:103:28: [2] (integer) atol: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). uint64_t const uto = atol(sto.c_str()); data/libmaus2-2.0.766+dfsg/src/test/testxz.cpp:29:3: [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 inbuf[8192]; data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/CircularBuffer.hpp:189:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(midptr, std::min(rspace,static_cast<uint64_t>(buffer.end()-midptr))); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/CircularBuffer.hpp:341:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(midptr, toread); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/CompactDecoder4.hpp:129:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). istr->read(reinterpret_cast<char *>(decodeBuffer.get()), toreadbytes); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/ConcatInputStreamBuffer.hpp:78:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). Pin->read(p,s); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/FileRemoval.cpp:34:40: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::string const fn = U.path.substr(strlen("//")); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/IStreamWrapper.hpp:52:24: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::libmaus2::ssize_t read(char * p, size_t c) data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/IStreamWrapper.hpp:54:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(p,c); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryFileAdapter.hpp:56:24: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::libmaus2::ssize_t read(char * buffer, size_t len) data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryInputOutputStreamBuffer.hpp:169:20: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). while ( (r=fd->read(buffer,count)) < 0 ) data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/MemoryInputStreamBuffer.hpp:230:43: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const uncompressedsize = fd->read( data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/OFStreamOutputStreamFactory.cpp:30:6: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(B.begin(),B.size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/OutputStreamFactoryContainer.cpp:35:6: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(B.begin(),B.size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInput.cpp:168:50: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::libmaus2::ssize_t libmaus2::aio::PosixFdInput::read(char * const buffer, uint64_t n) data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInput.cpp:176:42: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). r = ::libmaus2::posix::PosixFunctions::read(fd,buffer,n); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInput.hpp:81:24: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::libmaus2::ssize_t read(char * const buffer, uint64_t n); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInputOutputStreamBuffer.hpp:274:51: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). while ( (r=::libmaus2::posix::PosixFunctions::read(fd,buffer,count)) < 0 ) data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdInputStreamBuffer.hpp:237:46: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const uncompressedsize = stream.read( data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdOutputStreamBuffer.hpp:462:15: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). istr0.read(BU0.begin(),n); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdOutputStreamBuffer.hpp:463:15: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). istr1.read(BU1.begin(),n); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdOutputStreamBuffer.hpp:472:26: [1] (buffer) equal: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. else if ( ! std::equal(BU0.begin(),BU0.begin()+istr0.gcount(),BU1.begin()) ) data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/PosixFdOutputStreamFactory.cpp:30:6: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(B.begin(),B.size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/ReorderConcatGenericInput.hpp:92:49: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). reader->read( reinterpret_cast<char *>(pa), toreadbytes ); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/ReorderConcatGenericInput.hpp:213:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(input_type * B, uint64_t n) data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/ReorderConcatGenericInput.hpp:534:49: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). reader->read( reinterpret_cast<char *>(T), bufread*sizeof(input_type) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SingleFileFragmentMerge.hpp:81:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). pCIS->read(reinterpret_cast<char *>(&BC), sizeof(element_type)); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SingleFileFragmentMerge.hpp:102:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). pCIS->read(reinterpret_cast<char *>(&NBC), sizeof(element_type)); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SkipConcatInputStreamBuffer.hpp:77:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). Pin->read(p,s); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SynchronousFastReaderBase.hpp:274:18: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). fpt->first->read ( reinterpret_cast<char *>(pa), B.size() ); data/libmaus2-2.0.766+dfsg/src/libmaus2/aio/SynchronousGenericInput.hpp:84:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). istr.read ( reinterpret_cast<char *>(buffer.get()), toreadwords * sizeof(input_type)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignment.hpp:136:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(reinterpret_cast<char *>(D.begin()),blocksize); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignment.hpp:950:5: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(alt, tag, 2); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignment.hpp:1005:8: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(alt, tag, 2); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignment.hpp:1037:8: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(alt, tag, 2); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignment.hpp:1078:8: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(alt, tag, 2); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignment.hpp:1363:5: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). strncpy(alt, tag, 2); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoder.hpp:251:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). GZ.read(reinterpret_cast<char *>(alignment.D.begin()),alignment.blocksize); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoder.hpp:308:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). GZ.read(reinterpret_cast<char *>(alignment.D.begin()),alignment.blocksize); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderBase.hpp:425:24: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). 1 + namelen + 1 + strlen(ne) + 1 + // name line data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderBase.hpp:455:24: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). 1 + namelen + 1 + strlen(ne) + 1 + // name line data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderBase.hpp:1150:43: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). if ( altqual && (static_cast<int64_t>(strlen(altqual)) == static_cast<int64_t>(getLseq(D))) ) data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderBase.hpp:1171:43: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). if ( altqual && (static_cast<int64_t>(strlen(altqual)) == static_cast<int64_t>(getLseq(D))) ) data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderBase.hpp:3570:49: [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. for ( uint8_t const * qual = rqual; qual != equal; ++qual ) data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderBase.hpp:5582:33: [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). size_t const refidnamelen = strlen(refidname); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentDecoderBase.hpp:5607:34: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). size_t const nextrefidlen = strlen(nextrefid); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentEncoderBase.hpp:851:26: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). uint64_t const len = strlen(c); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentEncoderBase.hpp:881:26: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). uint64_t const len = strlen(c); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamAlignmentSnappyInput.hpp:67:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). GZ.read(reinterpret_cast<char *>(alignment.D.begin()),alignment.blocksize); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamHeader.hpp:474:33: [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). unsigned int const idlen = strlen(ID); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamHeaderLowMem.hpp:829:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(text,l_text); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamHeaderLowMem.hpp:932:33: [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). uint64_t const namesize = strlen(name); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamHeaderLowMem.hpp:959:32: [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). uint64_t const namesize = strlen(name); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamHeaderLowMem.hpp:994:24: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). ostr.write(hdtext,strlen(hdtext)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamHeaderLowMem.hpp:1136:24: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). ostr.write(hdtext,strlen(hdtext)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamHeaderLowMem.hpp:1498:33: [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). unsigned int const idlen = strlen(ID); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndex.hpp:71:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(&magic[0],sizeof(magic)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexGenerator.hpp:58:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(reinterpret_cast<char *>(&BC),sizeof(::libmaus2::bambam::BamIndexBinChunk)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexGenerator.hpp:90:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(reinterpret_cast<char *>(&BC),sizeof(::libmaus2::bambam::BamIndexBinChunk)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexGenerator.hpp:125:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(reinterpret_cast<char *>(&LC),sizeof(::libmaus2::bambam::BamIndexLinearChunk)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexGenerator.hpp:154:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(reinterpret_cast<char *>(&LC),sizeof(::libmaus2::bambam::BamIndexLinearChunk)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexGenerator.hpp:183:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(reinterpret_cast<char *>(&LC),sizeof(::libmaus2::bambam::BamIndexLinearChunk)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexGenerator.hpp:210:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(reinterpret_cast<char *>(&LC),sizeof(::libmaus2::bambam::BamIndexLinearChunk)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexGenerator.hpp:225:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(reinterpret_cast<char *>(&LC),sizeof(::libmaus2::bambam::BamIndexLinearChunk)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexGenerator.hpp:240:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(reinterpret_cast<char *>(&LC),sizeof(::libmaus2::bambam::BamIndexLinearChunk)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexGenerator.hpp:255:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read( data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexGenerator.hpp:276:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read( data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexGenerator.hpp:1048:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). binCIS.read(reinterpret_cast<char *>(&BC),sizeof(::libmaus2::bambam::BamIndexBinChunk)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamIndexGenerator.hpp:1120:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). linCIS.read(reinterpret_cast<char *>(&LC),sizeof(::libmaus2::bambam::BamIndexLinearChunk)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamSeqEncodeTable.hpp:45:13: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). A[i] = strlen(s); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamSeqEncodeTable.hpp:46:31: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). for ( uint64_t i = 0; i < strlen(s); ++i ) data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamSeqEncodeTable.hpp:48:31: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). for ( uint64_t i = 0; i < strlen(s); ++i ) data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamStreamingMarkDuplicates.hpp:358:19: [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). l1 = tag1 ? strlen(tag1) : 0; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/BamStreamingMarkDuplicates.hpp:363:20: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). l2 = tag2 ? strlen(tag2) : 0; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ChecksumsFactory.cpp:1212:15: [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). lenq = ::strlen(OQ); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ChromosomeVectorMerge.hpp:86:10: [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. bool equal(Chromosome const & CA, Chromosome const & CB) const data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ChromosomeVectorMerge.hpp:104:13: [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. return equal(V[A.first]->at(A.second),V[B.first]->at(B.second)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ChromosomeVectorMerge.hpp:125:19: [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. if ( ! comp.equal(V[0]->at(j),V[i]->at(j)) ) data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ChromosomeVectorMerge.hpp:256:22: [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. assert ( comp.equal(inchr,cvec[inchrr]) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ChromosomeVectorMerge.hpp:257:22: [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. assert ( comp.equal(inchr,chromosomes[outchrr]) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/GeneFlatFile.hpp:59:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(C.begin() + p, C.size()-p); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/MdNmRecalculation.hpp:236:15: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). fastr->read(B.begin(),pack); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ProgramHeaderLineSet.hpp:350:26: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). uint64_t const len = strlen(from); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsBase.hpp:508:22: [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). size_t const l = strlen(reinterpret_cast<char const *>(readname)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadEndsBase.hpp:1070:7: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). G.read(reinterpret_cast<char *>(this),sizeof(*this)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ReadGroup.hpp:188:12: [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. comp.equal(M[low],M[high]) data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:46:12: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). modelen = strlen(rmode); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:47:16: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). filenamelen = strlen(rfilename); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:61:26: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). referencefilenamelen = strlen(rreferencefilename); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:123:16: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). filenamelen = strlen(rfilename); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:133:26: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). referencefilenamelen = strlen(rreferencefilename); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:197:12: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). modelen = strlen(rmode); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:198:16: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). filenamelen = strlen(rfilename); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:212:26: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). referencefilenamelen = strlen(rreferencefilename); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:327:16: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). filenamelen = strlen(rfilename); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:337:26: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). referencefilenamelen = strlen(rreferencefilename); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:539:40: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). size_t const headerlen = headertext ? strlen(headertext) : 0; data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:614:37: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). encoder->filename = (char *)malloc(strlen(rfilename)+1); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:619:29: [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). memset(encoder->filename,0,strlen(rfilename)+1); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:620:37: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). memcpy(encoder->filename,rfilename,strlen(rfilename)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:622:33: [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). encoder->mode = (char *)malloc(strlen(rmode)+1); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:627:25: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). memset(encoder->mode,0,strlen(rmode)+1); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:628:29: [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). memcpy(encoder->mode,rmode,strlen(rmode)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:632:47: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). encoder->referencefilename = (char *)malloc(strlen(rreferencefilename)+1); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:637:39: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). memset(encoder->referencefilename,0,strlen(rreferencefilename)+1); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/Scram.c:638:56: [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). memcpy(encoder->referencefilename,rreferencefilename,strlen(rreferencefilename)); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/ScramInputContainer.hpp:200:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). pistr->read(out,bytestoread); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteReadEndsWorkPackageDispatcher.hpp:270:29: [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). size_t const len = strlen(TA1); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteReadEndsWorkPackageDispatcher.hpp:282:29: [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). size_t const len = strlen(TA2); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteWorkPackageDispatcher.hpp:241:29: [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). size_t const len = strlen(TA1); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteWorkPackageDispatcher.hpp:253:29: [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). size_t const len = strlen(TA2); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/GenericInputBlock.hpp:161:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(reinterpret_cast<char *>(pe),readsize); data/libmaus2-2.0.766+dfsg/src/libmaus2/bambam/parallel/InputBlock.hpp:80:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(C.begin(),payloadsize + 8); data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/ArrayDecode.hpp:337:23: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). out.put ( SBIS.read(k) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitIOInput.hpp:178:20: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). inline uint64_t read(uint64_t numbits) throw() data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitIOInput.hpp:215:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). return read(numbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitIOInput.hpp:301:20: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). inline uint64_t read(unsigned int numbits) data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitIOInput.hpp:342:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). return read(numbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitIOInput.hpp:483:20: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). inline uint64_t read(unsigned int numbits) data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/BitIOInput.hpp:524:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). return read(numbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/CompactDecoderBuffer.hpp:204:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read ( reinterpret_cast<char *>(C.getD()) , bytestoread ); data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/OutputBuffer.hpp:159:36: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read( reinterpret_cast<char *>(B.get()), n * sizeof(data_type) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/PacDecoderBuffer.hpp:191:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read ( reinterpret_cast<char *>(C.begin()) , bytestoread ); data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/readElias.hpp:92:34: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const log_1 = reader.read(log_2); data/libmaus2-2.0.766+dfsg/src/libmaus2/bitio/readElias.hpp:93:30: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const n = reader.read(log_1); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphDecoder.hpp:89:28: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const c = IA.read(64); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphDecoder.hpp:93:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const k = IA.read(64); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphDecoder.hpp:94:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const v = IA.read(64); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphDecoder.hpp:117:28: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const c = IA.read(64); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphDecoder.hpp:121:34: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). linkcntfreqs[i].first = IA.read(64); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphDecoder.hpp:122:35: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). linkcntfreqs[i].second = IA.read(64); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphDecoder.hpp:272:22: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). A[i].inv = IA.read(1); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphDecoder.hpp:274:23: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). absort[i] = IA.read(nb); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphDecoder.hpp:276:23: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). bbsort[i] = IA.read(nb); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphDecoder.hpp:278:27: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). arangesort[i] = IA.read(nb); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphDecoder.hpp:280:27: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). brangesort[i] = IA.read(nb); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/GraphEncoder.hpp:914:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ISI->read(C.begin(),C.size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/LasIntervals.hpp:195:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). pISI->read(reinterpret_cast<char *>(B.begin()),toread); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapDataInterface.hpp:557:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(reinterpret_cast<char *>(A.begin()),l); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/OverlapInfo.hpp:56:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(reinterpret_cast<char *>(this),sizeof(*this)); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/SimpleOverlapParser.hpp:89:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(Abuffer.begin(),toread); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/align/SimpleOverlapParser.hpp:93:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(Abuffer.begin(),Abuffer.size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:469:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). bpsstream.read(C + (rlen - (rlen+3)/4),(rlen+3)/4); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:520:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). bpsstream.read(C + (rlen - (rlen+3)/4),(rlen+3)/4); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:572:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). bpsstream.read(C,inbytes); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:625:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). bpsstream.read(C,inbytes); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:677:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). bpsstream.read(C + (rlen - (rlen+3)/4),(rlen+3)/4); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:791:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). bpsstream.read(C + (rlen - (rlen+3)/4),(rlen+3)/4); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:3065:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). Pidxfile->read(reinterpret_cast<char * >(B.begin()), (uhigh-ulow) * Read::serialisedSize); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:3386:15: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). dataISI.read( data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:3565:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). anno.read(Aname.begin(),slen); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/DatabaseFile.hpp:3592:14: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). Pdata->read ( reinterpret_cast<char *>(Adata->begin()), toread ); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/IQVDecoder.hpp:40:53: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). unsigned char getQualityForBlock(uint64_t const read, uint64_t const block) const data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/IQVDecoder.hpp:42:11: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if ( read < RL.size() ) data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/IQVDecoder.hpp:44:33: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const tqa = anno[read]; data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/IQVDecoder.hpp:51:67: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). lme.getStream() << "[E] IQVDecoder::getQualityForBlock(" << read << "," << block << "): unknown read id" << std::endl; data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/IQVDecoder.hpp:57:56: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). unsigned char getQualityForInterval(uint64_t const read, uint64_t const low, uint64_t const high) const data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/IQVDecoder.hpp:64:44: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). unsigned char u = getQualityForBlock(read,blocklow); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/IQVDecoder.hpp:67:42: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). u = std::max(u,getQualityForBlock(read,i)); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/IQVDecoder.hpp:77:56: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). unsigned char getQualityForInterval(uint64_t const read, uint64_t low, uint64_t high, bool const inv) const data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/IQVDecoder.hpp:82:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). low = RL[read]-low; data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/IQVDecoder.hpp:83:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). high = RL[read]-high; data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/IQVDecoder.hpp:86:35: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). return getQualityForInterval(read,low,high); data/libmaus2-2.0.766+dfsg/src/libmaus2/dazzler/db/Read.hpp:136:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(C.end() - (rlen+3)/4,(rlen+3)/4); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/CompactReadContainer.hpp:181:36: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const textread = RCGI.read(text.begin(),text.size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastABPGenerator.hpp:106:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(Bin.begin(),bs); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastABgzfDecoderBuffer.hpp:231:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). Pinf->read( data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAIndex.hpp:262:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(cur,re); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAIndex.hpp:327:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(cur,re); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAIndex.hpp:359:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(cur,re); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAInfo.hpp:53:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(B.begin(),sidlen); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAStreamSet.hpp:112:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(A->begin(),A->size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAStreamSet.hpp:184:11: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). str.read(B.begin(),B.size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAStreamSet.hpp:224:22: [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). e = e.substr(strlen("URL=")); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAStreamSet.hpp:259:14: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). PFIS.read(B.begin(),B.size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAToCompact4BigBandBiDir.hpp:351:18: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). seqtmpISI->read(B.begin(),tocopy); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAToCompact4BigBandBiDir.hpp:418:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). seqtmpISI->read(D.begin(),seqlen); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAToCompact4BigBandBiDir.hpp:434:14: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). seqtmp.read(B.begin(),tocopy); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastAToCompact4BigBandBiDir.hpp:493:14: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). seqtmp.read(B.begin(),tocopy); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaBPDecoder.hpp:54:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(&magic[0],8); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaBPDecoder.hpp:180:23: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). while ( (n = ptr->read(Bout.begin(),Bout.size())) ) data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaBPDecoder.hpp:250:30: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const r = ptr->read(p,todo); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaBPDecoder.hpp:283:23: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). while ( (n = ptr->read(Bout.begin(),Bout.size())) ) data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaBPDecoder.hpp:331:23: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). while ( (n = ptr->read(Bout.begin(),Bout.size())) ) data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaBPDecoder.hpp:351:23: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). while ( (r = ptr->read(p,n) ) ) data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaBPDecoder.hpp:370:23: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). while ( (r = ptr->read(p,n) ) ) data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaBPSequenceDecoder.hpp:54:24: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::libmaus2::ssize_t read(char * p, uint64_t const m) data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaBPSequenceDecoder.hpp:88:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(Bin.begin(),(toread+3)/4); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaBPSequenceDecoder.hpp:120:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(Bin.begin(),(toread+2)/3); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaBPSequenceDecoder.hpp:160:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(Bin.begin(),(toread+1)/2); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/FastaBPSequenceDecoder.hpp:214:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(reinterpret_cast<char *>(&crcbytes[0]),sizeof(crcbytes)); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/Phred.cpp:90:33: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). if ( lineostr->str().size() + strlen(",") + lostr.str().size() > linelength ) data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/RefPathLookup.hpp:79:20: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). e = e.substr(strlen("URL=")); data/libmaus2-2.0.766+dfsg/src/libmaus2/fastx/StreamFastReaderBase.hpp:109:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read ( reinterpret_cast<char *>(pa), B.size() ); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/CDS.hpp:96:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(reinterpret_cast<char *>(this),sizeof(CDS)); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/Exon.hpp:74:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(reinterpret_cast<char *>(this),sizeof(Exon)); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/ExonInterval.hpp:60:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(reinterpret_cast<char *>(this),sizeof(ExonInterval)); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GTFData.hpp:250:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(A.begin(),data.size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GTFData.hpp:317:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(Aid.begin(),Aid_o); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GTFData.hpp:561:35: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::ptrdiff_t const l_gene = strlen(c_gene); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GTFData.hpp:563:41: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::ptrdiff_t const l_transcript = strlen(c_transcript); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GTFData.hpp:565:35: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::ptrdiff_t const l_exon = strlen(c_exon); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GTFData.hpp:567:34: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::ptrdiff_t const l_CDS = strlen(c_CDS); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GTFData.hpp:570:38: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::ptrdiff_t const l_gene_id = strlen(c_gene_id); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GTFData.hpp:572:44: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::ptrdiff_t const l_transcript_id = strlen(c_transcript_id); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GTFData.hpp:574:40: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::ptrdiff_t const l_gene_name = strlen(c_gene_name); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GTFData.hpp:577:34: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::ptrdiff_t const l_tag = strlen(c_tag); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GTFData.hpp:580:55: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::ptrdiff_t const l_transcript_support_level = strlen(c_transcript_support_level); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GTFData.hpp:583:38: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::ptrdiff_t const l_exon_id = strlen(c_exon_id); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GTFData.hpp:585:42: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::ptrdiff_t const l_exon_number = strlen(c_exon_number); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/GTFData.hpp:1365:27: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::size_t const l = strlen(a); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/Gene.hpp:104:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(reinterpret_cast<char *>(this),sizeof(Gene)); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/Tag.hpp:68:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(reinterpret_cast<char *>(this),sizeof(Tag)); data/libmaus2-2.0.766+dfsg/src/libmaus2/gtf/Transcript.hpp:118:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(reinterpret_cast<char *>(this),sizeof(Transcript)); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/BitInputBuffer.hpp:112:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(unsigned int bits) data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/BitInputBuffer.hpp:175:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in->read ( reinterpret_cast<char *>(B.begin() + wordoffset) , bytelen ); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/FileStreamBaseType.hpp:53:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void read(char * const buf, uint64_t const n) data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/FileStreamBaseType.hpp:55:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(buf,n); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexDecoderDataArray.hpp:261:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). SBIS.read(entrybitoff); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexDecoderDataArray.hpp:263:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const pos = SBIS.read(posbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexDecoderDataArray.hpp:264:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const kcnt = SBIS.read(kbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexDecoderDataArray.hpp:265:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const vcnt = SBIS.read(vbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoader.hpp:221:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const pos = SBIS.read(posbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoader.hpp:222:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const kcnt = SBIS.read(kbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoader.hpp:223:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const vcnt = SBIS.read(vbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoader.hpp:301:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const pos = SBIS.read(posbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoader.hpp:302:33: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const kcnt = SBIS.read(kbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoader.hpp:303:33: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const vcnt = SBIS.read(vbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoader.hpp:366:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const pos = SBIS.read(posbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoader.hpp:367:33: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const kcnt = SBIS.read(kbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoader.hpp:368:33: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const vcnt = SBIS.read(vbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoader.hpp:385:40: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). /* uint64_t const pos = */ SBIS.read(posbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoader.hpp:386:38: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). index[numentries-1].kcnt = SBIS.read(kbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoader.hpp:387:38: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). index[numentries-1].vcnt = SBIS.read(vbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/IndexLoaderBase.cpp:43:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). indexistr.read( reinterpret_cast<char *>(&v) , 8 ); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/InputAdapter.hpp:50:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(unsigned int b) data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/InputAdapter.hpp:57:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). v |= PBIB->read(32); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/InputAdapter.hpp:64:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). v |= PBIB->read(b); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/InputAdapter.hpp:72:15: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). v = PBIB->read(32); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/InputAdapter.hpp:74:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). v |= PBIB->read(32); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFPhiPairDecoder.hpp:99:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). projector::set(B[i], SBIS.read(numbits)); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFPhiPairLCPDecoder.hpp:165:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). projector::set(B[i], SBIS.read(numbits)); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFRankLCPDecoder.hpp:164:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). projector::set(B[i], SBIS.read(numbits)); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFSupportBitDecoder.hpp:117:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(unsigned int numbits) data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFSupportBitDecoder.hpp:126:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). return read(1); data/libmaus2-2.0.766+dfsg/src/libmaus2/huffman/LFValueDecoder.hpp:167:25: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). B[i].value = SBIS.read(numbits); data/libmaus2-2.0.766+dfsg/src/libmaus2/index/ExternalMemoryIndexDecoder.hpp:141:20: [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. if ( ! ref.equal(check) ) data/libmaus2-2.0.766+dfsg/src/libmaus2/index/ExternalMemoryIndexDecoder.hpp:148:21: [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. assert( ref.equal(check) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/index/ExternalMemoryIndexRecord.hpp:66:9: [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. bool equal(ExternalMemoryIndexRecord const & O) const data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPCorLocalAligner.hpp:571:19: [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. assert ( std::equal(ATC0.ta,ATC0.ta + offa, ATCc.ta) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPCorLocalAligner.hpp:576:19: [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. assert ( std::equal(ATC0.ta,ATC0.ta + offa, ATCc.ta) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPCorLocalAligner.hpp:577:19: [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. assert ( std::equal(ATC1.ta+offb,ATC1.te, ATCc.ta + offa) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPCorLocalAligner.hpp:935:20: [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. assert ( std::equal( aa + m_c->apos, aa + m_c->apos + anak, ba + m_c->bpos ) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPCorLocalAligner.hpp:1059:21: [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. assert ( std::equal( aa + apos, aa + apos + anak, ba + bpos ) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPLocalAligner.hpp:567:19: [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. assert ( std::equal(ATC0.ta,ATC0.ta + offa, ATCc.ta) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPLocalAligner.hpp:572:19: [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. assert ( std::equal(ATC0.ta,ATC0.ta + offa, ATCc.ta) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPLocalAligner.hpp:573:19: [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. assert ( std::equal(ATC1.ta+offb,ATC1.te, ATCc.ta + offa) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPLocalAligner.hpp:931:20: [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. assert ( std::equal( aa + m_c->apos, aa + m_c->apos + anak, ba + m_c->bpos ) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/lcs/NNPLocalAligner.hpp:1055:21: [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. assert ( std::equal( aa + apos, aa + apos + anak, ba + bpos ) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflate.hpp:184:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * const decomp, uint64_t const n) data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateBase.hpp:61:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(reinterpret_cast<char *>(block.begin()),payloadsize + 8); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateBlock.hpp:173:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * const ldata, uint64_t const n) data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateDeflateParallel.hpp:264:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * const data, uint64_t const n) data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateHeaderBase.hpp:84:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(reinterpret_cast<char *>(header.begin()),getBgzfHeaderSize()); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateParallel.hpp:194:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * const data, uint64_t const n) data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateThreadPoolReader.hpp:130:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * p, uint64_t s) data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/BgzfInflateThreadPoolReader.hpp:180:24: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const n = read(&c,1); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/GzipSingleStream.hpp:59:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * buffer, uint64_t n) data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/GzipSingleStream.hpp:68:29: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t subred = infl.read(buffer,n); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/GzipStream.hpp:76:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * buffer, uint64_t n) data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/GzipStream.hpp:82:37: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t subred = singlestream.read(buffer,n); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/GzipStream.hpp:109:26: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t const red = read(reinterpret_cast<char *>(&c),1); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Inflate.hpp:133:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * buffer, uint64_t const n) data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Inflate.hpp:164:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read ( reinterpret_cast<char *>(inbuf.get()), inbuf.size() ); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Inflate.hpp:166:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if ( ! read ) data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Inflate.hpp:178:23: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). strm->setAvailIn(read); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/IstreamSource.hpp:65:18: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). pe = pa + in.read(pc,std::min(avail,A.size())); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/Lz4DecoderBuffer.hpp:194:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(cbuffer.begin(),compressedsize); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SimpleCompressedConcatInputStream.hpp:87:34: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). fragments[curstream].stream->read(C.begin(),comp); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SimpleCompressedConcatInputStream.hpp:155:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * p, uint64_t n) data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SimpleCompressedInputBlock.hpp:75:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(reinterpret_cast<char *>(I.begin()),compsize); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SimpleCompressedInputBlockConcat.hpp:104:11: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). Pcis->read(reinterpret_cast<char *>(block.I.begin()),block.compsize); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SimpleCompressedInputStream.hpp:81:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(C.begin(),comp); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SimpleCompressedInputStream.hpp:160:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * p, uint64_t n) data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyCompress.cpp:144:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(out,insize); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyFileInputStream.hpp:36:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * c, uint64_t const n) { return instream.read(c,n); } data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyFileInputStream.hpp:36:64: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * c, uint64_t const n) { return instream.read(c,n); } data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyInputStream.hpp:143:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * B, uint64_t n) data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyOffsetFileInputStream.hpp:57:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * c, uint64_t const n) { return instream.read(c,n); } data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyOffsetFileInputStream.hpp:57:64: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * c, uint64_t const n) { return instream.read(c,n); } data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyStringInputStream.hpp:39:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * c, uint64_t const n) { return instream.read(c,n); } data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/SnappyStringInputStream.hpp:39:64: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). uint64_t read(char * c, uint64_t const n) { return instream.read(c,n); } data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/StreamWrapperBuffer.hpp:87:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read(midptr, buffer.end()-midptr); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/XzDecoder.cpp:62:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(reinterpret_cast<char *>(Ainbuf.begin()),Ainbuf.size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/XzDecoder.cpp:75:33: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). size_t libmaus2::lz::XzDecoder::read( data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/XzDecoder.hpp:54:11: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). size_t read(uint8_t * A, size_t s); data/libmaus2-2.0.766+dfsg/src/libmaus2/lz/XzInputStreamBuffer.hpp:81:28: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). size_t const n = xzdec.read(reinterpret_cast<uint8_t *>(midptr), buffer.end()-midptr); data/libmaus2-2.0.766+dfsg/src/libmaus2/math/IntegerInterval.hpp:65:36: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). size_t const exptlen = ::std::strlen(expt); data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlInputStreamBuffer.cpp:39:30: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::size_t const n = COR.read(buffer.begin()+putbackspace,buffer.size()-putbackspace); data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlObject.cpp:141:46: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::size_t libmaus2::network::CurlObject::read( data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlObject.hpp:69:18: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::std::size_t read( data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlObjectReader.cpp:59:50: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::size_t libmaus2::network::CurlObjectReader::read(char * p, std::size_t n) data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlObjectReader.cpp:61:28: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::size_t const r = obj.read(p,n); data/libmaus2-2.0.766+dfsg/src/libmaus2/network/CurlObjectReader.hpp:47:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::size_t read(char * p, std::size_t n); data/libmaus2-2.0.766+dfsg/src/libmaus2/parallel/threadpool/input/ThreadPoolInput.hpp:241:23: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). inputinfo.in.read(ca,ptr->blocksize); data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixExecute.cpp:589:69: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::libmaus2::ssize_t const r = ::libmaus2::posix::PosixFunctions::read(stderrfd,tempmemerr+errread,toread); data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixExecute.cpp:620:69: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::libmaus2::ssize_t const r = ::libmaus2::posix::PosixFunctions::read(stdoutfd,tempmemout+outread,toread); data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixFunctions.cpp:474:54: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::libmaus2::ssize_t libmaus2::posix::PosixFunctions::read(int fd, void * buf, ::std::size_t count) data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixFunctions.cpp:476:11: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). return ::read(fd,buf,count); data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixFunctions.cpp:479:54: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::libmaus2::ssize_t libmaus2::posix::PosixFunctions::read(int fd, void * buf, ::std::size_t count) data/libmaus2-2.0.766+dfsg/src/libmaus2/posix/PosixFunctions.hpp:198:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). static ::libmaus2::ssize_t read(int fd, void * buf, ::std::size_t count); data/libmaus2-2.0.766+dfsg/src/libmaus2/serialize/Serialize.hpp:99:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read ( reinterpret_cast<char *>(p) , sizeof(N) ); return sizeof(N); data/libmaus2-2.0.766+dfsg/src/libmaus2/serialize/Serialize.hpp:103:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read ( reinterpret_cast<char *>(p) , sizeof(N) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/serialize/Serialize.hpp:138:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read ( reinterpret_cast<char *>(p+ i*bsunits), bsbytes ); data/libmaus2-2.0.766+dfsg/src/libmaus2/serialize/Serialize.hpp:142:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read ( reinterpret_cast<char *>(p+full*bsunits), restbytes ); data/libmaus2-2.0.766+dfsg/src/libmaus2/serialize/Serialize.hpp:164:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read ( reinterpret_cast<char *>(p+ i*bsunits), bsbytes ); data/libmaus2-2.0.766+dfsg/src/libmaus2/serialize/Serialize.hpp:177:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read ( reinterpret_cast<char *>(p+full*bsunits), restbytes ); data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/MergingReadBack.hpp:91:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). PCIS->read(reinterpret_cast<char *>(subblocks[b].pa),toread * sizeof(data_type)); data/libmaus2-2.0.766+dfsg/src/libmaus2/sorting/SemiExternalKeyTupleSort.hpp:226:11: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). conc.read(reinterpret_cast<char *>(AS.begin()),snum*sizeof(data_type)); data/libmaus2-2.0.766+dfsg/src/libmaus2/stacktrace/StackTraceBufferContainer.cpp:376:25: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ::ssize_t const r = ::read(rmk,pp,todo); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/BwtMergeBlockSortRequest.hpp:825:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). utfCIS->read(c,toread); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/GapArrayByteOverflowKeyAccessor.hpp:50:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(reinterpret_cast<char *>(&p[0]),1*sizeof(uint64_t)); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtComputeSSA.cpp:236:7: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(reinterpret_cast<char *>(&p0), sizeof(uint64_t)); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtComputeSSA.cpp:237:7: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(reinterpret_cast<char *>(&p1), sizeof(uint64_t)); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp:93:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(reinterpret_cast<char_type *>(B.begin()),toread); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp:138:23: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). HEF.write(SBIS->read(8),8); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp:2212:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CA.read(BA.begin(),BA.size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp:2213:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CB.read(BB.begin(),BB.size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp:2219:15: [1] (buffer) equal: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. ! std::equal(BA.begin(),BA.begin()+ca,BB.begin()) data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp:4326:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(reinterpret_cast<char_type *>(B),toread); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp:4374:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(reinterpret_cast<char_type *>(B.begin()),toread); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp:4496:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ininst.read(COA.begin() + low,high-low); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp:4506:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ininst.read(COA.begin(),fs); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp:4607:15: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). textstr.read(&A[0],A.size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp:4922:27: [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. assert ( mergetree->equal(*tptr) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp:4976:27: [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. assert ( mergetree->equal(*tptr) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp:5016:27: [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. assert ( mergetree->equal(*tptr) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtSelectSSA.cpp:239:7: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(reinterpret_cast<char *>(&p0), sizeof(uint64_t)); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/BwtSelectSSA.cpp:240:7: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(reinterpret_cast<char *>(&p1), sizeof(uint64_t)); data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyBaseBlock.hpp:36:10: [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. bool equal(MergeStrategyBlock const & O) const data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyBlock.hpp:237:18: [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. virtual bool equal(MergeStrategyBlock const & O) const = 0; data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeBlock.hpp:43:27: [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. if ( ! children[i]->equal(*(O.children[i])) ) data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeExternalBlock.hpp:46:10: [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. bool equal(MergeStrategyBlock const & O) const data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeInternalBlock.hpp:41:10: [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. bool equal(MergeStrategyBlock const & O) const data/libmaus2-2.0.766+dfsg/src/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeInternalSmallBlock.hpp:41:10: [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. bool equal(MergeStrategyBlock const & O) const data/libmaus2-2.0.766+dfsg/src/libmaus2/uint/uint.hpp:522:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read ( reinterpret_cast<char *>(&A[0]) , words * sizeof(uint64_t) ); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Base64.hpp:131:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(&tin[0],4); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Concat.cpp:31:6: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(buf.get(), buf.size()); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Concat.cpp:49:6: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(buf.get(), toread); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/CountGetObject.hpp:61:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void read(value_copy_type * q, uint64_t n) data/libmaus2-2.0.766+dfsg/src/libmaus2/util/CountGetObject.hpp:109:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void read(value_type * q, uint64_t n) data/libmaus2-2.0.766+dfsg/src/libmaus2/util/DynamicLoading.cpp:46:41: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). libmaus2::autoarray::AutoArray<char> D(strlen(libinfo.dli_fname)+1,true); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/DynamicLoading.cpp:47:50: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::copy(libinfo.dli_fname,libinfo.dli_fname + strlen(libinfo.dli_fname),D.begin()); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/GetFileSize.cpp:58:7: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). istr.read ( reinterpret_cast<char *>(A.get()), fs ); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/GetFileSize.hpp:99:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). istr.read ( reinterpret_cast<char *>(A.get()), n8 ); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/GetFileSize.hpp:126:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(buf.get(), tocopy); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/GetFileSize.hpp:177:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(buf.get(), tocopy); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/GetFileSize.hpp:227:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(buf.get(), tocopy); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/GetObject.hpp:70:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void read(value_type * q, uint64_t n) data/libmaus2-2.0.766+dfsg/src/libmaus2/util/LineBuffer.hpp:58:20: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::streamsize read(char * p, size_t n) data/libmaus2-2.0.766+dfsg/src/libmaus2/util/LineBuffer.hpp:60:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). file.read(p,n); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/LineBuffer.hpp:103:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). bufferptrin = bufferptra + read(bufferptra,bufsize); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/LineBuffer.hpp:125:32: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). bufferptrin = bufferptra + read(bufferptra,bufsize); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/LineBuffer.hpp:224:24: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). bufferptrin += read(bufferptrin,unused); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/OctetString.cpp:92:6: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(reinterpret_cast<char *>(A.begin()),blength); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/OctetString.cpp:109:6: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(reinterpret_cast<char *>(A.begin()),blength); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/OctetString.cpp:127:6: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(reinterpret_cast<char *>(A.begin()),symlength); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/SerialiseHelper.hpp:60:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(reinterpret_cast<char *>(&v),sizeof(v)); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/StreamGetObject.hpp:70:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). void read(value_type * q, uint64_t n) data/libmaus2-2.0.766+dfsg/src/libmaus2/util/StringSerialisation.cpp:47:5: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read ( A.get(), u ); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/SuccinctBorderArray.hpp:93:55: [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). SuccinctBorderArray(char const * s) : B(), S(B), n(strlen(s)) data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Utf8DecoderBuffer.cpp:145:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). stream.read ( reinterpret_cast<char *>(inbuffer.begin()) , bytestoread ); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Utf8String.cpp:77:6: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(reinterpret_cast<char *>(A.begin()),blength); data/libmaus2-2.0.766+dfsg/src/libmaus2/util/Utf8String.cpp:85:6: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(reinterpret_cast<char *>(A.begin()),blength); data/libmaus2-2.0.766+dfsg/src/libmaus2/vcf/VCFSortEntry.hpp:147:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in.read(A->begin(),n); data/libmaus2-2.0.766+dfsg/src/libmaus2/vep/VEPParser.hpp:110:6: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). > read() data/libmaus2-2.0.766+dfsg/src/libmaus2/wavelet/ImpExternalWaveletGeneratorCompactHuffmanParallel.hpp:322:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). istr.read(reinterpret_cast<char *>(inbuf.get()), readbytes); data/libmaus2-2.0.766+dfsg/src/libmaus2/wavelet/ImpExternalWaveletGeneratorHuffmanParallel.hpp:313:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). istr.read(reinterpret_cast<char *>(inbuf.get()), readbytes); data/libmaus2-2.0.766+dfsg/src/libmaus2/wavelet/Utf8ToImpCompactHuffmanWaveletTree.hpp:183:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). textCIS->read(reinterpret_cast<char *>(A.begin()),partsize); data/libmaus2-2.0.766+dfsg/src/libmaus2/wavelet/Utf8ToImpHuffmanWaveletTree.hpp:159:16: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). textCIS->read(reinterpret_cast<char *>(A.begin()),partsize); data/libmaus2-2.0.766+dfsg/src/test/testAIO.cpp:271:7: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(C.begin(),C.size()); data/libmaus2-2.0.766+dfsg/src/test/testAIO.cpp:285:7: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(C.begin(),C.size()); data/libmaus2-2.0.766+dfsg/src/test/testAIO.cpp:301:7: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(A.begin(),fs); data/libmaus2-2.0.766+dfsg/src/test/testAIO.cpp:347:26: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). assert ( url.size() >= strlen("mem:") ); data/libmaus2-2.0.766+dfsg/src/test/testAIO.cpp:420:21: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). uint64_t const l = strlen(text); data/libmaus2-2.0.766+dfsg/src/test/testAIO.cpp:440:21: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). uint64_t const l = strlen(text); data/libmaus2-2.0.766+dfsg/src/test/testAIO.cpp:461:21: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). uint64_t const l = strlen(text); data/libmaus2-2.0.766+dfsg/src/test/testBWTDyn.cpp:55:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). istr.read ( reinterpret_cast<char *>(buf.get()), c ); data/libmaus2-2.0.766+dfsg/src/test/testBWTDyn.cpp:188:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). istr.read ( reinterpret_cast<char *>(buf.get()), len ); data/libmaus2-2.0.766+dfsg/src/test/testBWTHufDyn.cpp:62:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). istr.read ( reinterpret_cast<char *>(buf.get()), c ); data/libmaus2-2.0.766+dfsg/src/test/testBWTHufDyn.cpp:189:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). istr.read ( reinterpret_cast<char *>(buf.get()), len ); data/libmaus2-2.0.766+dfsg/src/test/testBitIO.cpp:539:15: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). assert ( R.read(8) == (i & 0xFF) ); data/libmaus2-2.0.766+dfsg/src/test/testBitIO.cpp:576:15: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). assert ( R.read(8) == (i & 0xFF) ); data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:257:5: [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). strlen(a), data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:259:5: [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). strlen(b) data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:265:7: [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). a,strlen(a), data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:266:7: [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). b,strlen(b), data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:399:9: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). a,a+strlen(a), data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:400:9: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). b,b+strlen(b) data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:473:9: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). a,a+strlen(a), data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:474:9: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). b,b+strlen(b) data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:531:4: [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). strlen(a), data/libmaus2-2.0.766+dfsg/src/test/testalignerspeed.cpp:533:4: [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). strlen(b), data/libmaus2-2.0.766+dfsg/src/test/testbamdamage.cpp:20:31: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). while ( (bamdec.getStream().read(C.begin(),C.size())) && (red=bamdec.getStream().gcount()) ) data/libmaus2-2.0.766+dfsg/src/test/testbwtconstruction.cpp:86:18: [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. assert ( ::std::equal(ita,ite,r.begin()) ); data/libmaus2-2.0.766+dfsg/src/test/testbytetocompact.cpp:155:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read ( reinterpret_cast<char *>(B.begin()), lrange ); data/libmaus2-2.0.766+dfsg/src/test/testbytetocompact.cpp:211:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read ( reinterpret_cast<char *>(B.begin()), range ); data/libmaus2-2.0.766+dfsg/src/test/testdazzlerdb.cpp:252:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). ISI.read(block.begin(),block.size()); data/libmaus2-2.0.766+dfsg/src/test/testfastaparse.cpp:66:15: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). basestream.read(B.begin(),B.size()); data/libmaus2-2.0.766+dfsg/src/test/testfastarecode.cpp:117:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(reinterpret_cast<char *>(B.begin()), info.seqlen+1); data/libmaus2-2.0.766+dfsg/src/test/testftp.cpp:46:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). in->read(A.begin(),A.size()); data/libmaus2-2.0.766+dfsg/src/test/testgunzip.cpp:33:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). BGS.read(B.begin(),B.size()); data/libmaus2-2.0.766+dfsg/src/test/testkmp.cpp:229:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). istrm.read(cs.begin(),cs.size()); data/libmaus2-2.0.766+dfsg/src/test/testkmp.cpp:236:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). istrn.read(cc.begin(),n); data/libmaus2-2.0.766+dfsg/src/test/testlibcurl.cpp:40:10: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). CIS.read(B.begin(),B.size()); data/libmaus2-2.0.766+dfsg/src/test/testlz.cpp:401:21: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). while ( (r = BIDP.read(B.begin(),B.size())) ) data/libmaus2-2.0.766+dfsg/src/test/testlz.cpp:449:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::cin.read(B.begin(),B.size()); data/libmaus2-2.0.766+dfsg/src/test/testlz.cpp:473:19: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). while ( (d=BIP.read(reinterpret_cast<char *>(adata.begin()),adata.size())) != 0 ) data/libmaus2-2.0.766+dfsg/src/test/testlz.cpp:505:50: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). bdefl.write(reinterpret_cast<char const *>(str),strlen(str)); data/libmaus2-2.0.766+dfsg/src/test/testlz.cpp:507:50: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). bdefl.write(reinterpret_cast<char const *>(str),strlen(str)); data/libmaus2-2.0.766+dfsg/src/test/testmapperm.cpp:82:23: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::string const read(T.begin()+i,T.begin()+i+readlen); data/libmaus2-2.0.766+dfsg/src/test/testmapperm.cpp:87:17: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). -1,-1, -1, read, std::string(readlen,'H')); data/libmaus2-2.0.766+dfsg/src/test/testpacdecode.cpp:36:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). PDW.read(C.begin(),C.size()); data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp:31:46: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). sid = sid.substr(sid.find("orientation=") + strlen("orientation=")); data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp:94:61: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::string srange = name.substr(name.find("genome[") + strlen("genome[")); data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp:101:65: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). std::string const sto = srange.substr(srange.find("..") + strlen("..")); data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp:113:58: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read = libmaus2::fastx::reverseComplementUnmapped(read); data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp:116:70: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read = libmaus2::fastx::remapString(libmaus2::fastx::mapString(read)); data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp:118:87: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). (*readOSI) << '>' << readprolog << '/' << 0 /* read id */ << '/' << 0 << '_' << read.size() << " RQ=0.851\n"; data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp:119:36: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). writeStringInColumn(*readOSI,read,80); data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp:123:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read.begin(),read.end() data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp:123:21: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read.begin(),read.end() data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp:133:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read.size(), data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp:145:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read.begin(),read.size(), data/libmaus2-2.0.766+dfsg/src/test/testpairalign.cpp:145:21: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). read.begin(),read.size(), data/libmaus2-2.0.766+dfsg/src/test/testsimplecompressblock.cpp:40:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). std::cin.read(B.begin(),B.size()); data/libmaus2-2.0.766+dfsg/src/test/testsnappy.cpp:71:20: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). while ( (d = SISB.read(p,64*1024)) != 0 ) data/libmaus2-2.0.766+dfsg/src/test/testsnappyconcat.cpp:66:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). decomp.read(C.begin(),l0-(b_0+b_1)); data/libmaus2-2.0.766+dfsg/src/test/testvalidatebamindex.cpp:217:27: [1] (buffer) equal: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. std::cerr << "[R] " << (equal ? "equal" : "not equal") << std::endl; data/libmaus2-2.0.766+dfsg/src/test/testxz.cpp:35:9: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). xzin.read(&inbuf[0],bufsize); data/libmaus2-2.0.766+dfsg/src/test/testzlibconcat.cpp:66:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). decomp.read(C.begin(),l0-(b_0+b_1)); ANALYSIS SUMMARY: Hits = 831 Lines analyzed = 395578 in approximately 10.40 seconds (38049 lines/second) Physical Source Lines of Code (SLOC) = 287591 Hits@level = [0] 11 [1] 439 [2] 143 [3] 232 [4] 14 [5] 3 Hits@level+ = [0+] 842 [1+] 831 [2+] 392 [3+] 249 [4+] 17 [5+] 3 Hits/KSLOC@level+ = [0+] 2.92777 [1+] 2.88952 [2+] 1.36305 [3+] 0.865813 [4+] 0.0591117 [5+] 0.0104315 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.