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..
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AffineGap.cpp
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AffineGap.h
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AffineGapVectorized.cpp
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AffineGapVectorized.h
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AlignerContext.cpp
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AlignerContext.h
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AlignerOptions.cpp
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AlignerOptions.h
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AlignerStats.cpp
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AlignerStats.h
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AlignmentAdjuster.cpp
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AlignmentAdjuster.h
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AlignmentResult.cpp
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AlignmentResult.h
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ApproximateCounter.cpp
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ApproximateCounter.h
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Bam.cpp
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Bam.h
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BaseAligner.cpp
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BaseAligner.h
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BigAlloc.cpp
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BigAlloc.h
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BufferedAsync.cpp
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BufferedAsync.h
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ChimericPairedEndAligner.cpp
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ChimericPairedEndAligner.h
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CommandProcessor.cpp
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CommandProcessor.h
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Compat.cpp
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Compat.h
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DataReader.cpp
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DataReader.h
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DataWriter.cpp
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DataWriter.h
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Error.cpp
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Error.h
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FASTA.cpp
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FASTA.h
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FASTQ.cpp
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FASTQ.h
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FileFormat.h
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FixedSizeMap.h
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FixedSizeSet.h
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FixedSizeVector.h
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GenericFile.cpp
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GenericFile.h
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GenericFile_Blob.cpp
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GenericFile_Blob.h
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GenericFile_HDFS.cpp
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GenericFile_HDFS.h
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GenericFile_map.cpp
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GenericFile_map.h
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GenericFile_stdio.cpp
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GenericFile_stdio.h
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Genome.cpp
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Genome.h
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GenomeIndex.cpp
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GenomeIndex.h
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GzipDataWriter.cpp
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GzipDataWriter.h
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HashTable.cpp
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HashTable.h
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Histogram.cpp
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Histogram.h
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IntersectingPairedEndAligner.cpp
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IntersectingPairedEndAligner.h
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LandauVishkin.cpp
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LandauVishkin.h
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MultiInputReadSupplier.cpp
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MultiInputReadSupplier.h
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PairedAligner.cpp
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PairedAligner.h
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PairedEndAligner.h
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PairedReadMatcher.cpp
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ParallelTask.cpp
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ParallelTask.h
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PriorityQueue.h
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ProbabilityDistance.cpp
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ProbabilityDistance.h
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RangeSplitter.cpp
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RangeSplitter.h
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Read.cpp
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Read.h
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ReadReader.cpp
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ReadSupplierQueue.cpp
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ReadSupplierQueue.h
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ReadWriter.cpp
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SAM.cpp
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SAM.h
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SNAPLib.vcxproj
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SNAPLib.vcxproj.filters
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Seed.cpp
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Seed.h
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SeedSequencer.cpp
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SeedSequencer.h
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SingleAligner.cpp
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SingleAligner.h
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SortedDataWriter.cpp
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Tables.cpp
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Tables.h
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Util.cpp
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Util.h
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VariableSizeMap.h
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VariableSizeVector.h
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WindowsFileMapper.h
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directions.h
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exit.cpp
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exit.h
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mapq.cpp
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mapq.h
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options.h
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stdafx.cpp
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stdafx.h
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targetver.h
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