include/libmaus2/LibMausConfig.hpp
include/libmaus2/LibMausWindows.hpp
include/libmaus2/aio/ArrayFile.hpp
include/libmaus2/aio/ArrayFileContainer.hpp
include/libmaus2/aio/ArrayFileSet.hpp
include/libmaus2/aio/ArrayInputStream.hpp
include/libmaus2/aio/ArrayInputStreamBuffer.hpp
include/libmaus2/aio/ArrayInputStreamFactory.hpp
include/libmaus2/aio/Buffer.hpp
include/libmaus2/aio/BufferedOutput.hpp
include/libmaus2/aio/CharArrayInputStream.hpp
include/libmaus2/aio/CharArrayInputStreamBuffer.hpp
include/libmaus2/aio/CharArrayOutputStream.hpp
include/libmaus2/aio/CharArrayOutputStreamBuffer.hpp
include/libmaus2/aio/CircularBuffer.hpp
include/libmaus2/aio/CircularWrapper.hpp
include/libmaus2/aio/CompactDecoder4.hpp
include/libmaus2/aio/CompactEncoder4.hpp
include/libmaus2/aio/ConcatInputStream.hpp
include/libmaus2/aio/ConcatInputStreamBuffer.hpp
include/libmaus2/aio/CountOutputStream.hpp
include/libmaus2/aio/CountOutputStreamBuffer.hpp
include/libmaus2/aio/DebugLineOutputStream.hpp
include/libmaus2/aio/DebugLineOutputStreamBuffer.hpp
include/libmaus2/aio/FStreamInputOutputStreamFactory.hpp
include/libmaus2/aio/FileFragment.hpp
include/libmaus2/aio/FileRemoval.hpp
include/libmaus2/aio/GenericPeeker.hpp
include/libmaus2/aio/GetLength.hpp
include/libmaus2/aio/IFStreamInputStreamFactory.hpp
include/libmaus2/aio/IStreamWrapper.hpp
include/libmaus2/aio/InputOutputStream.hpp
include/libmaus2/aio/InputOutputStreamFactory.hpp
include/libmaus2/aio/InputOutputStreamFactoryContainer.hpp
include/libmaus2/aio/InputOutputStreamInstance.hpp
include/libmaus2/aio/InputOutputStreamPointerWrapper.hpp
include/libmaus2/aio/InputOutputStreamWrapper.hpp
include/libmaus2/aio/InputStream.hpp
include/libmaus2/aio/InputStreamFactory.hpp
include/libmaus2/aio/InputStreamFactoryContainer.hpp
include/libmaus2/aio/InputStreamInstance.hpp
include/libmaus2/aio/InputStreamInstanceAtOffset.hpp
include/libmaus2/aio/InputStreamObject.hpp
include/libmaus2/aio/InputStreamObjectAllocator.hpp
include/libmaus2/aio/InputStreamObjectTypeInfo.hpp
include/libmaus2/aio/InputStreamPointerWrapper.hpp
include/libmaus2/aio/InputStreamWrapper.hpp
include/libmaus2/aio/LineSplittingPosixFdOutputStream.hpp
include/libmaus2/aio/LineSplittingPosixFdOutputStreamBuffer.hpp
include/libmaus2/aio/MemoryBackedOutputStream.hpp
include/libmaus2/aio/MemoryBackedOutputStreamBuffer.hpp
include/libmaus2/aio/MemoryFile.hpp
include/libmaus2/aio/MemoryFileAdapter.hpp
include/libmaus2/aio/MemoryFileContainer.hpp
include/libmaus2/aio/MemoryInputOutputStream.hpp
include/libmaus2/aio/MemoryInputOutputStreamBuffer.hpp
include/libmaus2/aio/MemoryInputOutputStreamFactory.hpp
include/libmaus2/aio/MemoryInputStream.hpp
include/libmaus2/aio/MemoryInputStreamBuffer.hpp
include/libmaus2/aio/MemoryInputStreamFactory.hpp
include/libmaus2/aio/MemoryOutputStream.hpp
include/libmaus2/aio/MemoryOutputStreamBuffer.hpp
include/libmaus2/aio/MemoryOutputStreamFactory.hpp
include/libmaus2/aio/NamedTemporaryFile.hpp
include/libmaus2/aio/NamedTemporaryFileAllocator.hpp
include/libmaus2/aio/NamedTemporaryFileTypeInfo.hpp
include/libmaus2/aio/OFStreamOutputStreamFactory.hpp
include/libmaus2/aio/OutputStream.hpp
include/libmaus2/aio/OutputStreamFactory.hpp
include/libmaus2/aio/OutputStreamFactoryContainer.hpp
include/libmaus2/aio/OutputStreamInstance.hpp
include/libmaus2/aio/OutputStreamInstanceArray.hpp
include/libmaus2/aio/OutputStreamPointerWrapper.hpp
include/libmaus2/aio/OutputStreamWrapper.hpp
include/libmaus2/aio/PairFileDecoder.hpp
include/libmaus2/aio/PosixFdInput.hpp
include/libmaus2/aio/PosixFdInputOutputStream.hpp
include/libmaus2/aio/PosixFdInputOutputStreamBuffer.hpp
include/libmaus2/aio/PosixFdInputOutputStreamFactory.hpp
include/libmaus2/aio/PosixFdInputStream.hpp
include/libmaus2/aio/PosixFdInputStreamBuffer.hpp
include/libmaus2/aio/PosixFdInputStreamFactory.hpp
include/libmaus2/aio/PosixFdInputWrapper.hpp
include/libmaus2/aio/PosixFdOutputStream.hpp
include/libmaus2/aio/PosixFdOutputStreamBuffer.hpp
include/libmaus2/aio/PosixFdOutputStreamFactory.hpp
include/libmaus2/aio/PutOutputIterator.hpp
include/libmaus2/aio/ReorderConcatGenericInput.hpp
include/libmaus2/aio/SecrecyCache.hpp
include/libmaus2/aio/SecrecyInputStreamFactory.hpp
include/libmaus2/aio/SecrecyOutputStreamFactory.hpp
include/libmaus2/aio/SerialisedPeeker.hpp
include/libmaus2/aio/SingleFileFragmentMerge.hpp
include/libmaus2/aio/SizeMonitorThread.hpp
include/libmaus2/aio/SkipConcatInputStream.hpp
include/libmaus2/aio/SkipConcatInputStreamBuffer.hpp
include/libmaus2/aio/SplitWriter.hpp
include/libmaus2/aio/StreamLock.hpp
include/libmaus2/aio/SynchronousFastReaderBase.hpp
include/libmaus2/aio/SynchronousGenericInput.hpp
include/libmaus2/aio/SynchronousGenericOutput.hpp
include/libmaus2/aio/TempFileArray.hpp
include/libmaus2/aio/URLObject.hpp
include/libmaus2/aio/WriteCompactArray.hpp
include/libmaus2/alignment/BamLineInfo.hpp
include/libmaus2/alignment/FMIIntervalComparator.hpp
include/libmaus2/alignment/FactorMatchInfo.hpp
include/libmaus2/alignment/FactorMatchInfoPosComparator.hpp
include/libmaus2/alignment/KmerInfo.hpp
include/libmaus2/alignment/KmerTuple.hpp
include/libmaus2/alignment/SimpleLocalAligner.hpp
include/libmaus2/arch/CacheLineSize.hpp
include/libmaus2/arch/I386Features.hpp
include/libmaus2/arch/PageSize.hpp
include/libmaus2/autoarray/AutoArray.hpp
include/libmaus2/autoarray/AutoArray2d.hpp
include/libmaus2/autoarray/AutoArrayAllocType.hpp
include/libmaus2/autoarray/AutoArrayMultiMap.hpp
include/libmaus2/avl/AVLSet.hpp
include/libmaus2/avl/AtomicAVLMap.hpp
include/libmaus2/avl/AtomicAVLPtrValueMap.hpp
include/libmaus2/avl/AtomicAVLSet.hpp
include/libmaus2/bambam/AdapterFilter.hpp
include/libmaus2/bambam/AdapterOffsetStrand.hpp
include/libmaus2/bambam/AlignmentValidity.hpp
include/libmaus2/bambam/BamAccessor.hpp
include/libmaus2/bambam/BamAlignment.hpp
include/libmaus2/bambam/BamAlignmentComparator.hpp
include/libmaus2/bambam/BamAlignmentDecoder.hpp
include/libmaus2/bambam/BamAlignmentDecoderBase.hpp
include/libmaus2/bambam/BamAlignmentDecoderFactory.hpp
include/libmaus2/bambam/BamAlignmentDecoderInfo.hpp
include/libmaus2/bambam/BamAlignmentEncoderBase.hpp
include/libmaus2/bambam/BamAlignmentExpungeCallback.hpp
include/libmaus2/bambam/BamAlignmentFilter.hpp
include/libmaus2/bambam/BamAlignmentFixedSizeData.hpp
include/libmaus2/bambam/BamAlignmentFreeList.hpp
include/libmaus2/bambam/BamAlignmentHashComparator.hpp
include/libmaus2/bambam/BamAlignmentHeapComparator.hpp
include/libmaus2/bambam/BamAlignmentInputCallbackBam.hpp
include/libmaus2/bambam/BamAlignmentInputCallbackSnappy.hpp
include/libmaus2/bambam/BamAlignmentInputPositionCallbackNull.hpp
include/libmaus2/bambam/BamAlignmentInputPositionUpdateCallback.hpp
include/libmaus2/bambam/BamAlignmentListNode.hpp
include/libmaus2/bambam/BamAlignmentNameComparator.hpp
include/libmaus2/bambam/BamAlignmentNameHIComparator.hpp
include/libmaus2/bambam/BamAlignmentNameLexicographicComparator.hpp
include/libmaus2/bambam/BamAlignmentPairFreeList.hpp
include/libmaus2/bambam/BamAlignmentPairListNode.hpp
include/libmaus2/bambam/BamAlignmentPosComparator.hpp
include/libmaus2/bambam/BamAlignmentPrinter.hpp
include/libmaus2/bambam/BamAlignmentReadGroupFilter.hpp
include/libmaus2/bambam/BamAlignmentReg2Bin.hpp
include/libmaus2/bambam/BamAlignmentSnappyInput.hpp
include/libmaus2/bambam/BamAlignmentSortingCircularHashEntryOverflow.hpp
include/libmaus2/bambam/BamAlignmentTagComparator.hpp
include/libmaus2/bambam/BamAlignmentTagOnlyComparator.hpp
include/libmaus2/bambam/BamAuxFilterVector.hpp
include/libmaus2/bambam/BamAuxSortingBuffer.hpp
include/libmaus2/bambam/BamAuxSortingBufferEntry.hpp
include/libmaus2/bambam/BamBlockWriterBase.hpp
include/libmaus2/bambam/BamBlockWriterBaseFactory.hpp
include/libmaus2/bambam/BamCat.hpp
include/libmaus2/bambam/BamCatHeader.hpp
include/libmaus2/bambam/BamDecoder.hpp
include/libmaus2/bambam/BamDefaultAdapters.hpp
include/libmaus2/bambam/BamEntryContainer.hpp
include/libmaus2/bambam/BamFlagBase.hpp
include/libmaus2/bambam/BamFormatAuxiliary.hpp
include/libmaus2/bambam/BamHeader.hpp
include/libmaus2/bambam/BamHeaderLowMem.hpp
include/libmaus2/bambam/BamHeaderParserState.hpp
include/libmaus2/bambam/BamHeaderParserStateBase.hpp
include/libmaus2/bambam/BamHeaderReadGroupInterface.hpp
include/libmaus2/bambam/BamHeaderUpdate.hpp
include/libmaus2/bambam/BamIndex.hpp
include/libmaus2/bambam/BamIndexBin.hpp
include/libmaus2/bambam/BamIndexBinChunk.hpp
include/libmaus2/bambam/BamIndexGenerator.hpp
include/libmaus2/bambam/BamIndexLinear.hpp
include/libmaus2/bambam/BamIndexLinearChunk.hpp
include/libmaus2/bambam/BamIndexMetaInfo.hpp
include/libmaus2/bambam/BamIndexRef.hpp
include/libmaus2/bambam/BamMergeCoordinate.hpp
include/libmaus2/bambam/BamMergeQueryName.hpp
include/libmaus2/bambam/BamMergeTemplate.hpp
include/libmaus2/bambam/BamMultiAlignmentDecoderFactory.hpp
include/libmaus2/bambam/BamNumExtractor.hpp
include/libmaus2/bambam/BamNumericalIndexBase.hpp
include/libmaus2/bambam/BamNumericalIndexDecoder.hpp
include/libmaus2/bambam/BamNumericalIndexGenerator.hpp
include/libmaus2/bambam/BamParallelRewrite.hpp
include/libmaus2/bambam/BamPeeker.hpp
include/libmaus2/bambam/BamRange.hpp
include/libmaus2/bambam/BamRangeDecoder.hpp
include/libmaus2/bambam/BamRangeParser.hpp
include/libmaus2/bambam/BamRawDecoder.hpp
include/libmaus2/bambam/BamRawPeeker.hpp
include/libmaus2/bambam/BamSeqEncodeTable.hpp
include/libmaus2/bambam/BamStreamingMarkDuplicates.hpp
include/libmaus2/bambam/BamStreamingMarkDuplicatesSupport.hpp
include/libmaus2/bambam/BamToFastqOutputFileSet.hpp
include/libmaus2/bambam/BamWriter.hpp
include/libmaus2/bambam/BgzfDeflateOutputCallbackBamIndex.hpp
include/libmaus2/bambam/BgzfDeflateOutputCallbackBamNumericalIndex.hpp
include/libmaus2/bambam/ChecksumsFactory.hpp
include/libmaus2/bambam/ChecksumsInterface.hpp
include/libmaus2/bambam/ChecksumsInterfaceAllocator.hpp
include/libmaus2/bambam/ChecksumsInterfaceTypeInfo.hpp
include/libmaus2/bambam/Chromosome.hpp
include/libmaus2/bambam/ChromosomeVectorMerge.hpp
include/libmaus2/bambam/CigarDecoder.hpp
include/libmaus2/bambam/CigarOperation.hpp
include/libmaus2/bambam/CigarRunLengthDecoder.hpp
include/libmaus2/bambam/CigarStringParser.hpp
include/libmaus2/bambam/CigarStringReader.hpp
include/libmaus2/bambam/CircularHashCollatingBamDecoder.hpp
include/libmaus2/bambam/CollatingBamDecoderAlignmentInputCallback.hpp
include/libmaus2/bambam/CompactReadEndsBase.hpp
include/libmaus2/bambam/CompactReadEndsComparator.hpp
include/libmaus2/bambam/CramRange.hpp
include/libmaus2/bambam/DecoderBase.hpp
include/libmaus2/bambam/DupMarkBase.hpp
include/libmaus2/bambam/DupSetCallback.hpp
include/libmaus2/bambam/DupSetCallbackSet.hpp
include/libmaus2/bambam/DupSetCallbackSharedVector.hpp
include/libmaus2/bambam/DupSetCallbackStream.hpp
include/libmaus2/bambam/DupSetCallbackVector.hpp
include/libmaus2/bambam/DuplicationMetrics.hpp
include/libmaus2/bambam/EncoderBase.hpp
include/libmaus2/bambam/GeneFlatFile.hpp
include/libmaus2/bambam/GeneFlatFileEntry.hpp
include/libmaus2/bambam/HeaderLine.hpp
include/libmaus2/bambam/MdNmRecalculation.hpp
include/libmaus2/bambam/MdStringComputationContext.hpp
include/libmaus2/bambam/MergeQueueElement.hpp
include/libmaus2/bambam/OptName.hpp
include/libmaus2/bambam/OptNameReader.hpp
include/libmaus2/bambam/OpticalComparator.hpp
include/libmaus2/bambam/PileQualityVectorElement.hpp
include/libmaus2/bambam/PileVectorElement.hpp
include/libmaus2/bambam/ProgramHeaderLineSet.hpp
include/libmaus2/bambam/ReadEnds.hpp
include/libmaus2/bambam/ReadEndsBase.hpp
include/libmaus2/bambam/ReadEndsBaseLongHashAttributeComparator.hpp
include/libmaus2/bambam/ReadEndsBasePointerComparator.hpp
include/libmaus2/bambam/ReadEndsBaseShortHashAttributeComparator.hpp
include/libmaus2/bambam/ReadEndsBlockDecoderBase.hpp
include/libmaus2/bambam/ReadEndsBlockDecoderBaseCollection.hpp
include/libmaus2/bambam/ReadEndsBlockDecoderBaseCollectionInfo.hpp
include/libmaus2/bambam/ReadEndsBlockDecoderBaseCollectionInfoBase.hpp
include/libmaus2/bambam/ReadEndsBlockIndexSet.hpp
include/libmaus2/bambam/ReadEndsContainer.hpp
include/libmaus2/bambam/ReadEndsContainerBase.hpp
include/libmaus2/bambam/ReadEndsFreeList.hpp
include/libmaus2/bambam/ReadEndsHeapPairComparator.hpp
include/libmaus2/bambam/ReadEndsListNode.hpp
include/libmaus2/bambam/ReadEndsStreamDecoder.hpp
include/libmaus2/bambam/ReadEndsStreamDecoderBase.hpp
include/libmaus2/bambam/ReadEndsStreamDecoderFileBase.hpp
include/libmaus2/bambam/ReadGroup.hpp
include/libmaus2/bambam/RgInfo.hpp
include/libmaus2/bambam/SamDecoder.hpp
include/libmaus2/bambam/SamDecoderWrapper.hpp
include/libmaus2/bambam/SamEncoder.hpp
include/libmaus2/bambam/SamInfo.hpp
include/libmaus2/bambam/SamInfoAllocator.hpp
include/libmaus2/bambam/SamInfoBase.hpp
include/libmaus2/bambam/SamInfoTypeInfo.hpp
include/libmaus2/bambam/SamPrintableTable.hpp
include/libmaus2/bambam/SamZPrintableTable.hpp
include/libmaus2/bambam/Scram.h
include/libmaus2/bambam/ScramDecoder.hpp
include/libmaus2/bambam/ScramEncoder.hpp
include/libmaus2/bambam/ScramInputContainer.hpp
include/libmaus2/bambam/SeqChksumPrimeNumbers.hpp
include/libmaus2/bambam/SeqChksumUpdateContext.hpp
include/libmaus2/bambam/SnappyAlignmentMergeInput.hpp
include/libmaus2/bambam/SortedFragDecoder.hpp
include/libmaus2/bambam/StrCmpNum.hpp
include/libmaus2/bambam/StrCmpNumRecode.hpp
include/libmaus2/bambam/parallel/AddDuplicationMetricsInterface.hpp
include/libmaus2/bambam/parallel/AddPendingCompressBufferWriteInterface.hpp
include/libmaus2/bambam/parallel/AddWritePendingBgzfBlockInterface.hpp
include/libmaus2/bambam/parallel/AlignmentBlockCompressPackage.hpp
include/libmaus2/bambam/parallel/AlignmentBlockCompressPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/AlignmentBuffer.hpp
include/libmaus2/bambam/parallel/AlignmentBufferAllocator.hpp
include/libmaus2/bambam/parallel/AlignmentBufferHeapComparator.hpp
include/libmaus2/bambam/parallel/AlignmentBufferReinsertInterface.hpp
include/libmaus2/bambam/parallel/AlignmentBufferReturnInterface.hpp
include/libmaus2/bambam/parallel/AlignmentBufferTypeInfo.hpp
include/libmaus2/bambam/parallel/AlignmentRewriteBuffer.hpp
include/libmaus2/bambam/parallel/AlignmentRewriteBufferAddPendingInterface.hpp
include/libmaus2/bambam/parallel/AlignmentRewriteBufferAllocator.hpp
include/libmaus2/bambam/parallel/AlignmentRewriteBufferCoordinateComparator.hpp
include/libmaus2/bambam/parallel/AlignmentRewriteBufferPosComparator.hpp
include/libmaus2/bambam/parallel/AlignmentRewriteBufferReinsertForFillingInterface.hpp
include/libmaus2/bambam/parallel/AlignmentRewritePosMergeSortPackage.hpp
include/libmaus2/bambam/parallel/AlignmentRewritePosSortBaseSortPackage.hpp
include/libmaus2/bambam/parallel/AlignmentRewritePosSortContext.hpp
include/libmaus2/bambam/parallel/AlignmentRewritePosSortContextBaseBlockSortedInterface.hpp
include/libmaus2/bambam/parallel/AlignmentRewritePosSortContextMergePackageFinished.hpp
include/libmaus2/bambam/parallel/BamBlockIndexingBlockFinishedInterface.hpp
include/libmaus2/bambam/parallel/BamBlockIndexingWorkPackage.hpp
include/libmaus2/bambam/parallel/BamBlockIndexingWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/BamBlockIndexingWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/BamBlockNumericalIndexingBlockFinishedInterface.hpp
include/libmaus2/bambam/parallel/BamBlockNumericalIndexingWorkPackage.hpp
include/libmaus2/bambam/parallel/BamBlockNumericalIndexingWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/BamBlockNumericalIndexingWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/BaseMergeSortWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/BaseSortWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/BaseSortWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/BgzfInflateZStreamBaseGetInterface.hpp
include/libmaus2/bambam/parallel/BgzfInflateZStreamBaseReturnInterface.hpp
include/libmaus2/bambam/parallel/BgzfLinearMemCompressWorkPackage.hpp
include/libmaus2/bambam/parallel/BgzfLinearMemCompressWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/BgzfLinearMemCompressWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/BgzfOutputBlockWrittenInterface.hpp
include/libmaus2/bambam/parallel/BlockCompressPackageDispatcher.hpp
include/libmaus2/bambam/parallel/BlockMergeControl.hpp
include/libmaus2/bambam/parallel/BlockMergeControlTypeBase.hpp
include/libmaus2/bambam/parallel/BlockSortControl.hpp
include/libmaus2/bambam/parallel/BlockSortControlBase.hpp
include/libmaus2/bambam/parallel/ChecksumsInterfaceGetInterface.hpp
include/libmaus2/bambam/parallel/ChecksumsInterfacePutInterface.hpp
include/libmaus2/bambam/parallel/CompressBuffer.hpp
include/libmaus2/bambam/parallel/CompressBufferAllocator.hpp
include/libmaus2/bambam/parallel/CompressBufferHeapComparator.hpp
include/libmaus2/bambam/parallel/CompressionPendingElement.hpp
include/libmaus2/bambam/parallel/ControlInputInfo.hpp
include/libmaus2/bambam/parallel/CramEncodingSupportData.hpp
include/libmaus2/bambam/parallel/CramEncodingWorkPackage.hpp
include/libmaus2/bambam/parallel/CramEncodingWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/CramEncodingWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/CramInterface.h
include/libmaus2/bambam/parallel/CramOutputBlock.hpp
include/libmaus2/bambam/parallel/CramOutputBlockChecksumComputedInterface.hpp
include/libmaus2/bambam/parallel/CramOutputBlockChecksumPackage.hpp
include/libmaus2/bambam/parallel/CramOutputBlockChecksumPackageDispatcher.hpp
include/libmaus2/bambam/parallel/CramOutputBlockChecksumPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/CramOutputBlockIdComparator.hpp
include/libmaus2/bambam/parallel/CramOutputBlockSizeComparator.hpp
include/libmaus2/bambam/parallel/CramOutputBlockWritePackage.hpp
include/libmaus2/bambam/parallel/CramOutputBlockWritePackageDispatcher.hpp
include/libmaus2/bambam/parallel/CramOutputBlockWritePackageFinishedInterface.hpp
include/libmaus2/bambam/parallel/CramOutputBlockWritePackageReturnInterface.hpp
include/libmaus2/bambam/parallel/CramPassPointerObject.hpp
include/libmaus2/bambam/parallel/CramPassPointerObjectAllocator.hpp
include/libmaus2/bambam/parallel/CramPassPointerObjectComparator.hpp
include/libmaus2/bambam/parallel/CramPassPointerObjectTypeInfo.hpp
include/libmaus2/bambam/parallel/DecompressBlockWorkPackage.hpp
include/libmaus2/bambam/parallel/DecompressBlockWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/DecompressBlockWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/DecompressBlocksWorkPackage.hpp
include/libmaus2/bambam/parallel/DecompressBlocksWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/DecompressBlocksWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/DecompressedBlock.hpp
include/libmaus2/bambam/parallel/DecompressedBlockAddPendingInterface.hpp
include/libmaus2/bambam/parallel/DecompressedBlockAllocator.hpp
include/libmaus2/bambam/parallel/DecompressedBlockHeapComparator.hpp
include/libmaus2/bambam/parallel/DecompressedBlockReorderHeapComparator.hpp
include/libmaus2/bambam/parallel/DecompressedBlockReturnInterface.hpp
include/libmaus2/bambam/parallel/DecompressedBlockTypeInfo.hpp
include/libmaus2/bambam/parallel/DecompressedPendingObject.hpp
include/libmaus2/bambam/parallel/DecompressedPendingObjectHeapComparator.hpp
include/libmaus2/bambam/parallel/FastQInputDesc.hpp
include/libmaus2/bambam/parallel/FastQInputDescBase.hpp
include/libmaus2/bambam/parallel/FastqInputPackage.hpp
include/libmaus2/bambam/parallel/FastqInputPackageAddPendingInterface.hpp
include/libmaus2/bambam/parallel/FastqInputPackageDispatcher.hpp
include/libmaus2/bambam/parallel/FastqInputPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/FastqParsePackage.hpp
include/libmaus2/bambam/parallel/FastqParsePackageDispatcher.hpp
include/libmaus2/bambam/parallel/FastqParsePackageFinishedInterface.hpp
include/libmaus2/bambam/parallel/FastqParsePackageReturnInterface.hpp
include/libmaus2/bambam/parallel/FastqToBamControl.hpp
include/libmaus2/bambam/parallel/FastqToBamControlInputBlockHeapComparator.hpp
include/libmaus2/bambam/parallel/FastqToBamControlSubReadPending.hpp
include/libmaus2/bambam/parallel/FastqToBamControlSubReadPendingHeapComparator.hpp
include/libmaus2/bambam/parallel/FileChecksumBlockFinishedInterface.hpp
include/libmaus2/bambam/parallel/FileChecksumBlockWorkPackage.hpp
include/libmaus2/bambam/parallel/FileChecksumBlockWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/FileChecksumBlockWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/FragReadEndsContainerFlushFinishedInterface.hpp
include/libmaus2/bambam/parallel/FragReadEndsContainerFlushWorkPackage.hpp
include/libmaus2/bambam/parallel/FragReadEndsContainerFlushWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/FragReadEndsContainerFlushWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/FragReadEndsMergeWorkPackage.hpp
include/libmaus2/bambam/parallel/FragReadEndsMergeWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/FragReadEndsMergeWorkPackageFinishedInterface.hpp
include/libmaus2/bambam/parallel/FragReadEndsMergeWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBuffer.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferAllocator.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferBaseSortPackage.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferBaseSortWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferBaseSortWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferFragment.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferHeapComparator.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferMergeSortPackage.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferMergeSortWorkPackage.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferMergeSortWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferMergeSortWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferNameComparator.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferPointerTypeSwitch.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferPointerTypeSwitchHelper.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferPosComparator.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferQueryNameComparator.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferReorderWorkPackage.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferReorderWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferReorderWorkPackageFinishedInterface.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferReorderWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteFragmentCompleteInterface.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteReadEndsWorkPackage.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteReadEndsWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteReadEndsWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteUpdateInterval.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteWorkPackage.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferRewriteWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferSortContext.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferSortContextBaseBlockSortedInterface.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferSortContextMergePackageFinished.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferSortFinishedInterface.hpp
include/libmaus2/bambam/parallel/FragmentAlignmentBufferTypeInfo.hpp
include/libmaus2/bambam/parallel/GenericInputBamParseObject.hpp
include/libmaus2/bambam/parallel/GenericInputBamParseWorkPackage.hpp
include/libmaus2/bambam/parallel/GenericInputBamParseWorkPackageBlockParsedInterface.hpp
include/libmaus2/bambam/parallel/GenericInputBamParseWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/GenericInputBamParseWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/GenericInputBase.hpp
include/libmaus2/bambam/parallel/GenericInputBgzfDecompressionWorkPackage.hpp
include/libmaus2/bambam/parallel/GenericInputBgzfDecompressionWorkPackageDecompressedBlockReturnInterface.hpp
include/libmaus2/bambam/parallel/GenericInputBgzfDecompressionWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/GenericInputBgzfDecompressionWorkPackageMemInputBlockReturnInterface.hpp
include/libmaus2/bambam/parallel/GenericInputBgzfDecompressionWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/GenericInputBgzfDecompressionWorkSubBlockDecompressionFinishedInterface.hpp
include/libmaus2/bambam/parallel/GenericInputBlock.hpp
include/libmaus2/bambam/parallel/GenericInputBlockAllocator.hpp
include/libmaus2/bambam/parallel/GenericInputBlockFillResult.hpp
include/libmaus2/bambam/parallel/GenericInputBlockSubBlockInfo.hpp
include/libmaus2/bambam/parallel/GenericInputBlockTypeInfo.hpp
include/libmaus2/bambam/parallel/GenericInputControlBlockCompressionFinishedInterface.hpp
include/libmaus2/bambam/parallel/GenericInputControlBlockCompressionWorkPackage.hpp
include/libmaus2/bambam/parallel/GenericInputControlBlockCompressionWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/GenericInputControlBlockCompressionWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/GenericInputControlBlockWritePackage.hpp
include/libmaus2/bambam/parallel/GenericInputControlBlockWritePackageBlockWrittenInterface.hpp
include/libmaus2/bambam/parallel/GenericInputControlBlockWritePackageDispatcher.hpp
include/libmaus2/bambam/parallel/GenericInputControlBlockWritePackageReturnInterface.hpp
include/libmaus2/bambam/parallel/GenericInputControlBlocksWritePackage.hpp
include/libmaus2/bambam/parallel/GenericInputControlBlocksWritePackageDispatcher.hpp
include/libmaus2/bambam/parallel/GenericInputControlBlocksWritePackageReturnInterface.hpp
include/libmaus2/bambam/parallel/GenericInputControlCompressionPending.hpp
include/libmaus2/bambam/parallel/GenericInputControlCompressionPendingHeapComparator.hpp
include/libmaus2/bambam/parallel/GenericInputControlGetCompressorInterface.hpp
include/libmaus2/bambam/parallel/GenericInputControlMergeBlockFinishedInterface.hpp
include/libmaus2/bambam/parallel/GenericInputControlMergeHeapEntry.hpp
include/libmaus2/bambam/parallel/GenericInputControlMergeRequeue.hpp
include/libmaus2/bambam/parallel/GenericInputControlPutCompressorInterface.hpp
include/libmaus2/bambam/parallel/GenericInputControlReadAddPendingInterface.hpp
include/libmaus2/bambam/parallel/GenericInputControlReadWorkPackage.hpp
include/libmaus2/bambam/parallel/GenericInputControlReadWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/GenericInputControlReadWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/GenericInputControlReorderWorkPackage.hpp
include/libmaus2/bambam/parallel/GenericInputControlReorderWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/GenericInputControlReorderWorkPackageFinishedInterface.hpp
include/libmaus2/bambam/parallel/GenericInputControlReorderWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/GenericInputControlSetMergeStallSlotInterface.hpp
include/libmaus2/bambam/parallel/GenericInputControlStreamInfo.hpp
include/libmaus2/bambam/parallel/GenericInputControlSubBlockPending.hpp
include/libmaus2/bambam/parallel/GenericInputControlSubBlockPendingHeapComparator.hpp
include/libmaus2/bambam/parallel/GenericInputHeapComparator.hpp
include/libmaus2/bambam/parallel/GenericInputMergeDecompressedBlockReturnInterface.hpp
include/libmaus2/bambam/parallel/GenericInputMergeWorkPackage.hpp
include/libmaus2/bambam/parallel/GenericInputMergeWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/GenericInputMergeWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/GenericInputMergeWorkRequest.hpp
include/libmaus2/bambam/parallel/GenericInputSingleData.hpp
include/libmaus2/bambam/parallel/GenericInputSingleDataBamParseInfo.hpp
include/libmaus2/bambam/parallel/GetBgzfDeflateZStreamBaseInterface.hpp
include/libmaus2/bambam/parallel/InputBlock.hpp
include/libmaus2/bambam/parallel/InputBlockAddPendingInterface.hpp
include/libmaus2/bambam/parallel/InputBlockAllocator.hpp
include/libmaus2/bambam/parallel/InputBlockReturnInterface.hpp
include/libmaus2/bambam/parallel/InputBlockTypeInfo.hpp
include/libmaus2/bambam/parallel/InputBlockWorkPackage.hpp
include/libmaus2/bambam/parallel/InputBlockWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/InputBlockWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/MemInputBlock.hpp
include/libmaus2/bambam/parallel/MergeSortWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/PairReadEndsContainerFlushFinishedInterface.hpp
include/libmaus2/bambam/parallel/PairReadEndsContainerFlushWorkPackage.hpp
include/libmaus2/bambam/parallel/PairReadEndsContainerFlushWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/PairReadEndsContainerFlushWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/PairReadEndsMergeWorkPackage.hpp
include/libmaus2/bambam/parallel/PairReadEndsMergeWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/PairReadEndsMergeWorkPackageFinishedInterface.hpp
include/libmaus2/bambam/parallel/PairReadEndsMergeWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/ParseBlockWorkPackage.hpp
include/libmaus2/bambam/parallel/ParseBlockWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/ParseInfo.hpp
include/libmaus2/bambam/parallel/ParseInfoHeaderCompleteCallback.hpp
include/libmaus2/bambam/parallel/ParsePackageReturnInterface.hpp
include/libmaus2/bambam/parallel/ParsedBlockAddPendingInterface.hpp
include/libmaus2/bambam/parallel/ParsedBlockStallInterface.hpp
include/libmaus2/bambam/parallel/PushBackSpace.hpp
include/libmaus2/bambam/parallel/PutBgzfDeflateZStreamBaseInterface.hpp
include/libmaus2/bambam/parallel/ReadEndsContainerAllocator.hpp
include/libmaus2/bambam/parallel/ReadEndsContainerFreeListInterface.hpp
include/libmaus2/bambam/parallel/ReadEndsContainerTypeInfo.hpp
include/libmaus2/bambam/parallel/ReadEndsMergeRequest.hpp
include/libmaus2/bambam/parallel/RefIdInterval.hpp
include/libmaus2/bambam/parallel/RequeReadInterface.hpp
include/libmaus2/bambam/parallel/ReturnBgzfOutputBufferInterface.hpp
include/libmaus2/bambam/parallel/ReturnCompressionPendingElementInterface.hpp
include/libmaus2/bambam/parallel/ReturnRewriteBufferInterface.hpp
include/libmaus2/bambam/parallel/RewriteBlockWorkPackage.hpp
include/libmaus2/bambam/parallel/RewriteBlockWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/RewritePackageReturnInterface.hpp
include/libmaus2/bambam/parallel/SamEncoderObject.hpp
include/libmaus2/bambam/parallel/SamEncodingWorkPackage.hpp
include/libmaus2/bambam/parallel/SamEncodingWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/SamEncodingWorkPackageWrapper.hpp
include/libmaus2/bambam/parallel/SamEncodingWorkPackageWrapperReturnInterface.hpp
include/libmaus2/bambam/parallel/SamParseDecompressedBlockFinishedInterface.hpp
include/libmaus2/bambam/parallel/SamParseFragmentParsedInterface.hpp
include/libmaus2/bambam/parallel/SamParseGetSamInfoInterface.hpp
include/libmaus2/bambam/parallel/SamParsePending.hpp
include/libmaus2/bambam/parallel/SamParsePendingHeapComparator.hpp
include/libmaus2/bambam/parallel/SamParsePutSamInfoInterface.hpp
include/libmaus2/bambam/parallel/SamParseWorkPackage.hpp
include/libmaus2/bambam/parallel/SamParseWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/SamParseWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/ScramCramEncoding.hpp
include/libmaus2/bambam/parallel/SmallLinearBlockCompressionPendingObject.hpp
include/libmaus2/bambam/parallel/SmallLinearBlockCompressionPendingObjectFinishedInterface.hpp
include/libmaus2/bambam/parallel/SmallLinearBlockCompressionPendingObjectHeapComparator.hpp
include/libmaus2/bambam/parallel/SortControl.hpp
include/libmaus2/bambam/parallel/SortFinishedInterface.hpp
include/libmaus2/bambam/parallel/ValidateBlockAddPendingInterface.hpp
include/libmaus2/bambam/parallel/ValidateBlockFragmentAddPendingInterface.hpp
include/libmaus2/bambam/parallel/ValidateBlockFragmentPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/ValidateBlockFragmentWorkPackage.hpp
include/libmaus2/bambam/parallel/ValidateBlockFragmentWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/ValidateBlockWorkPackage.hpp
include/libmaus2/bambam/parallel/ValidateBlockWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/ValidatePackageReturnInterface.hpp
include/libmaus2/bambam/parallel/ValidationFragment.hpp
include/libmaus2/bambam/parallel/WriteBlockWorkPackage.hpp
include/libmaus2/bambam/parallel/WriteBlockWorkPackageDispatcher.hpp
include/libmaus2/bambam/parallel/WriteBlockWorkPackageReturnInterface.hpp
include/libmaus2/bambam/parallel/WritePendingObject.hpp
include/libmaus2/bambam/parallel/WritePendingObjectHeapComparator.hpp
include/libmaus2/bed/BED.hpp
include/libmaus2/bitbtree/bitbtree.hpp
include/libmaus2/bitio/ArrayDecode.hpp
include/libmaus2/bitio/BitIO.hpp
include/libmaus2/bitio/BitIOInput.hpp
include/libmaus2/bitio/BitIOOutput.hpp
include/libmaus2/bitio/BitSet.hpp
include/libmaus2/bitio/BitStreamFileDecoder.hpp
include/libmaus2/bitio/BitVector.hpp
include/libmaus2/bitio/BitVectorConcat.hpp
include/libmaus2/bitio/BitVectorInput.hpp
include/libmaus2/bitio/BitVectorOutput.hpp
include/libmaus2/bitio/BitWriter.hpp
include/libmaus2/bitio/BufferIterator.hpp
include/libmaus2/bitio/CheckedBitWriter.hpp
include/libmaus2/bitio/Clz.hpp
include/libmaus2/bitio/CompactArray.hpp
include/libmaus2/bitio/CompactArrayBase.hpp
include/libmaus2/bitio/CompactArrayWriter.hpp
include/libmaus2/bitio/CompactArrayWriterFile.hpp
include/libmaus2/bitio/CompactDecoderBuffer.hpp
include/libmaus2/bitio/CompactOffsetArray.hpp
include/libmaus2/bitio/CompactOffsetOneArray.hpp
include/libmaus2/bitio/CompactQueue.hpp
include/libmaus2/bitio/CompactSparseArray.hpp
include/libmaus2/bitio/Ctz.hpp
include/libmaus2/bitio/FastWriteBitWriter.hpp
include/libmaus2/bitio/MarkerFastWriteBitWriter.hpp
include/libmaus2/bitio/OutputBuffer.hpp
include/libmaus2/bitio/PacDecoderBuffer.hpp
include/libmaus2/bitio/ReverseTable.hpp
include/libmaus2/bitio/SignedCompactArray.hpp
include/libmaus2/bitio/SwapWordBitBlock.hpp
include/libmaus2/bitio/getBit.hpp
include/libmaus2/bitio/getBits.hpp
include/libmaus2/bitio/putBit.hpp
include/libmaus2/bitio/putBits.hpp
include/libmaus2/bitio/readElias.hpp
include/libmaus2/bitio/swapBitBlocksByReversal.hpp
include/libmaus2/btree/btree.hpp
include/libmaus2/clustering/HashCreation.hpp
include/libmaus2/clustering/HashCreationBase.hpp
include/libmaus2/clustering/KMeans.hpp
include/libmaus2/clustering/KmerBase.hpp
include/libmaus2/clustering/ProduceEdgeRequest.hpp
include/libmaus2/cumfreq/DynamicCumulativeFrequencies.hpp
include/libmaus2/cumfreq/SlowCumFreq.hpp
include/libmaus2/dazzler/align/AlignmentFile.hpp
include/libmaus2/dazzler/align/AlignmentFileCat.hpp
include/libmaus2/dazzler/align/AlignmentFileConstants.hpp
include/libmaus2/dazzler/align/AlignmentFileDecoder.hpp
include/libmaus2/dazzler/align/AlignmentFileRegion.hpp
include/libmaus2/dazzler/align/AlignmentFileSymmetryCheck.hpp
include/libmaus2/dazzler/align/AlignmentSplitWriter.hpp
include/libmaus2/dazzler/align/AlignmentWriter.hpp
include/libmaus2/dazzler/align/AlignmentWriterArray.hpp
include/libmaus2/dazzler/align/ApproximateRun.hpp
include/libmaus2/dazzler/align/ApproximateRunPartContainer.hpp
include/libmaus2/dazzler/align/BinIndexDecoder.hpp
include/libmaus2/dazzler/align/CompactRunPartContainer.hpp
include/libmaus2/dazzler/align/DalignerIndexDecoder.hpp
include/libmaus2/dazzler/align/FilterUnique.hpp
include/libmaus2/dazzler/align/GetTransitiveStrict.hpp
include/libmaus2/dazzler/align/GraphCheck.hpp
include/libmaus2/dazzler/align/GraphDecoder.hpp
include/libmaus2/dazzler/align/GraphDecoderContext.hpp
include/libmaus2/dazzler/align/GraphDecoderContextAllocator.hpp
include/libmaus2/dazzler/align/GraphDecoderContextTypeInfo.hpp
include/libmaus2/dazzler/align/GraphEncoder.hpp
include/libmaus2/dazzler/align/LASToBamConverterBase.hpp
include/libmaus2/dazzler/align/LasFileRange.hpp
include/libmaus2/dazzler/align/LasIntervals.hpp
include/libmaus2/dazzler/align/LasMerge2.hpp
include/libmaus2/dazzler/align/LasRangeDecoder.hpp
include/libmaus2/dazzler/align/LasSort2.hpp
include/libmaus2/dazzler/align/LasSort2Cascade.hpp
include/libmaus2/dazzler/align/Overlap.hpp
include/libmaus2/dazzler/align/OverlapAdapter.hpp
include/libmaus2/dazzler/align/OverlapData.hpp
include/libmaus2/dazzler/align/OverlapDataInterface.hpp
include/libmaus2/dazzler/align/OverlapHeader.hpp
include/libmaus2/dazzler/align/OverlapHeapComparator.hpp
include/libmaus2/dazzler/align/OverlapIndexer.hpp
include/libmaus2/dazzler/align/OverlapIndexerBase.hpp
include/libmaus2/dazzler/align/OverlapInfo.hpp
include/libmaus2/dazzler/align/OverlapInfoIndexer.hpp
include/libmaus2/dazzler/align/OverlapMeta.hpp
include/libmaus2/dazzler/align/OverlapMetaIteratorGet.hpp
include/libmaus2/dazzler/align/OverlapParser.hpp
include/libmaus2/dazzler/align/OverlapProperCheck.hpp
include/libmaus2/dazzler/align/Path.hpp
include/libmaus2/dazzler/align/ReadIntervals.hpp
include/libmaus2/dazzler/align/ReadIntervalsVector.hpp
include/libmaus2/dazzler/align/RefMapEntry.hpp
include/libmaus2/dazzler/align/RefMapEntryVector.hpp
include/libmaus2/dazzler/align/SimpleOverlapParser.hpp
include/libmaus2/dazzler/align/SimpleOverlapVectorParser.hpp
include/libmaus2/dazzler/align/SortOrderCheck.hpp
include/libmaus2/dazzler/align/SortingOverlapBlockInput.hpp
include/libmaus2/dazzler/align/SortingOverlapOutputBuffer.hpp
include/libmaus2/dazzler/align/SortingOverlapOutputBufferMerger.hpp
include/libmaus2/dazzler/align/SubIntervalResult.hpp
include/libmaus2/dazzler/align/Tandem.hpp
include/libmaus2/dazzler/align/TandemVector.hpp
include/libmaus2/dazzler/align/TandemVectorPartContainer.hpp
include/libmaus2/dazzler/align/TraceBlock.hpp
include/libmaus2/dazzler/align/TraceBlockVectorCache.hpp
include/libmaus2/dazzler/align/TracePoint.hpp
include/libmaus2/dazzler/align/TrueOverlap.hpp
include/libmaus2/dazzler/align/TrueOverlapStats.hpp
include/libmaus2/dazzler/db/DatabaseFile.hpp
include/libmaus2/dazzler/db/FastaInfo.hpp
include/libmaus2/dazzler/db/GetByteCounter.hpp
include/libmaus2/dazzler/db/IQVDecoder.hpp
include/libmaus2/dazzler/db/IndexBase.hpp
include/libmaus2/dazzler/db/InputBase.hpp
include/libmaus2/dazzler/db/InqualContainer.hpp
include/libmaus2/dazzler/db/OutputBase.hpp
include/libmaus2/dazzler/db/PartTrackContainer.hpp
include/libmaus2/dazzler/db/Read.hpp
include/libmaus2/dazzler/db/ReadContainer.hpp
include/libmaus2/dazzler/db/ReadLRUContainer.hpp
include/libmaus2/dazzler/db/SatsContainer.hpp
include/libmaus2/dazzler/db/StringTrackWriter.hpp
include/libmaus2/dazzler/db/Track.hpp
include/libmaus2/dazzler/db/TrackAnno.hpp
include/libmaus2/dazzler/db/TrackAnnoInterface.hpp
include/libmaus2/dazzler/db/TrackExtra.hpp
include/libmaus2/dazzler/stringgraph/ContainmentInfo.hpp
include/libmaus2/dazzler/stringgraph/Edge.hpp
include/libmaus2/dazzler/stringgraph/OverlapNode.hpp
include/libmaus2/dazzler/stringgraph/StringGraph.hpp
include/libmaus2/dazzler/stringgraph/TraversalElement.hpp
include/libmaus2/deleter/Deleter.hpp
include/libmaus2/demangle/Demangle.hpp
include/libmaus2/digest/CRC32.hpp
include/libmaus2/digest/CRC32C.hpp
include/libmaus2/digest/CRC32C_Core.hpp
include/libmaus2/digest/CRC32_Core.hpp
include/libmaus2/digest/DigestBase.hpp
include/libmaus2/digest/DigestFactory.hpp
include/libmaus2/digest/DigestFactoryContainer.hpp
include/libmaus2/digest/DigestFactoryInterface.hpp
include/libmaus2/digest/DigestInterface.hpp
include/libmaus2/digest/Digests.hpp
include/libmaus2/digest/MurmurHash3_x64_128.hpp
include/libmaus2/digest/Null.hpp
include/libmaus2/digest/SHA1.hpp
include/libmaus2/digest/SHA2_224.hpp
include/libmaus2/digest/SHA2_256.hpp
include/libmaus2/digest/SHA2_384.hpp
include/libmaus2/digest/SHA2_512.hpp
include/libmaus2/digest/SHA3_256.hpp
include/libmaus2/digest/md5.h
include/libmaus2/digest/md5.hpp
include/libmaus2/eta/LinearETA.hpp
include/libmaus2/exception/LibMausException.hpp
include/libmaus2/fastx/BgzfFastAIndexEntry.hpp
include/libmaus2/fastx/BgzfFastAIndexEntryIdComparator.hpp
include/libmaus2/fastx/BgzfFastAIndexEntryNameComparator.hpp
include/libmaus2/fastx/CharBuffer.hpp
include/libmaus2/fastx/CharTermTable.hpp
include/libmaus2/fastx/CompactFastDecoder.hpp
include/libmaus2/fastx/CompactFastDecoderBase.hpp
include/libmaus2/fastx/CompactFastEncoder.hpp
include/libmaus2/fastx/CompactFastQBlockGenerator.hpp
include/libmaus2/fastx/CompactFastQContainer.hpp
include/libmaus2/fastx/CompactFastQContainerDictionary.hpp
include/libmaus2/fastx/CompactFastQContainerDictionaryCreator.hpp
include/libmaus2/fastx/CompactFastQContext.hpp
include/libmaus2/fastx/CompactFastQDecoderBase.hpp
include/libmaus2/fastx/CompactFastQHeader.hpp
include/libmaus2/fastx/CompactFastQMultiBlockReader.hpp
include/libmaus2/fastx/CompactFastQSingleBlockReader.hpp
include/libmaus2/fastx/CompactFastReplace.hpp
include/libmaus2/fastx/CompactFastTerminator.hpp
include/libmaus2/fastx/CompactReadContainer.hpp
include/libmaus2/fastx/ComputeFastXIntervals.hpp
include/libmaus2/fastx/ConcatWriter.hpp
include/libmaus2/fastx/CoordinateCache.hpp
include/libmaus2/fastx/CoordinateCacheBiDir.hpp
include/libmaus2/fastx/DNAIndexMetaData.hpp
include/libmaus2/fastx/DNAIndexMetaDataBigBand.hpp
include/libmaus2/fastx/DNAIndexMetaDataBigBandBiDir.hpp
include/libmaus2/fastx/DNAIndexMetaDataSequence.hpp
include/libmaus2/fastx/FASTQEntry.hpp
include/libmaus2/fastx/FastABPConstants.hpp
include/libmaus2/fastx/FastABPGenerator.hpp
include/libmaus2/fastx/FastABgzfDecoder.hpp
include/libmaus2/fastx/FastABgzfDecoderBuffer.hpp
include/libmaus2/fastx/FastABgzfIndex.hpp
include/libmaus2/fastx/FastABgzfIndexEntry.hpp
include/libmaus2/fastx/FastADefinedBasesTable.hpp
include/libmaus2/fastx/FastAIndex.hpp
include/libmaus2/fastx/FastAIndexEntry.hpp
include/libmaus2/fastx/FastAIndexGenerator.hpp
include/libmaus2/fastx/FastAInfo.hpp
include/libmaus2/fastx/FastALineParser.hpp
include/libmaus2/fastx/FastALineParserLineInfo.hpp
include/libmaus2/fastx/FastAMapTable.hpp
include/libmaus2/fastx/FastAMatchTable.hpp
include/libmaus2/fastx/FastAReader.hpp
include/libmaus2/fastx/FastAReaderSplit.hpp
include/libmaus2/fastx/FastAStream.hpp
include/libmaus2/fastx/FastAStreamSet.hpp
include/libmaus2/fastx/FastAStreamWrapper.hpp
include/libmaus2/fastx/FastAToCompact4BigBand.hpp
include/libmaus2/fastx/FastAToCompact4BigBandBiDir.hpp
include/libmaus2/fastx/FastATwoBitTable.hpp
include/libmaus2/fastx/FastFirstToLastReverseAdapter.hpp
include/libmaus2/fastx/FastIDBlock.hpp
include/libmaus2/fastx/FastInterval.hpp
include/libmaus2/fastx/FastQBgzfWriter.hpp
include/libmaus2/fastx/FastQElement.hpp
include/libmaus2/fastx/FastQReader.hpp
include/libmaus2/fastx/FastQReaderSplit.hpp
include/libmaus2/fastx/FastaBPDecoder.hpp
include/libmaus2/fastx/FastaBPSequenceDecoder.hpp
include/libmaus2/fastx/FastaPeeker.hpp
include/libmaus2/fastx/FastqPeeker.hpp
include/libmaus2/fastx/FirstWhiteSpaceSlashStrip.hpp
include/libmaus2/fastx/FqWeightQuantiser.hpp
include/libmaus2/fastx/GCContent.hpp
include/libmaus2/fastx/GzipFileFastQReader.hpp
include/libmaus2/fastx/GzipStreamFastQReader.hpp
include/libmaus2/fastx/KmerCount.hpp
include/libmaus2/fastx/KmerFreqInWindowStats.hpp
include/libmaus2/fastx/KmerRepeatDetector.hpp
include/libmaus2/fastx/LineBufferFastAReader.hpp
include/libmaus2/fastx/MultiWordDNABitBuffer.hpp
include/libmaus2/fastx/NameInfo.hpp
include/libmaus2/fastx/NameInfoBase.hpp
include/libmaus2/fastx/Pattern.hpp
include/libmaus2/fastx/PatternBlock.hpp
include/libmaus2/fastx/Phred.hpp
include/libmaus2/fastx/QReorder.hpp
include/libmaus2/fastx/ReadContainer.hpp
include/libmaus2/fastx/RefPathLookup.hpp
include/libmaus2/fastx/RefPathToken.hpp
include/libmaus2/fastx/RefPathTokenVector.hpp
include/libmaus2/fastx/RefPathTokenVectorSequence.hpp
include/libmaus2/fastx/SingleWordDNABitBuffer.hpp
include/libmaus2/fastx/SlashStrip.hpp
include/libmaus2/fastx/SpaceTable.hpp
include/libmaus2/fastx/StreamFastAReader.hpp
include/libmaus2/fastx/StreamFastQReader.hpp
include/libmaus2/fastx/StreamFastReaderBase.hpp
include/libmaus2/fastx/SubSamplingFastReader.hpp
include/libmaus2/fastx/acgtnMap.hpp
include/libmaus2/fastx/isFastQ.hpp
include/libmaus2/fm/BiIndex.hpp
include/libmaus2/fm/BidirectionalDnaIndexTemplate.hpp
include/libmaus2/fm/BidirectionalIndexInterval.hpp
include/libmaus2/fm/BidirectionalIndexIntervalSymbol.hpp
include/libmaus2/fm/DictionaryInfo.hpp
include/libmaus2/fm/DictionaryInfoImpCompactHuffmanWaveletTree.hpp
include/libmaus2/fm/FA4CompactSampledSuffixArray.hpp
include/libmaus2/fm/FM.hpp
include/libmaus2/fm/KmerCache.hpp
include/libmaus2/fm/MausFmToBwaConversion.hpp
include/libmaus2/fm/SampledISA.hpp
include/libmaus2/fm/SampledSA.hpp
include/libmaus2/gamma/FlaggedInterval.hpp
include/libmaus2/gamma/GammaDecoder.hpp
include/libmaus2/gamma/GammaDecoderBase.hpp
include/libmaus2/gamma/GammaDifferenceDecoder.hpp
include/libmaus2/gamma/GammaDifferenceEncoder.hpp
include/libmaus2/gamma/GammaDifferenceMerge.hpp
include/libmaus2/gamma/GammaDifferenceOutputBuffer.hpp
include/libmaus2/gamma/GammaEncoder.hpp
include/libmaus2/gamma/GammaEncoderBase.hpp
include/libmaus2/gamma/GammaFlaggedIntervalDecoder.hpp
include/libmaus2/gamma/GammaFlaggedIntervalEncoder.hpp
include/libmaus2/gamma/GammaFlaggedPartitionDecoder.hpp
include/libmaus2/gamma/GammaFlaggedPartitionEncoder.hpp
include/libmaus2/gamma/GammaGapDecoder.hpp
include/libmaus2/gamma/GammaGapEncoder.hpp
include/libmaus2/gamma/GammaGenericBase.hpp
include/libmaus2/gamma/GammaGenericClz.hpp
include/libmaus2/gamma/GammaGenericDecoder.hpp
include/libmaus2/gamma/GammaGenericEncoder.hpp
include/libmaus2/gamma/GammaIntervalDecoder.hpp
include/libmaus2/gamma/GammaIntervalEncoder.hpp
include/libmaus2/gamma/GammaPDDecoder.hpp
include/libmaus2/gamma/GammaPDEncoder.hpp
include/libmaus2/gamma/GammaPDIndexDecoder.hpp
include/libmaus2/gamma/GammaPDIndexDecoderBase.hpp
include/libmaus2/gamma/GammaPartitionDecoder.hpp
include/libmaus2/gamma/GammaPartitionEncoder.hpp
include/libmaus2/gamma/GammaRLDecoder.hpp
include/libmaus2/gamma/GammaRLEncoder.hpp
include/libmaus2/gamma/Interval.hpp
include/libmaus2/gamma/SimpleGammaDecoder.hpp
include/libmaus2/gamma/SimpleGammaDecoderData.hpp
include/libmaus2/gamma/SimpleGammaEncoder.hpp
include/libmaus2/gamma/SimpleGammaEncoderArray.hpp
include/libmaus2/gamma/SimpleGammaEncoderData.hpp
include/libmaus2/gamma/SparseGammaGapBlockEncoder.hpp
include/libmaus2/gamma/SparseGammaGapConcatDecoder.hpp
include/libmaus2/gamma/SparseGammaGapDecoder.hpp
include/libmaus2/gamma/SparseGammaGapEncoder.hpp
include/libmaus2/gamma/SparseGammaGapFile.hpp
include/libmaus2/gamma/SparseGammaGapFileIndexDecoder.hpp
include/libmaus2/gamma/SparseGammaGapFileIndexDecoderEntry.hpp
include/libmaus2/gamma/SparseGammaGapFileIndexMultiDecoder.hpp
include/libmaus2/gamma/SparseGammaGapFileLevelSet.hpp
include/libmaus2/gamma/SparseGammaGapFileSet.hpp
include/libmaus2/gamma/SparseGammaGapMerge.hpp
include/libmaus2/gamma/SparseGammaGapMultiFile.hpp
include/libmaus2/gamma/SparseGammaGapMultiFileLevelSet.hpp
include/libmaus2/gamma/SparseGammaGapMultiFileSet.hpp
include/libmaus2/geometry/IntervalTree.hpp
include/libmaus2/geometry/RangeSet.hpp
include/libmaus2/graph/IdentityTargetProjector.hpp
include/libmaus2/graph/ReachableVertices.hpp
include/libmaus2/graph/StronglyConnectedComponents.hpp
include/libmaus2/graph/TopologicalSorting.hpp
include/libmaus2/gtf/BAMGTFMap.hpp
include/libmaus2/gtf/CDS.hpp
include/libmaus2/gtf/Exon.hpp
include/libmaus2/gtf/ExonIdOffsetComparator.hpp
include/libmaus2/gtf/ExonInfo.hpp
include/libmaus2/gtf/ExonInterval.hpp
include/libmaus2/gtf/ExonSubInfo.hpp
include/libmaus2/gtf/GTFData.hpp
include/libmaus2/gtf/Gene.hpp
include/libmaus2/gtf/GeneChrComparator.hpp
include/libmaus2/gtf/GeneRangeSets.hpp
include/libmaus2/gtf/IntervalList.hpp
include/libmaus2/gtf/IntervalListSet.hpp
include/libmaus2/gtf/RangeSets.hpp
include/libmaus2/gtf/Tag.hpp
include/libmaus2/gtf/Transcript.hpp
include/libmaus2/gtf/TranscriptRangeSets.hpp
include/libmaus2/hashing/CircularHash.hpp
include/libmaus2/hashing/ConstantStringHash.hpp
include/libmaus2/hashing/Crc32.hpp
include/libmaus2/hashing/MurmurHash3.h
include/libmaus2/hashing/hash.hpp
include/libmaus2/huffman/BitInputBuffer.hpp
include/libmaus2/huffman/CanonicalEncoder.hpp
include/libmaus2/huffman/CompressTable.hpp
include/libmaus2/huffman/DecodeTable.hpp
include/libmaus2/huffman/EncodeTable.hpp
include/libmaus2/huffman/FileStreamBaseType.hpp
include/libmaus2/huffman/GapDecoder.hpp
include/libmaus2/huffman/GapDecoderIndexBase.hpp
include/libmaus2/huffman/GapEncoder.hpp
include/libmaus2/huffman/HuffmanBase.hpp
include/libmaus2/huffman/HuffmanEncoderFile.hpp
include/libmaus2/huffman/HuffmanInputFile.hpp
include/libmaus2/huffman/HuffmanSorting.hpp
include/libmaus2/huffman/HuffmanTree.hpp
include/libmaus2/huffman/HuffmanTreeInnerNode.hpp
include/libmaus2/huffman/HuffmanTreeLeaf.hpp
include/libmaus2/huffman/HuffmanTreeLeafComparator.hpp
include/libmaus2/huffman/HuffmanTreeNode.hpp
include/libmaus2/huffman/IndexDecoderDataArray.hpp
include/libmaus2/huffman/IndexEntry.hpp
include/libmaus2/huffman/IndexLoader.hpp
include/libmaus2/huffman/IndexLoaderBase.hpp
include/libmaus2/huffman/IndexWriter.hpp
include/libmaus2/huffman/InputAdapter.hpp
include/libmaus2/huffman/KvInitResult.hpp
include/libmaus2/huffman/LFInfo.hpp
include/libmaus2/huffman/LFPhiPair.hpp
include/libmaus2/huffman/LFPhiPairDecoder.hpp
include/libmaus2/huffman/LFPhiPairEncoder.hpp
include/libmaus2/huffman/LFPhiPairLCP.hpp
include/libmaus2/huffman/LFPhiPairLCPDecoder.hpp
include/libmaus2/huffman/LFPhiPairLCPEncoder.hpp
include/libmaus2/huffman/LFRankLCP.hpp
include/libmaus2/huffman/LFRankLCPDecoder.hpp
include/libmaus2/huffman/LFRankLCPEncoder.hpp
include/libmaus2/huffman/LFRankPos.hpp
include/libmaus2/huffman/LFRankPosDecoder.hpp
include/libmaus2/huffman/LFRankPosEncoder.hpp
include/libmaus2/huffman/LFSetBit.hpp
include/libmaus2/huffman/LFSetBitDecoder.hpp
include/libmaus2/huffman/LFSetBitEncoder.hpp
include/libmaus2/huffman/LFSupportBitDecoder.hpp
include/libmaus2/huffman/LFSupportDecoder.hpp
include/libmaus2/huffman/LFSupportEncoder.hpp
include/libmaus2/huffman/LFSymRankPos.hpp
include/libmaus2/huffman/LFSymRankPosDecoder.hpp
include/libmaus2/huffman/LFSymRankPosEncoder.hpp
include/libmaus2/huffman/LFValue.hpp
include/libmaus2/huffman/LFValueDecoder.hpp
include/libmaus2/huffman/LFValueEncoder.hpp
include/libmaus2/huffman/OutputAdapter.hpp
include/libmaus2/huffman/PairAddSecond.hpp
include/libmaus2/huffman/RLDecoder.hpp
include/libmaus2/huffman/RLDecoderIndexBase.hpp
include/libmaus2/huffman/RLEncoder.hpp
include/libmaus2/huffman/RLInitType.hpp
include/libmaus2/huffman/RLRun.hpp
include/libmaus2/huffman/SymBit.hpp
include/libmaus2/huffman/SymBitDecoder.hpp
include/libmaus2/huffman/SymBitEncoder.hpp
include/libmaus2/huffman/SymBitRun.hpp
include/libmaus2/huffman/SymCount.hpp
include/libmaus2/huffman/SymCountDecoder.hpp
include/libmaus2/huffman/SymCountEncoder.hpp
include/libmaus2/huffman/SymCountRun.hpp
include/libmaus2/huffman/hufEncodeString.hpp
include/libmaus2/huffman/huffman.hpp
include/libmaus2/index/ExternalMemoryIndexDecoder.hpp
include/libmaus2/index/ExternalMemoryIndexDecoderFindLargestSmallerResult.hpp
include/libmaus2/index/ExternalMemoryIndexGenerator.hpp
include/libmaus2/index/ExternalMemoryIndexRecord.hpp
include/libmaus2/lcp/ComputeSuccinctLCPResult.hpp
include/libmaus2/lcp/LCP.hpp
include/libmaus2/lcp/PLCPBitDecoder.hpp
include/libmaus2/lcp/SuccinctLCP.hpp
include/libmaus2/lcp/WaveletLCP.hpp
include/libmaus2/lcp/WaveletLCPResult.hpp
include/libmaus2/lcs/Aligner.hpp
include/libmaus2/lcs/AlignerFactory.hpp
include/libmaus2/lcs/AlignmentOneAgainstManyAVX2.hpp
include/libmaus2/lcs/AlignmentOneAgainstManyFactory.hpp
include/libmaus2/lcs/AlignmentOneAgainstManyGeneric.hpp
include/libmaus2/lcs/AlignmentOneAgainstManyInterface.hpp
include/libmaus2/lcs/AlignmentPrint.hpp
include/libmaus2/lcs/AlignmentStatistics.hpp
include/libmaus2/lcs/AlignmentTraceContainer.hpp
include/libmaus2/lcs/BandedAligner.hpp
include/libmaus2/lcs/BandedAlignerFactory.hpp
include/libmaus2/lcs/BandedEditDistance.hpp
include/libmaus2/lcs/BandedLocalEditDistance.hpp
include/libmaus2/lcs/BaseConstants.hpp
include/libmaus2/lcs/BitVector.hpp
include/libmaus2/lcs/BitVectorResultCallbackInterface.hpp
include/libmaus2/lcs/Chain.hpp
include/libmaus2/lcs/ChainAddQueueElement.hpp
include/libmaus2/lcs/ChainAddQueueElementHeapComparator.hpp
include/libmaus2/lcs/ChainAlignment.hpp
include/libmaus2/lcs/ChainLeftMostComparator.hpp
include/libmaus2/lcs/ChainNode.hpp
include/libmaus2/lcs/ChainNodeInfo.hpp
include/libmaus2/lcs/ChainNodeInfoSet.hpp
include/libmaus2/lcs/ChainRemoveQueueElement.hpp
include/libmaus2/lcs/ChainRemoveQueueElementComparator.hpp
include/libmaus2/lcs/ChainSplayTreeNode.hpp
include/libmaus2/lcs/ChainSplayTreeNodeComparator.hpp
include/libmaus2/lcs/CheckSelf.hpp
include/libmaus2/lcs/DistNodeType.hpp
include/libmaus2/lcs/EditDistance.hpp
include/libmaus2/lcs/EditDistancePriorityType.hpp
include/libmaus2/lcs/EditDistanceResult.hpp
include/libmaus2/lcs/EditDistanceTraceContainer.hpp
include/libmaus2/lcs/GenericAlignmentPrint.hpp
include/libmaus2/lcs/GenericEditDistance.hpp
include/libmaus2/lcs/LCS.hpp
include/libmaus2/lcs/LCSDynamic.hpp
include/libmaus2/lcs/LCSRef.hpp
include/libmaus2/lcs/LocalAlignmentPrint.hpp
include/libmaus2/lcs/LocalAlignmentTraceContainer.hpp
include/libmaus2/lcs/LocalBaseConstants.hpp
include/libmaus2/lcs/LocalEditDistance.hpp
include/libmaus2/lcs/LocalEditDistanceResult.hpp
include/libmaus2/lcs/LocalEditDistanceTraceContainer.hpp
include/libmaus2/lcs/LocalPenaltyConstants.hpp
include/libmaus2/lcs/MetaEditDistance.hpp
include/libmaus2/lcs/MetaLocalEditDistance.hpp
include/libmaus2/lcs/NNP.hpp
include/libmaus2/lcs/NNPAlignResult.hpp
include/libmaus2/lcs/NNPCor.hpp
include/libmaus2/lcs/NNPCorL.hpp
include/libmaus2/lcs/NNPCorLocalAligner.hpp
include/libmaus2/lcs/NNPLocalAligner.hpp
include/libmaus2/lcs/NNPTraceContainer.hpp
include/libmaus2/lcs/NNPTraceElement.hpp
include/libmaus2/lcs/NP.hpp
include/libmaus2/lcs/NPL.hpp
include/libmaus2/lcs/NPLLinMem.hpp
include/libmaus2/lcs/NPLNoTrace.hpp
include/libmaus2/lcs/NPLSelf.hpp
include/libmaus2/lcs/NPLinMem.hpp
include/libmaus2/lcs/NPNoTrace.hpp
include/libmaus2/lcs/OverlapOrientation.hpp
include/libmaus2/lcs/PenaltyConstants.hpp
include/libmaus2/lcs/PosMapping.hpp
include/libmaus2/lcs/SMEMProcessor.hpp
include/libmaus2/lcs/ScoreBandedAligner.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreTemplate.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreY256_16.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreY256_16_def.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentScoreY256_16_undef.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentTemplate.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentX128_16.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentX128_16_def.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentX128_16_undef.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentX128_8.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentX128_8_def.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentX128_8_undef.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_16.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_16_def.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_16_undef.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_8.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_8_def.hpp
include/libmaus2/lcs/SimdX86BandedGlobalAlignmentY256_8_undef.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentConstants128.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentConstants256.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentScoreConstants256.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentTemplate.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentX128_16.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentX128_16_def.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentX128_16_undef.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentX128_8.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentX128_8_def.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentX128_8_undef.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentY256_16.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentY256_16_def.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentY256_16_undef.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentY256_8.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentY256_8_def.hpp
include/libmaus2/lcs/SimdX86GlobalAlignmentY256_8_undef.hpp
include/libmaus2/lcs/SuffixArrayLCS.hpp
include/libmaus2/lcs/SuffixPrefix.hpp
include/libmaus2/lcs/SuffixPrefixAlignmentPrint.hpp
include/libmaus2/lcs/SuffixPrefixResult.hpp
include/libmaus2/lcs/TraceContainer.hpp
include/libmaus2/lcs/TwoSidedNPL.hpp
include/libmaus2/lf/DArray.hpp
include/libmaus2/lf/HuffmanLF.hpp
include/libmaus2/lf/ImpCacheLineRankLF.hpp
include/libmaus2/lf/ImpCacheLineRankLFNonZero.hpp
include/libmaus2/lf/ImpCompactHuffmanWaveletLF.hpp
include/libmaus2/lf/ImpHuffmanWaveletLF.hpp
include/libmaus2/lf/ImpWTLF.hpp
include/libmaus2/lf/LF.hpp
include/libmaus2/lf/LFBase.hpp
include/libmaus2/lf/LFZero.hpp
include/libmaus2/lf/MultiRankCacheLF.hpp
include/libmaus2/lf/MultiRankLF.hpp
include/libmaus2/lf/QuickLF.hpp
include/libmaus2/lf/RLIndexLF.hpp
include/libmaus2/lru/FileBunchLRU.hpp
include/libmaus2/lru/LRU.hpp
include/libmaus2/lru/SparseLRU.hpp
include/libmaus2/lru/SparseLRUFileBunch.hpp
include/libmaus2/lz/BgzfChunkInputStream.hpp
include/libmaus2/lz/BgzfChunkInputStreamBuffer.hpp
include/libmaus2/lz/BgzfConstants.hpp
include/libmaus2/lz/BgzfDeflate.hpp
include/libmaus2/lz/BgzfDeflateBase.hpp
include/libmaus2/lz/BgzfDeflateBlockIdComparator.hpp
include/libmaus2/lz/BgzfDeflateBlockIdInfo.hpp
include/libmaus2/lz/BgzfDeflateHeaderFunctions.hpp
include/libmaus2/lz/BgzfDeflateInputBufferBase.hpp
include/libmaus2/lz/BgzfDeflateOutputBufferBase.hpp
include/libmaus2/lz/BgzfDeflateOutputBufferBaseAllocator.hpp
include/libmaus2/lz/BgzfDeflateOutputBufferBaseTypeInfo.hpp
include/libmaus2/lz/BgzfDeflateOutputCallback.hpp
include/libmaus2/lz/BgzfDeflateOutputCallbackMD5.hpp
include/libmaus2/lz/BgzfDeflateParallel.hpp
include/libmaus2/lz/BgzfDeflateParallelContext.hpp
include/libmaus2/lz/BgzfDeflateParallelThread.hpp
include/libmaus2/lz/BgzfDeflateZStreamBase.hpp
include/libmaus2/lz/BgzfDeflateZStreamBaseAllocator.hpp
include/libmaus2/lz/BgzfDeflateZStreamBaseFlushInfo.hpp
include/libmaus2/lz/BgzfDeflateZStreamBaseTypeInfo.hpp
include/libmaus2/lz/BgzfInflate.hpp
include/libmaus2/lz/BgzfInflateBase.hpp
include/libmaus2/lz/BgzfInflateBaseAllocator.hpp
include/libmaus2/lz/BgzfInflateBaseTypeInfo.hpp
include/libmaus2/lz/BgzfInflateBlock.hpp
include/libmaus2/lz/BgzfInflateBlockIdComparator.hpp
include/libmaus2/lz/BgzfInflateBlockIdInfo.hpp
include/libmaus2/lz/BgzfInflateDecompressPackageDispatcher.hpp
include/libmaus2/lz/BgzfInflateDeflateParallel.hpp
include/libmaus2/lz/BgzfInflateDeflateParallelInputStream.hpp
include/libmaus2/lz/BgzfInflateDeflateParallelThread.hpp
include/libmaus2/lz/BgzfInflateDeflateParallelWrapper.hpp
include/libmaus2/lz/BgzfInflateFile.hpp
include/libmaus2/lz/BgzfInflateHeaderBase.hpp
include/libmaus2/lz/BgzfInflateInfo.hpp
include/libmaus2/lz/BgzfInflateParallel.hpp
include/libmaus2/lz/BgzfInflateParallelContext.hpp
include/libmaus2/lz/BgzfInflateParallelStream.hpp
include/libmaus2/lz/BgzfInflateParallelThread.hpp
include/libmaus2/lz/BgzfInflateParallelWrapper.hpp
include/libmaus2/lz/BgzfInflateReadPackageDispatcher.hpp
include/libmaus2/lz/BgzfInflateStream.hpp
include/libmaus2/lz/BgzfInflateThreadPoolReader.hpp
include/libmaus2/lz/BgzfInflateWrapper.hpp
include/libmaus2/lz/BgzfInflateZStreamBase.hpp
include/libmaus2/lz/BgzfInflateZStreamBaseAllocator.hpp
include/libmaus2/lz/BgzfInflateZStreamBaseTypeInfo.hpp
include/libmaus2/lz/BgzfInputContext.hpp
include/libmaus2/lz/BgzfParallelRecodeDeflateBase.hpp
include/libmaus2/lz/BgzfRecode.hpp
include/libmaus2/lz/BgzfRecodeParallel.hpp
include/libmaus2/lz/BgzfStreamWrapper.hpp
include/libmaus2/lz/BgzfThreadOpBase.hpp
include/libmaus2/lz/BgzfVirtualOffset.hpp
include/libmaus2/lz/BufferedGzipStream.hpp
include/libmaus2/lz/BufferedGzipStreamBuffer.hpp
include/libmaus2/lz/BufferedGzipStreamWrapper.hpp
include/libmaus2/lz/CompressorObject.hpp
include/libmaus2/lz/CompressorObjectFactory.hpp
include/libmaus2/lz/CompressorObjectFreeListAllocator.hpp
include/libmaus2/lz/CompressorObjectFreeListAllocatorFactory.hpp
include/libmaus2/lz/DecompressorObject.hpp
include/libmaus2/lz/DecompressorObjectFactory.hpp
include/libmaus2/lz/DeflateDefaults.hpp
include/libmaus2/lz/GzipHeader.hpp
include/libmaus2/lz/GzipOutputStream.hpp
include/libmaus2/lz/GzipOutputStreamBuffer.hpp
include/libmaus2/lz/GzipSingleStream.hpp
include/libmaus2/lz/GzipStream.hpp
include/libmaus2/lz/GzipStreamWrapper.hpp
include/libmaus2/lz/Inflate.hpp
include/libmaus2/lz/IsGzip.hpp
include/libmaus2/lz/IstreamSource.hpp
include/libmaus2/lz/LineSplittingGzipOutputStream.hpp
include/libmaus2/lz/LineSplittingGzipOutputStreamBuffer.hpp
include/libmaus2/lz/Lz4Base.hpp
include/libmaus2/lz/Lz4Compress.hpp
include/libmaus2/lz/Lz4CompressStream.hpp
include/libmaus2/lz/Lz4CompressStreamBuffer.hpp
include/libmaus2/lz/Lz4CompressWrapper.hpp
include/libmaus2/lz/Lz4Decoder.hpp
include/libmaus2/lz/Lz4DecoderBuffer.hpp
include/libmaus2/lz/Lz4Index.hpp
include/libmaus2/lz/PlainOrGzipStream.hpp
include/libmaus2/lz/PlainOrGzipStreamBufferWrapper.hpp
include/libmaus2/lz/SimpleCompressedConcatInputStream.hpp
include/libmaus2/lz/SimpleCompressedConcatInputStreamFragment.hpp
include/libmaus2/lz/SimpleCompressedInputBlock.hpp
include/libmaus2/lz/SimpleCompressedInputBlockConcat.hpp
include/libmaus2/lz/SimpleCompressedInputBlockConcatBlock.hpp
include/libmaus2/lz/SimpleCompressedInputStream.hpp
include/libmaus2/lz/SimpleCompressedOutputStream.hpp
include/libmaus2/lz/SimpleCompressedStreamInterval.hpp
include/libmaus2/lz/SimpleCompressedStreamNamedInterval.hpp
include/libmaus2/lz/SnappyCompress.hpp
include/libmaus2/lz/SnappyCompressorObject.hpp
include/libmaus2/lz/SnappyCompressorObjectFactory.hpp
include/libmaus2/lz/SnappyCompressorObjectFactoryWrapper.hpp
include/libmaus2/lz/SnappyCompressorObjectFreeListAllocator.hpp
include/libmaus2/lz/SnappyDecompressorObject.hpp
include/libmaus2/lz/SnappyDecompressorObjectFactory.hpp
include/libmaus2/lz/SnappyFileInputStream.hpp
include/libmaus2/lz/SnappyFileOutputStream.hpp
include/libmaus2/lz/SnappyInputStream.hpp
include/libmaus2/lz/SnappyInputStreamArray.hpp
include/libmaus2/lz/SnappyInputStreamArrayFile.hpp
include/libmaus2/lz/SnappyOffsetFileInputStream.hpp
include/libmaus2/lz/SnappyOutputStream.hpp
include/libmaus2/lz/SnappyStringInputStream.hpp
include/libmaus2/lz/StdOstreamSink.hpp
include/libmaus2/lz/StreamWrapper.hpp
include/libmaus2/lz/StreamWrapperBuffer.hpp
include/libmaus2/lz/XzDecoder.hpp
include/libmaus2/lz/XzInputStream.hpp
include/libmaus2/lz/XzInputStreamBuffer.hpp
include/libmaus2/lz/ZlibCompressorObject.hpp
include/libmaus2/lz/ZlibCompressorObjectFactory.hpp
include/libmaus2/lz/ZlibCompressorObjectFactoryWrapper.hpp
include/libmaus2/lz/ZlibCompressorObjectFreeListAllocator.hpp
include/libmaus2/lz/ZlibDecompressorObject.hpp
include/libmaus2/lz/ZlibDecompressorObjectFactory.hpp
include/libmaus2/lz/ZlibInterface.hpp
include/libmaus2/math/Bernoulli.hpp
include/libmaus2/math/BernoulliNumber.hpp
include/libmaus2/math/ClusteredBernoulli.hpp
include/libmaus2/math/ConstantSumCombinatorics.hpp
include/libmaus2/math/Convolution.hpp
include/libmaus2/math/DecimalNumberParser.hpp
include/libmaus2/math/Distribution.hpp
include/libmaus2/math/DoubleCode.hpp
include/libmaus2/math/Faulhaber.hpp
include/libmaus2/math/GeneralisedBernoulli.hpp
include/libmaus2/math/GeneralisedClusterBernoulli.hpp
include/libmaus2/math/GmpFloat.hpp
include/libmaus2/math/GmpInteger.hpp
include/libmaus2/math/HistogramBuckets.hpp
include/libmaus2/math/IPower.hpp
include/libmaus2/math/IntegerInterval.hpp
include/libmaus2/math/LGammaCache.hpp
include/libmaus2/math/Log.hpp
include/libmaus2/math/LogNormalDistribution.hpp
include/libmaus2/math/Matrix.hpp
include/libmaus2/math/MetaLog.hpp
include/libmaus2/math/NormalDistribution.hpp
include/libmaus2/math/Rational.hpp
include/libmaus2/math/RationalPolynomialSupport.hpp
include/libmaus2/math/RepetetiveKmerFreqEstimate.hpp
include/libmaus2/math/UnsignedInteger.hpp
include/libmaus2/math/binom.hpp
include/libmaus2/math/bitsPerNum.hpp
include/libmaus2/math/gcd.hpp
include/libmaus2/math/iabs.hpp
include/libmaus2/math/ilog.hpp
include/libmaus2/math/ipow.hpp
include/libmaus2/math/isqrt.hpp
include/libmaus2/math/lowbits.hpp
include/libmaus2/math/numbits.hpp
include/libmaus2/math/primes16.hpp
include/libmaus2/network/CurlInitObject.hpp
include/libmaus2/network/CurlInputStream.hpp
include/libmaus2/network/CurlInputStreamBuffer.hpp
include/libmaus2/network/CurlObject.hpp
include/libmaus2/network/CurlObjectReader.hpp
include/libmaus2/network/CurlObjectThreadCallable.hpp
include/libmaus2/network/CurlOutputBlock.hpp
include/libmaus2/network/CurlResponseAcceptor.hpp
include/libmaus2/network/FileUrl.hpp
include/libmaus2/network/FtpCurlResponseAcceptor.hpp
include/libmaus2/network/GetHostName.hpp
include/libmaus2/network/HttpCurlResponseAcceptor.hpp
include/libmaus2/network/UrlBase.hpp
include/libmaus2/network/UrlInputStream.hpp
include/libmaus2/network/UrlInputStreamBufferWrapper.hpp
include/libmaus2/network/UrlInputStreamFactory.hpp
include/libmaus2/parallel/AtomicPtrHeap.hpp
include/libmaus2/parallel/AtomicPtrQueue.hpp
include/libmaus2/parallel/AtomicPtrStack.hpp
include/libmaus2/parallel/AtomicQueue.hpp
include/libmaus2/parallel/AtomicStack.hpp
include/libmaus2/parallel/LockedBool.hpp
include/libmaus2/parallel/LockedCounter.hpp
include/libmaus2/parallel/LockedFreeList.hpp
include/libmaus2/parallel/LockedGrowingFreeList.hpp
include/libmaus2/parallel/LockedHeap.hpp
include/libmaus2/parallel/LockedQueue.hpp
include/libmaus2/parallel/NumCpus.hpp
include/libmaus2/parallel/OMPNumThreadsScope.hpp
include/libmaus2/parallel/SimpleThreadPool.hpp
include/libmaus2/parallel/SimpleThreadPoolBase.hpp
include/libmaus2/parallel/SimpleThreadPoolInterface.hpp
include/libmaus2/parallel/SimpleThreadPoolInterfaceEnqueTermInterface.hpp
include/libmaus2/parallel/SimpleThreadPoolThread.hpp
include/libmaus2/parallel/SimpleThreadPoolThreadId.hpp
include/libmaus2/parallel/SimpleThreadPoolThreadIdNode.hpp
include/libmaus2/parallel/SimpleThreadPoolThreadIdTree.hpp
include/libmaus2/parallel/SimpleThreadPoolWorkPackageFreeList.hpp
include/libmaus2/parallel/SimpleThreadWorkPackage.hpp
include/libmaus2/parallel/SimpleThreadWorkPackageComparator.hpp
include/libmaus2/parallel/SimpleThreadWorkPackageDispatcher.hpp
include/libmaus2/parallel/StdBasicSpinLock.hpp
include/libmaus2/parallel/StdMutex.hpp
include/libmaus2/parallel/StdSemaphore.hpp
include/libmaus2/parallel/StdSpinLock.hpp
include/libmaus2/parallel/StdSynchronousConditionQueue.hpp
include/libmaus2/parallel/StdSynchronousHeap.hpp
include/libmaus2/parallel/StdSynchronousQueue.hpp
include/libmaus2/parallel/StdTerminatableSynchronousHeap.hpp
include/libmaus2/parallel/StdTerminatableSynchronousQueue.hpp
include/libmaus2/parallel/StdThread.hpp
include/libmaus2/parallel/SynchronousCounter.hpp
include/libmaus2/parallel/threadpool/LockedMap.hpp
include/libmaus2/parallel/threadpool/ThreadPool.hpp
include/libmaus2/parallel/threadpool/ThreadPoolDispatcher.hpp
include/libmaus2/parallel/threadpool/ThreadWorkPackage.hpp
include/libmaus2/parallel/threadpool/ThreadWorkPackageData.hpp
include/libmaus2/parallel/threadpool/bam/BamHeaderSeqData.hpp
include/libmaus2/parallel/threadpool/bam/BamParseContext.hpp
include/libmaus2/parallel/threadpool/bam/BamParseHeaderData.hpp
include/libmaus2/parallel/threadpool/bam/BamParseOutputQueue.hpp
include/libmaus2/parallel/threadpool/bam/BamParsePackageData.hpp
include/libmaus2/parallel/threadpool/bam/BamParsePackageDataDispatcher.hpp
include/libmaus2/parallel/threadpool/bam/BamParsePackageDataHandler.hpp
include/libmaus2/parallel/threadpool/bam/ThreadPoolBamParseControl.hpp
include/libmaus2/parallel/threadpool/bam/ThreadPoolBamParseHandler.hpp
include/libmaus2/parallel/threadpool/bam/ThreadPoolBamParseTrivialReturnHandler.hpp
include/libmaus2/parallel/threadpool/bgzf/BgzfBlockInfo.hpp
include/libmaus2/parallel/threadpool/bgzf/BgzfBlockInfoEnqueDecompressHandler.hpp
include/libmaus2/parallel/threadpool/bgzf/BgzfBlockInfoHandlerInterface.hpp
include/libmaus2/parallel/threadpool/bgzf/BgzfBlockInfoTrivialReturnHandler.hpp
include/libmaus2/parallel/threadpool/bgzf/BgzfBlockSummary.hpp
include/libmaus2/parallel/threadpool/bgzf/BgzfDataDecompressedInterface.hpp
include/libmaus2/parallel/threadpool/bgzf/BgzfDataDecompressedTrivialReturnInterface.hpp
include/libmaus2/parallel/threadpool/bgzf/BgzfDecompressContext.hpp
include/libmaus2/parallel/threadpool/bgzf/BgzfDecompressPackageData.hpp
include/libmaus2/parallel/threadpool/bgzf/BgzfDecompressPackageDataDispatcher.hpp
include/libmaus2/parallel/threadpool/bgzf/BgzfDecompressedBlock.hpp
include/libmaus2/parallel/threadpool/bgzf/BgzfHeaderDecoder.hpp
include/libmaus2/parallel/threadpool/bgzf/BgzfHeaderDecoderBase.hpp
include/libmaus2/parallel/threadpool/bgzf/BgzfInputReadInterface.hpp
include/libmaus2/parallel/threadpool/bgzf/BgzfInputThreadControl.hpp
include/libmaus2/parallel/threadpool/bgzf/GenericBlock.hpp
include/libmaus2/parallel/threadpool/bgzf/ReadInfo.hpp
include/libmaus2/parallel/threadpool/bgzf/ThreadPoolBGZFDecompressControl.hpp
include/libmaus2/parallel/threadpool/bgzf/ThreadPoolBGZFReadControl.hpp
include/libmaus2/parallel/threadpool/cram/CramEncodingWorkPackageData.hpp
include/libmaus2/parallel/threadpool/cram/CramEncodingWorkPackageDispatcher.hpp
include/libmaus2/parallel/threadpool/cram/CramEnqueuePackageData.hpp
include/libmaus2/parallel/threadpool/cram/CramEnqueuePackageDataDispatcher.hpp
include/libmaus2/parallel/threadpool/cram/CramEnqueuePackageDataHandler.hpp
include/libmaus2/parallel/threadpool/cram/ThreadPoolCramEnqueueControl.hpp
include/libmaus2/parallel/threadpool/input/InputThreadCallbackInterface.hpp
include/libmaus2/parallel/threadpool/input/InputThreadControl.hpp
include/libmaus2/parallel/threadpool/input/InputThreadPackageData.hpp
include/libmaus2/parallel/threadpool/input/InputThreadPackageDispatcher.hpp
include/libmaus2/parallel/threadpool/input/InputThreadTrivialReturnInterface.hpp
include/libmaus2/parallel/threadpool/input/ThreadPoolInputBlock.hpp
include/libmaus2/parallel/threadpool/input/ThreadPoolInputInfo.hpp
include/libmaus2/posix/PosixExecute.hpp
include/libmaus2/posix/PosixFunctions.hpp
include/libmaus2/protein/Align.hpp
include/libmaus2/protein/AlignGlobal.hpp
include/libmaus2/protein/Blosum62.hpp
include/libmaus2/protein/CodonMapper.hpp
include/libmaus2/protein/ProteinAlignment.hpp
include/libmaus2/quantisation/ClusterComputation.hpp
include/libmaus2/quantisation/KmeansDataType.hpp
include/libmaus2/quantisation/Quantiser.hpp
include/libmaus2/random/DNABaseNoiseSpiker.hpp
include/libmaus2/random/GaussianRandom.hpp
include/libmaus2/random/LogNormalRandom.hpp
include/libmaus2/random/Poisson.hpp
include/libmaus2/random/Random.hpp
include/libmaus2/random/UniformUnitRandom.hpp
include/libmaus2/rank/BSwapBase.hpp
include/libmaus2/rank/CacheLineRank.hpp
include/libmaus2/rank/ChooseCache.hpp
include/libmaus2/rank/CodeBase.hpp
include/libmaus2/rank/DNARank.hpp
include/libmaus2/rank/DNARankBiDir.hpp
include/libmaus2/rank/DNARankBiDirRange.hpp
include/libmaus2/rank/DNARankBiDirRangeSizeComparator.hpp
include/libmaus2/rank/DNARankGetPosition.hpp
include/libmaus2/rank/DNARankKmerCache.hpp
include/libmaus2/rank/DNARankMEM.hpp
include/libmaus2/rank/DNARankMEMPosComparator.hpp
include/libmaus2/rank/DNARankSMEMComputation.hpp
include/libmaus2/rank/DNARankSMEMContext.hpp
include/libmaus2/rank/DNARankSuffixTreeNodeEnumerator.hpp
include/libmaus2/rank/DNARankSuffixTreeNodeEnumeratorQueueElement.hpp
include/libmaus2/rank/DecodeCache.hpp
include/libmaus2/rank/ERank.hpp
include/libmaus2/rank/ERank2.hpp
include/libmaus2/rank/ERank22.hpp
include/libmaus2/rank/ERank222.hpp
include/libmaus2/rank/ERank222B.hpp
include/libmaus2/rank/ERank222BAppend.hpp
include/libmaus2/rank/ERank222BAppendDynamic.hpp
include/libmaus2/rank/ERank222BBase.hpp
include/libmaus2/rank/ERank222BP.hpp
include/libmaus2/rank/ERank22B.hpp
include/libmaus2/rank/ERank3.hpp
include/libmaus2/rank/ERank3C.hpp
include/libmaus2/rank/ERankBase.hpp
include/libmaus2/rank/EncodeCache.hpp
include/libmaus2/rank/FastRank.hpp
include/libmaus2/rank/ImpCacheLineRank.hpp
include/libmaus2/rank/Proc01.hpp
include/libmaus2/rank/RankTable.hpp
include/libmaus2/rank/RunLengthBitVector.hpp
include/libmaus2/rank/RunLengthBitVectorBase.hpp
include/libmaus2/rank/RunLengthBitVectorGenerator.hpp
include/libmaus2/rank/RunLengthBitVectorGeneratorBase.hpp
include/libmaus2/rank/RunLengthBitVectorGeneratorGammaBase.hpp
include/libmaus2/rank/RunLengthBitVectorStream.hpp
include/libmaus2/rank/log2table.hpp
include/libmaus2/rank/popcnt.hpp
include/libmaus2/rl/RLIndex.hpp
include/libmaus2/rmq/CartesianTree.hpp
include/libmaus2/rmq/QuickDynamicRMQ.hpp
include/libmaus2/rmq/RMMTree.hpp
include/libmaus2/select/ESelect222B.hpp
include/libmaus2/select/ESelectBase.hpp
include/libmaus2/select/ESelectSimple.hpp
include/libmaus2/select/ImpCacheLineSelectSupport.hpp
include/libmaus2/serialize/Serialize.hpp
include/libmaus2/sorting/InPlaceParallelSort.hpp
include/libmaus2/sorting/InterleavedRadixSort.hpp
include/libmaus2/sorting/MergeStepBinSearchResult.hpp
include/libmaus2/sorting/MergingReadBack.hpp
include/libmaus2/sorting/PairFileSorting.hpp
include/libmaus2/sorting/ParallelExternalRadixSort.hpp
include/libmaus2/sorting/ParallelRadixSort.hpp
include/libmaus2/sorting/ParallelRunLengthRadixSort.hpp
include/libmaus2/sorting/ParallelRunLengthRadixUnsort.hpp
include/libmaus2/sorting/ParallelStableSort.hpp
include/libmaus2/sorting/RankSearch.hpp
include/libmaus2/sorting/SemiExternalKeyTupleSort.hpp
include/libmaus2/sorting/SerialRadixSort64.hpp
include/libmaus2/sorting/SortingBufferedOutputFile.hpp
include/libmaus2/sorting/sorting.hpp
include/libmaus2/stacktrace/StackLineTranslator.hpp
include/libmaus2/stacktrace/StackTrace.hpp
include/libmaus2/stacktrace/StackTraceBufferContainer.hpp
include/libmaus2/suffixsort/BwtMergeBlockSortRequest.hpp
include/libmaus2/suffixsort/BwtMergeBlockSortRequestBase.hpp
include/libmaus2/suffixsort/BwtMergeBlockSortResult.hpp
include/libmaus2/suffixsort/BwtMergeEnumBase.hpp
include/libmaus2/suffixsort/BwtMergeTempFileNameSet.hpp
include/libmaus2/suffixsort/BwtMergeTempFileNameSetVector.hpp
include/libmaus2/suffixsort/BwtMergeZBlock.hpp
include/libmaus2/suffixsort/BwtMergeZBlockRequest.hpp
include/libmaus2/suffixsort/BwtMergeZBlockRequestVector.hpp
include/libmaus2/suffixsort/ByteInputTypes.hpp
include/libmaus2/suffixsort/CircularBwt.hpp
include/libmaus2/suffixsort/CircularSuffixComparator.hpp
include/libmaus2/suffixsort/CompactInputTypes.hpp
include/libmaus2/suffixsort/GapArrayByte.hpp
include/libmaus2/suffixsort/GapArrayByteDecoder.hpp
include/libmaus2/suffixsort/GapArrayByteDecoderBuffer.hpp
include/libmaus2/suffixsort/GapArrayByteOverflowKeyAccessor.hpp
include/libmaus2/suffixsort/GapMergePacket.hpp
include/libmaus2/suffixsort/Lz4InputTypes.hpp
include/libmaus2/suffixsort/PacInputTypes.hpp
include/libmaus2/suffixsort/PacTermInputTypes.hpp
include/libmaus2/suffixsort/SkewSuffixSort.hpp
include/libmaus2/suffixsort/SmallestRotation.hpp
include/libmaus2/suffixsort/Utf8InputTypes.hpp
include/libmaus2/suffixsort/bwtb3m/BWTB3MBase.hpp
include/libmaus2/suffixsort/bwtb3m/BaseBlockSortThread.hpp
include/libmaus2/suffixsort/bwtb3m/BaseBlockSorting.hpp
include/libmaus2/suffixsort/bwtb3m/BwtComputeSSA.hpp
include/libmaus2/suffixsort/bwtb3m/BwtMergeComputeSampledSA.hpp
include/libmaus2/suffixsort/bwtb3m/BwtMergeIsaBase.hpp
include/libmaus2/suffixsort/bwtb3m/BwtMergeIsaParallelBase.hpp
include/libmaus2/suffixsort/bwtb3m/BwtMergeParallelGapFragMerge.hpp
include/libmaus2/suffixsort/bwtb3m/BwtMergeSort.hpp
include/libmaus2/suffixsort/bwtb3m/BwtMergeSortOptions.hpp
include/libmaus2/suffixsort/bwtb3m/BwtMergeSortResult.hpp
include/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
include/libmaus2/suffixsort/bwtb3m/BwtSelectSSA.hpp
include/libmaus2/suffixsort/bwtb3m/GapArrayWrapper.hpp
include/libmaus2/suffixsort/bwtb3m/InputTypesForward.hpp
include/libmaus2/suffixsort/bwtb3m/MergeStrategyBaseBlock.hpp
include/libmaus2/suffixsort/bwtb3m/MergeStrategyBlock.hpp
include/libmaus2/suffixsort/bwtb3m/MergeStrategyConstruction.hpp
include/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeBlock.hpp
include/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeExternalBlock.hpp
include/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeGapRequest.hpp
include/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeGapRequestQueryObject.hpp
include/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeInput.hpp
include/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeInternalBlock.hpp
include/libmaus2/suffixsort/bwtb3m/MergeStrategyMergeInternalSmallBlock.hpp
include/libmaus2/suffixsort/bwtb3m/MergeTree.hpp
include/libmaus2/suffixsort/bwtb3m/PreIsaAdapter.hpp
include/libmaus2/suffixsort/divsufsort.hpp
include/libmaus2/suffixtree/CompressedSuffixTree.hpp
include/libmaus2/sv/sv.hpp
include/libmaus2/timing/RealTimeClock.hpp
include/libmaus2/trie/SimpleTrie.hpp
include/libmaus2/trie/TrieState.hpp
include/libmaus2/types/types.hpp
include/libmaus2/uint/uint.hpp
include/libmaus2/util/AlphaDigitTable.hpp
include/libmaus2/util/AlphaTable.hpp
include/libmaus2/util/ArgInfo.hpp
include/libmaus2/util/ArgInfoParseBase.hpp
include/libmaus2/util/ArgParser.hpp
include/libmaus2/util/ArrayIterator.hpp
include/libmaus2/util/AtomicArray.hpp
include/libmaus2/util/AutoArrayCharBaseAllocator.hpp
include/libmaus2/util/AutoArrayCharBaseTypeInfo.hpp
include/libmaus2/util/AutoArrayUInt8TBaseAllocator.hpp
include/libmaus2/util/AutoArrayUInt8TBaseTypeInfo.hpp
include/libmaus2/util/Base64.hpp
include/libmaus2/util/BitList.hpp
include/libmaus2/util/BitsPerNum.hpp
include/libmaus2/util/BorderArray.hpp
include/libmaus2/util/CompactNumberArray.hpp
include/libmaus2/util/Concat.hpp
include/libmaus2/util/ConcatRequest.hpp
include/libmaus2/util/ConsoleColor.hpp
include/libmaus2/util/ContainerDescription.hpp
include/libmaus2/util/ContainerDescriptionList.hpp
include/libmaus2/util/ContainerElementFreeList.hpp
include/libmaus2/util/ContainerGetObject.hpp
include/libmaus2/util/CountGetObject.hpp
include/libmaus2/util/CountPutIterator.hpp
include/libmaus2/util/CountPutObject.hpp
include/libmaus2/util/DigitTable.hpp
include/libmaus2/util/DirectoryStructure.hpp
include/libmaus2/util/DynamicLoading.hpp
include/libmaus2/util/Enumerator.hpp
include/libmaus2/util/FileEnumerator.hpp
include/libmaus2/util/FileTempFileContainer.hpp
include/libmaus2/util/FiniteSizeHeap.hpp
include/libmaus2/util/FreeList.hpp
include/libmaus2/util/GenericIntervalTree.hpp
include/libmaus2/util/GenericSerialisation.hpp
include/libmaus2/util/GetCObject.hpp
include/libmaus2/util/GetFileSize.hpp
include/libmaus2/util/GrowingFreeList.hpp
include/libmaus2/util/Histogram.hpp
include/libmaus2/util/HistogramSet.hpp
include/libmaus2/util/ImpCompactNumberArray.hpp
include/libmaus2/util/IncreasingList.hpp
include/libmaus2/util/IntervalTree.hpp
include/libmaus2/util/KMP.hpp
include/libmaus2/util/LELoad.hpp
include/libmaus2/util/LineAccessor.hpp
include/libmaus2/util/LineBuffer.hpp
include/libmaus2/util/LocalTempContainer.hpp
include/libmaus2/util/LongestIncreasingSubsequence.hpp
include/libmaus2/util/LongestIncreasingSubsequenceExtendedResult.hpp
include/libmaus2/util/LookupIntervalTree.hpp
include/libmaus2/util/MemTempFileContainer.hpp
include/libmaus2/util/MemUsage.hpp
include/libmaus2/util/MemoryStatistics.hpp
include/libmaus2/util/MoveStack.hpp
include/libmaus2/util/NotDigitOrTermTable.hpp
include/libmaus2/util/NumberMapSerialisation.hpp
include/libmaus2/util/NumberSerialisation.hpp
include/libmaus2/util/NumberToString.hpp
include/libmaus2/util/Object.hpp
include/libmaus2/util/OctetString.hpp
include/libmaus2/util/OffsetArray.hpp
include/libmaus2/util/OutputFileNameTools.hpp
include/libmaus2/util/PathTools.hpp
include/libmaus2/util/PrefixSums.hpp
include/libmaus2/util/PushBuffer.hpp
include/libmaus2/util/PutObject.hpp
include/libmaus2/util/PutObjectReverse.hpp
include/libmaus2/util/Queue.hpp
include/libmaus2/util/ReverseAdapter.hpp
include/libmaus2/util/ReverseByteOrder.hpp
include/libmaus2/util/SaturatingCounter.hpp
include/libmaus2/util/SerialiseHelper.hpp
include/libmaus2/util/SimpleBloomFilter.hpp
include/libmaus2/util/SimpleCountingHash.hpp
include/libmaus2/util/SimpleHashMap.hpp
include/libmaus2/util/SimpleHashMapConstants.hpp
include/libmaus2/util/SimpleHashMapDisplaceMaskFunction.hpp
include/libmaus2/util/SimpleHashMapHashCompute.hpp
include/libmaus2/util/SimpleHashMapInsDel.hpp
include/libmaus2/util/SimpleHashMapKeyPrint.hpp
include/libmaus2/util/SimpleHashMapNumberCast.hpp
include/libmaus2/util/SimpleHashSet.hpp
include/libmaus2/util/SimpleHashSetInsDel.hpp
include/libmaus2/util/SimpleQueue.hpp
include/libmaus2/util/SplayTree.hpp
include/libmaus2/util/StreamGetObject.hpp
include/libmaus2/util/StringAllocTypes.hpp
include/libmaus2/util/StringMapCompare.hpp
include/libmaus2/util/StringSerialisation.hpp
include/libmaus2/util/SuccinctBorderArray.hpp
include/libmaus2/util/TabEntry.hpp
include/libmaus2/util/TempFileContainer.hpp
include/libmaus2/util/TempFileNameGenerator.hpp
include/libmaus2/util/TempFileNameGeneratorState.hpp
include/libmaus2/util/TempFileRemovalContainer.hpp
include/libmaus2/util/Terminal.hpp
include/libmaus2/util/ToUpperTable.hpp
include/libmaus2/util/U.hpp
include/libmaus2/util/UnitNum.hpp
include/libmaus2/util/UnsignedCharVariant.hpp
include/libmaus2/util/UnsignedIntegerIndexIterator.hpp
include/libmaus2/util/Utf8BlockIndex.hpp
include/libmaus2/util/Utf8BlockIndexDecoder.hpp
include/libmaus2/util/Utf8DecoderBuffer.hpp
include/libmaus2/util/Utf8DecoderWrapper.hpp
include/libmaus2/util/Utf8String.hpp
include/libmaus2/util/Utf8StringPairAdapter.hpp
include/libmaus2/util/VarBitList.hpp
include/libmaus2/util/VarList.hpp
include/libmaus2/util/WriteableString.hpp
include/libmaus2/util/atomic_shared_ptr.hpp
include/libmaus2/util/iterator.hpp
include/libmaus2/util/nstat.hpp
include/libmaus2/util/stringFunctions.hpp
include/libmaus2/util/unordered_map.hpp
include/libmaus2/util/unordered_set.hpp
include/libmaus2/util/utf8.hpp
include/libmaus2/vcf/TabixIndex.hpp
include/libmaus2/vcf/VCFParser.hpp
include/libmaus2/vcf/VCFSortEntry.hpp
include/libmaus2/vcf/VCFSorter.hpp
include/libmaus2/vep/VEPCoordinate.hpp
include/libmaus2/vep/VEPParser.hpp
include/libmaus2/wavelet/DynamicHuffmanWaveletTree.hpp
include/libmaus2/wavelet/DynamicWaveletTree.hpp
include/libmaus2/wavelet/ExternalWaveletGenerator.hpp
include/libmaus2/wavelet/HuffmanWaveletTree.hpp
include/libmaus2/wavelet/ImpCompactHuffmanWaveletTree.hpp
include/libmaus2/wavelet/ImpExternalWaveletGenerator.hpp
include/libmaus2/wavelet/ImpExternalWaveletGeneratorCompactHuffman.hpp
include/libmaus2/wavelet/ImpExternalWaveletGeneratorCompactHuffmanParallel.hpp
include/libmaus2/wavelet/ImpExternalWaveletGeneratorHuffman.hpp
include/libmaus2/wavelet/ImpExternalWaveletGeneratorHuffmanParallel.hpp
include/libmaus2/wavelet/ImpHuffmanWaveletTree.hpp
include/libmaus2/wavelet/ImpWaveletTree.hpp
include/libmaus2/wavelet/RlToHwtBase.hpp
include/libmaus2/wavelet/RlToHwtTermRequest.hpp
include/libmaus2/wavelet/Utf8ToImpCompactHuffmanWaveletTree.hpp
include/libmaus2/wavelet/Utf8ToImpHuffmanWaveletTree.hpp
include/libmaus2/wavelet/WaveletTree.hpp
include/libmaus2/wavelet/toWaveletTreeBits.hpp
lib/libmaus2.a
lib/libmaus2.so
lib/libmaus2.so.2
lib/libmaus2.so.2.0.813
lib/libmaus2_arch.a
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lib/libmaus2_arch.so.2.0.813
lib/libmaus2_autoarray.a
lib/libmaus2_autoarray.so
lib/libmaus2_autoarray.so.2
lib/libmaus2_autoarray.so.2.0.813
lib/libmaus2_demangle.a
lib/libmaus2_demangle.so
lib/libmaus2_demangle.so.2
lib/libmaus2_demangle.so.2.0.813
lib/libmaus2_exception.a
lib/libmaus2_exception.so
lib/libmaus2_exception.so.2
lib/libmaus2_exception.so.2.0.813
lib/libmaus2_parallel.a
lib/libmaus2_parallel.so
lib/libmaus2_parallel.so.2
lib/libmaus2_parallel.so.2.0.813
lib/libmaus2_posix.a
lib/libmaus2_posix.so
lib/libmaus2_posix.so.2
lib/libmaus2_posix.so.2.0.813
lib/libmaus2_simd_align_128.a
lib/libmaus2_simd_align_128.so
lib/libmaus2_simd_align_128.so.2
lib/libmaus2_simd_align_128.so.2.0.813
lib/libmaus2_simd_align_256.a
lib/libmaus2_simd_align_256.so
lib/libmaus2_simd_align_256.so.2
lib/libmaus2_simd_align_256.so.2.0.813
lib/libmaus2_stacktrace.a
lib/libmaus2_stacktrace.so
lib/libmaus2_stacktrace.so.2
lib/libmaus2_stacktrace.so.2.0.813
lib/pkgconfig/libmaus2.pc
share/doc/libmaus2/changelog.gz
