├── .gitignore ├── COPYING ├── LICENSE ├── Makefile ├── README.md ├── SNAPLib ├── Aligner.h ├── AlignerContext.cpp ├── AlignerContext.h ├── AlignerOptions.cpp ├── AlignerOptions.h ├── AlignerStats.cpp ├── AlignerStats.h ├── AlignmentFilter.cpp ├── AlignmentFilter.h ├── ApproximateCounter.cpp ├── ApproximateCounter.h ├── Bam.cpp ├── Bam.h ├── BaseAligner.cpp ├── BaseAligner.h ├── BiasTables.cpp ├── BigAlloc.cpp ├── BigAlloc.h ├── BufferedAsync.cpp ├── BufferedAsync.h ├── ChimericPairedEndAligner.cpp ├── ChimericPairedEndAligner.h ├── Compat.cpp ├── Compat.h ├── ContaminationFilter.cpp ├── ContaminationFilter.h ├── DataReader.cpp ├── DataReader.h ├── DataWriter.cpp ├── DataWriter.h ├── FASTA.cpp ├── FASTA.h ├── FASTQ.cpp ├── FASTQ.h ├── FileFormat.h ├── FixedSizeMap.h ├── FixedSizeSet.h ├── FixedSizeVector.h ├── GTFReader.cpp ├── GTFReader.h ├── Genome.cpp ├── Genome.h ├── GenomeIndex.cpp ├── GenomeIndex.h ├── GzipDataWriter.cpp ├── GzipDataWriter.h ├── HashTable.cpp ├── HashTable.h ├── Histogram.cpp ├── Histogram.h ├── IntersectingPairedEndAligner.cpp ├── IntersectingPairedEndAligner.h ├── IntervalTree.h ├── LandauVishkin.cpp ├── LandauVishkin.h ├── MultiInputReadSupplier.cpp ├── MultiInputReadSupplier.h ├── PairedAligner.cpp ├── PairedAligner.h ├── PairedEndAligner.h ├── PairedReadMatcher.cpp ├── ParallelTask.cpp ├── ParallelTask.h ├── PriorityQueue.h ├── ProbabilityDistance.cpp ├── ProbabilityDistance.h ├── Range.cpp ├── Range.h ├── RangeSplitter.cpp ├── RangeSplitter.h ├── Read.cpp ├── Read.h ├── ReadReader.cpp ├── ReadSupplierQueue.cpp ├── ReadSupplierQueue.h ├── ReadWriter.cpp ├── SAM.cpp ├── SAM.h ├── SNAPLib.vcxproj ├── SNAPLib.vcxproj.filters ├── Seed.cpp ├── Seed.h ├── SeedSequencer.cpp ├── SeedSequencer.h ├── SingleAligner.cpp ├── SingleAligner.h ├── SortedDataWriter.cpp ├── Tables.cpp ├── Tables.h ├── Util.cpp ├── Util.h ├── VariableSizeMap.h ├── VariableSizeVector.h ├── WGsim.cpp ├── WGsim.h ├── WindowsFileMapper.h ├── directions.h ├── exit.cpp ├── exit.h ├── mapq.cpp ├── mapq.h ├── options.h ├── stdafx.cpp ├── stdafx.h └── targetver.h ├── apps ├── ComputeROC │ ├── .gitignore │ ├── ComputeROC.cpp │ ├── ComputeROC.vcxproj │ ├── ComputeROC.vcxproj.filters │ ├── stdafx.cpp │ ├── stdafx.h │ └── targetver.h ├── DistanceHist │ ├── DistanceHist.cpp │ ├── DistanceHist.vcxproj │ ├── DistanceHist.vcxproj.filters │ ├── stdafx.cpp │ ├── stdafx.h │ └── targetver.h ├── ExtractReads │ ├── ExtractReads.cpp │ ├── ExtractReads.vcxproj │ ├── ExtractReads.vcxproj.filters │ ├── stdafx.cpp │ ├── stdafx.h │ └── targetver.h ├── snap │ ├── Main.cpp │ ├── snap.vcxproj │ ├── snap.vcxproj.filters │ ├── stdafx.cpp │ └── stdafx.h ├── stringz │ ├── GoodRandom.cpp │ ├── GoodRandom.h │ ├── stdafx.cpp │ ├── stdafx.h │ ├── stringz.cpp │ ├── stringz.vcxproj │ ├── stringz.vcxproj.filters │ └── targetver.h └── wc │ ├── stdafx.cpp │ ├── stdafx.h │ ├── targetver.h │ ├── wc.cpp │ ├── wc.vcxproj │ └── wc.vcxproj.filters ├── docs ├── Manual.docx ├── Manual.pdf ├── 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