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./alignment/MappingMetrics.hpp
./alignment/algorithms/alignment/AffineGuidedAlign.hpp
./alignment/algorithms/alignment/AffineKBandAlign.hpp
./alignment/algorithms/alignment/AlignmentFormats.hpp
./alignment/algorithms/alignment/AlignmentUtils.hpp
./alignment/algorithms/alignment/AlignmentUtilsImpl.hpp
./alignment/algorithms/alignment/BaseScoreFunction.hpp
./alignment/algorithms/alignment/DistanceMatrixScoreFunction.hpp
./alignment/algorithms/alignment/DistanceMatrixScoreFunctionImpl.hpp
./alignment/algorithms/alignment/ExtendAlign.hpp
./alignment/algorithms/alignment/FullQVAlign.hpp
./alignment/algorithms/alignment/GraphPaper.hpp
./alignment/algorithms/alignment/GraphPaperImpl.hpp
./alignment/algorithms/alignment/GuidedAlign.hpp
./alignment/algorithms/alignment/IDSScoreFunction.hpp
./alignment/algorithms/alignment/KBandAlign.hpp
./alignment/algorithms/alignment/OneGapAlignment.hpp
./alignment/algorithms/alignment/QualityValueScoreFunction.hpp
./alignment/algorithms/alignment/SDPAlign.hpp
./alignment/algorithms/alignment/SDPAlignImpl.hpp
./alignment/algorithms/alignment/SWAlign.hpp
./alignment/algorithms/alignment/SWAlignImpl.hpp
./alignment/algorithms/alignment/ScoreMatrices.hpp
./alignment/algorithms/alignment/StringToScoreMatrix.hpp
./alignment/algorithms/alignment/sdp/FragmentSort.hpp
./alignment/algorithms/alignment/sdp/FragmentSortImpl.hpp
./alignment/algorithms/alignment/sdp/SDPColumn.hpp
./alignment/algorithms/alignment/sdp/SDPFragment.hpp
./alignment/algorithms/alignment/sdp/SDPSet.hpp
./alignment/algorithms/alignment/sdp/SDPSetImpl.hpp
./alignment/algorithms/alignment/sdp/SparseDynamicProgramming.hpp
./alignment/algorithms/alignment/sdp/SparseDynamicProgrammingImpl.hpp
./alignment/algorithms/anchoring/BWTSearch.hpp
./alignment/algorithms/anchoring/BWTSearchImpl.hpp
./alignment/algorithms/anchoring/BasicEndpoint.hpp
./alignment/algorithms/anchoring/BasicEndpointImpl.hpp
./alignment/algorithms/anchoring/ClusterProbability.hpp
./alignment/algorithms/anchoring/Coordinate.hpp
./alignment/algorithms/anchoring/FindMaxInterval.hpp
./alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp
./alignment/algorithms/anchoring/GlobalChain.hpp
./alignment/algorithms/anchoring/GlobalChainImpl.hpp
./alignment/algorithms/anchoring/LISPValue.hpp
./alignment/algorithms/anchoring/LISPValueImpl.hpp
./alignment/algorithms/anchoring/LISPValueWeightor.hpp
./alignment/algorithms/anchoring/LISPValueWeightorImpl.hpp
./alignment/algorithms/anchoring/LISQValueWeightor.hpp
./alignment/algorithms/anchoring/LISSizeWeightor.hpp
./alignment/algorithms/anchoring/LISSizeWeightorImpl.hpp
./alignment/algorithms/anchoring/LongestIncreasingSubsequence.hpp
./alignment/algorithms/anchoring/LongestIncreasingSubsequenceImpl.hpp
./alignment/algorithms/anchoring/MapBySuffixArray.hpp
./alignment/algorithms/anchoring/MapBySuffixArrayImpl.hpp
./alignment/algorithms/anchoring/PrioritySearchTree.hpp
./alignment/algorithms/anchoring/PrioritySearchTreeImpl.hpp
./alignment/algorithms/anchoring/ScoreAnchors.hpp
./alignment/algorithms/anchoring/ScoreAnchorsImpl.hpp
./alignment/algorithms/compare/CompareStrings.hpp
./alignment/algorithms/sorting/DifferenceCovers.hpp
./alignment/algorithms/sorting/Karkkainen.hpp
./alignment/algorithms/sorting/LightweightSuffixArray.hpp
./alignment/algorithms/sorting/MultikeyQuicksort.hpp
./alignment/algorithms/sorting/qsufsort.hpp
./alignment/anchoring/AnchorParameters.hpp
./alignment/bwt/BWT.hpp
./alignment/bwt/Occ.hpp
./alignment/bwt/PackedHash.hpp
./alignment/bwt/Pos.hpp
./alignment/datastructures/alignment/Alignment.hpp
./alignment/datastructures/alignment/AlignmentCandidate.hpp
./alignment/datastructures/alignment/AlignmentContext.hpp
./alignment/datastructures/alignment/AlignmentMap.hpp
./alignment/datastructures/alignment/AlignmentStats.hpp
./alignment/datastructures/alignment/CmpFile.hpp
./alignment/datastructures/alignment/FilterCriteria.hpp
./alignment/datastructures/alignment/SAMToAlignmentCandidateAdapter.hpp
./alignment/datastructures/alignmentset/AlignmentSetToCmpH5Adapter.hpp
./alignment/datastructures/alignmentset/AlignmentSetToCmpH5AdapterImpl.hpp
./alignment/datastructures/alignmentset/SAMQVConversion.hpp
./alignment/datastructures/alignmentset/SAMSupplementalQVList.hpp
./alignment/datastructures/anchoring/AnchorParameters.hpp
./alignment/datastructures/anchoring/ClusterList.hpp
./alignment/datastructures/anchoring/MatchPos.hpp
./alignment/datastructures/anchoring/WeightedInterval.hpp
./alignment/files/BaseSequenceIO.hpp
./alignment/files/CCSIterator.hpp
./alignment/files/FragmentCCSIterator.hpp
./alignment/files/ReaderAgglomerate.hpp
./alignment/files/ReaderAgglomerateImpl.hpp
./alignment/format/BAMPrinter.hpp
./alignment/format/BAMPrinterImpl.hpp
./alignment/format/CompareSequencesPrinter.hpp
./alignment/format/CompareSequencesPrinterImpl.hpp
./alignment/format/IntervalPrinter.hpp
./alignment/format/SAMHeaderPrinter.hpp
./alignment/format/SAMPrinter.hpp
./alignment/format/SAMPrinterImpl.hpp
./alignment/format/StickAlignmentPrinter.hpp
./alignment/format/SummaryPrinter.hpp
./alignment/format/VulgarPrinter.hpp
./alignment/format/XMLPrinter.hpp
./alignment/ipc/SharedMemoryAllocator.hpp
./alignment/qvs/QualityValueProfile.hpp
./alignment/simulator/CDFMap.hpp
./alignment/simulator/ContextOutputList.hpp
./alignment/simulator/ContextSample.hpp
./alignment/simulator/ContextSet.hpp
./alignment/simulator/LengthHistogram.hpp
./alignment/simulator/OutputList.hpp
./alignment/simulator/OutputSample.hpp
./alignment/simulator/OutputSampleList.hpp
./alignment/simulator/OutputSampleListSet.hpp
./alignment/simulator/QualitySample.hpp
./alignment/statistics/AnchorDistributionTable.hpp
./alignment/statistics/LookupAnchorDistribution.hpp
./alignment/statistics/StatUtils.hpp
./alignment/statistics/StatUtilsImpl.hpp
./alignment/statistics/VarianceAccumulator.hpp
./alignment/statistics/VarianceAccumulatorImpl.hpp
./alignment/statistics/cdfs.hpp
./alignment/statistics/pdfs.hpp
./alignment/suffixarray/LCPTable.hpp
./alignment/suffixarray/SharedSuffixArray.hpp
./alignment/suffixarray/SuffixArray.hpp
./alignment/suffixarray/SuffixArrayTypes.hpp
./alignment/suffixarray/ssort.hpp
./alignment/tuples/BaseTuple.hpp
./alignment/tuples/CompressedDNATuple.hpp
./alignment/tuples/DNATuple.hpp
./alignment/tuples/DNATupleImpl.hpp
./alignment/tuples/HashedTupleList.hpp
./alignment/tuples/HashedTupleListImpl.hpp
./alignment/tuples/TupleCountTable.hpp
./alignment/tuples/TupleCountTableImpl.hpp
./alignment/tuples/TupleList.hpp
./alignment/tuples/TupleListImpl.hpp
./alignment/tuples/TupleMatching.hpp
./alignment/tuples/TupleMatchingImpl.hpp
./alignment/tuples/TupleMetrics.hpp
./alignment/utils/FileOfFileNames.hpp
./alignment/utils/FileUtils.hpp
./alignment/utils/LogUtils.hpp
./alignment/utils/PhredUtils.hpp
./alignment/utils/RangeUtils.hpp
./alignment/utils/RegionUtils.hpp
./alignment/utils/RegionUtilsImpl.hpp
./alignment/utils/SimpleXMLUtils.hpp
./hdf/BufferedHDF2DArray.hpp
./hdf/BufferedHDF2DArrayImpl.hpp
./hdf/BufferedHDFArray.hpp
./hdf/BufferedHDFArrayImpl.hpp
./hdf/DatasetCollection.hpp
./hdf/DatasetCollectionImpl.hpp
./hdf/HDF2DArray.hpp
./hdf/HDFAlnGroup.hpp
./hdf/HDFAlnGroupGroup.hpp
./hdf/HDFAlnInfoGroup.hpp
./hdf/HDFArray.hpp
./hdf/HDFAtom.hpp
./hdf/HDFAttributable.hpp
./hdf/HDFBasReader.hpp
./hdf/HDFBasWriter.hpp
./hdf/HDFBaseCallsWriter.hpp
./hdf/HDFBaxWriter.hpp
./hdf/HDFCCSReader.hpp
./hdf/HDFCmpExperimentGroup.hpp
./hdf/HDFCmpData.hpp
./hdf/HDFCmpFile.hpp
./hdf/HDFCmpReader.hpp
./hdf/HDFCmpRootGroup.hpp
./hdf/HDFCmpRefAlignmentGroup.hpp
./hdf/HDFCmpSupportedFields.hpp
./hdf/HDFCommonFG.hpp
./hdf/HDFConfig.hpp
./hdf/HDFData.hpp
./hdf/HDFFile.hpp
./hdf/HDFGroup.hpp
./hdf/HDFFileLogGroup.hpp
./hdf/HDFMovieInfoGroup.hpp
./hdf/HDFPlsReader.hpp
./hdf/HDFNewBasReader.hpp
./hdf/HDFPlsWriter.hpp
./hdf/HDFPulseCallsWriter.hpp
./hdf/HDFPulseDataFile.hpp
./hdf/HDFPulseWriter.hpp
./hdf/HDFRefGroupGroup.hpp
./hdf/HDFRefInfoGroup.hpp
./hdf/HDFRegionTableReader.hpp
./hdf/HDFRegionTableWriter.hpp
./hdf/HDFRegionsWriter.hpp
./hdf/HDFSMRTSequenceReader.hpp
./hdf/HDFScanDataReader.hpp
./hdf/HDFScanDataWriter.hpp
./hdf/HDFUtils.hpp
./hdf/HDFWriteBuffer.hpp
./hdf/HDFSentinalFile.hpp
./hdf/HDFWriterBase.hpp
./hdf/HDFZMWMetricsWriter.hpp
./hdf/HDFZMWReader.hpp
./hdf/HDFZMWWriter.hpp
./pbdata/CCSSequence.hpp
./pbdata/ChangeListID.hpp
./pbdata/CommandLineParser.hpp
./pbdata/Compare4BitCompressed.hpp
./pbdata/CompressedDNASequence.hpp
./pbdata/CompressedSequence.hpp
./pbdata/CompressedSequenceImpl.hpp
./pbdata/DNASequence.hpp
./pbdata/FASTAReader.hpp
./pbdata/FASTASequence.hpp
./pbdata/FASTQReader.hpp
./pbdata/FASTQSequence.hpp
./pbdata/GFFFile.hpp
./pbdata/MD5Utils.hpp
./pbdata/MD5UtilsImpl.hpp
./pbdata/NucConversion.hpp
./pbdata/PackedDNASequence.hpp
./pbdata/ReverseCompressIndex.hpp
./pbdata/SMRTSequence.hpp
./pbdata/SeqUtils.hpp
./pbdata/SeqUtilsImpl.hpp
./pbdata/StringUtils.hpp
./pbdata/VectorUtils.hpp
./pbdata/alignment/CmpAlignment.hpp
./pbdata/alignment/CmpAlignmentImpl.hpp
./pbdata/amos/AfgBasWriter.hpp
./pbdata/loadpulses/MetricField.hpp
./pbdata/loadpulses/MovieAlnIndexLookupTable.hpp
./pbdata/matrix/FlatMatrix.hpp
./pbdata/matrix/FlatMatrixImpl.hpp
./pbdata/matrix/Matrix.hpp
./pbdata/matrix/MatrixImpl.hpp
./pbdata/metagenome/FindRandomSequence.hpp
./pbdata/metagenome/SequenceIndexDatabase.hpp
./pbdata/metagenome/SequenceIndexDatabaseImpl.hpp
./pbdata/metagenome/TitleTable.hpp
./pbdata/qvs/QualityTransform.hpp
./pbdata/qvs/QualityValue.hpp
./pbdata/qvs/QualityValueVector.hpp
./pbdata/qvs/QualityValueVectorImpl.hpp
./pbdata/reads/BaseFile.hpp
./pbdata/reads/BaseFileImpl.hpp
./pbdata/reads/HoleXY.hpp
./pbdata/reads/PulseBaseCommon.hpp
./pbdata/reads/PulseFile.hpp
./pbdata/reads/PulseFileImpl.hpp
./pbdata/reads/ReadInterval.hpp
./pbdata/reads/ReadType.hpp
./pbdata/reads/RegionAnnotation.hpp
./pbdata/reads/RegionAnnotations.hpp
./pbdata/reads/RegionTable.hpp
./pbdata/reads/RegionTypeMap.hpp
./pbdata/reads/ScanData.hpp
./pbdata/reads/ZMWGroupEntry.hpp
./pbdata/reads/AcqParams.hpp
./pbdata/saf/AlnGroup.hpp
./pbdata/saf/AlnInfo.hpp
./pbdata/saf/MovieInfo.hpp
./pbdata/saf/RefGroup.hpp
./pbdata/saf/RefInfo.hpp
./pbdata/sam/AlignmentSet.hpp
./pbdata/sam/AlignmentSetImpl.hpp
./pbdata/sam/ReadGroup.hpp
./pbdata/sam/ReferenceSequence.hpp
./pbdata/sam/SAMAlignment.hpp
./pbdata/sam/SAMHeader.hpp
./pbdata/sam/SAMKeywordValuePair.hpp
./pbdata/sam/SAMKeywordValuePairImpl.hpp
./pbdata/sam/SAMReader.hpp
./pbdata/sam/SAMReaderImpl.hpp
./pbdata/utils.hpp
./pbdata/utils/BitUtils.hpp
./pbdata/utils/SMRTReadUtils.hpp
./pbdata/utils/SMRTTitle.hpp
./pbdata/utils/TimeUtils.hpp
./pbdata/utilsImpl.hpp
./alignment/algorithms/alignment/sdp/NonoverlappingSparseDynamicProgramming.h
./alignment/algorithms/alignment/sdp/VariableLengthSDPFragment.h
./alignment/datastructures/alignment/AlignedPair.h
./alignment/datastructures/alignment/AlignmentGapList.h
./alignment/datastructures/alignment/ByteAlignment.h
./alignment/datastructures/alignment/CmpIndexedStringTable.h
./alignment/datastructures/alignment/CmpReadGroupTable.h
./alignment/datastructures/alignment/CmpRefSeqTable.h
./alignment/datastructures/alignment/Path.h
./alignment/query/PbiFilterZmwGroupQuery.h
./alignment/query/SequentialZmwGroupQuery.h
./alignment/tuples/CountedTuple.h
./alignment/tuples/DNATupleList.h
./alignment/tuples/TupleMask.h
./alignment/tuples/TupleOperations.h
./alignment/tuples/TupleTranslations.h
./alignment/tuples/tuple.h
./pbdata/Enumerations.h
./pbdata/PacBioDefs.h
./pbdata/Types.h
./pbdata/defs.h
./pbdata/sam/CigarString.h
./pbdata/sam/SAMFlag.h
pbdata/libconfig.h
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