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usr/
usr/bin/
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usr/bin/taxsize.sh
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usr/bin/tetramerfreq.sh
usr/bin/textfile.sh
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usr/bin/unicode2ascii.sh
usr/bin/unzip.sh
usr/bin/vcf2gff.sh
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usr/bin/webcheck.sh
usr/bin/wobblealigner.sh
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usr/share/
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usr/share/doc/bbmap/RestartingServers.txt
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usr/share/doc/bbmap/guides/CallVariantsGuide.txt
usr/share/doc/bbmap/guides/ClumpifyGuide.txt
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usr/share/java/bbmap/current/aligner/BandedAlignerConcise.java
usr/share/java/bbmap/current/aligner/BandedAlignerInt.class
usr/share/java/bbmap/current/aligner/BandedAlignerInt.java
usr/share/java/bbmap/current/aligner/BandedAlignerM.class
usr/share/java/bbmap/current/aligner/BandedAlignerM.java
usr/share/java/bbmap/current/aligner/BandedByteAligner.class
usr/share/java/bbmap/current/aligner/BandedByteAligner.java
usr/share/java/bbmap/current/aligner/BandedPlusAligner.class
usr/share/java/bbmap/current/aligner/BandedPlusAligner.java
usr/share/java/bbmap/current/aligner/BandedPlusAligner2.class
usr/share/java/bbmap/current/aligner/BandedPlusAligner2.java
usr/share/java/bbmap/current/aligner/BandedPlusAligner3.class
usr/share/java/bbmap/current/aligner/BandedPlusAligner3.java
usr/share/java/bbmap/current/aligner/BandedPlusAlignerInt.class
usr/share/java/bbmap/current/aligner/BandedPlusAlignerInt.java
usr/share/java/bbmap/current/aligner/ClippingTest.class
usr/share/java/bbmap/current/aligner/ClippingTest.java
usr/share/java/bbmap/current/aligner/CrossCutAligner.class
usr/share/java/bbmap/current/aligner/CrossCutAligner.java
usr/share/java/bbmap/current/aligner/DiagonalAligner$ExtzResult.class
usr/share/java/bbmap/current/aligner/DiagonalAligner.class
usr/share/java/bbmap/current/aligner/DiagonalAligner.java
usr/share/java/bbmap/current/aligner/DriftingAligner.class
usr/share/java/bbmap/current/aligner/DriftingAligner.java
usr/share/java/bbmap/current/aligner/DriftingAlignerConcise.class
usr/share/java/bbmap/current/aligner/DriftingAlignerConcise.java
usr/share/java/bbmap/current/aligner/DriftingAlignerM.class
usr/share/java/bbmap/current/aligner/DriftingAlignerM.java
usr/share/java/bbmap/current/aligner/DriftingPlusAligner.class
usr/share/java/bbmap/current/aligner/DriftingPlusAligner.java
usr/share/java/bbmap/current/aligner/DriftingPlusAligner2.class
usr/share/java/bbmap/current/aligner/DriftingPlusAligner2.java
usr/share/java/bbmap/current/aligner/DriftingPlusAligner3.class
usr/share/java/bbmap/current/aligner/DriftingPlusAligner3.java
usr/share/java/bbmap/current/aligner/Eh.class
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usr/share/java/bbmap/current/aligner/Factory.java
usr/share/java/bbmap/current/aligner/FlatAligner.class
usr/share/java/bbmap/current/aligner/FlatAligner.java
usr/share/java/bbmap/current/aligner/FlatAligner2.class
usr/share/java/bbmap/current/aligner/FlatAligner2.java
usr/share/java/bbmap/current/aligner/GlocalAligner.class
usr/share/java/bbmap/current/aligner/GlocalAligner.java
usr/share/java/bbmap/current/aligner/GlocalAlignerConcise.class
usr/share/java/bbmap/current/aligner/GlocalAlignerConcise.java
usr/share/java/bbmap/current/aligner/GlocalAlignerInt.class
usr/share/java/bbmap/current/aligner/GlocalAlignerInt.java
usr/share/java/bbmap/current/aligner/GlocalAlignerOld.class
usr/share/java/bbmap/current/aligner/GlocalAlignerOld.java
usr/share/java/bbmap/current/aligner/GlocalPlusAligner.class
usr/share/java/bbmap/current/aligner/GlocalPlusAligner.java
usr/share/java/bbmap/current/aligner/GlocalPlusAligner2.class
usr/share/java/bbmap/current/aligner/GlocalPlusAligner2.java
usr/share/java/bbmap/current/aligner/GlocalPlusAligner3.class
usr/share/java/bbmap/current/aligner/GlocalPlusAligner3.java
usr/share/java/bbmap/current/aligner/GlocalPlusAligner4.class
usr/share/java/bbmap/current/aligner/GlocalPlusAligner4.java
usr/share/java/bbmap/current/aligner/GlocalPlusAligner5.class
usr/share/java/bbmap/current/aligner/GlocalPlusAligner5.java
usr/share/java/bbmap/current/aligner/IDAligner.class
usr/share/java/bbmap/current/aligner/IDAligner.java
usr/share/java/bbmap/current/aligner/IndelFreeAligner$ProcessThread.class
usr/share/java/bbmap/current/aligner/IndelFreeAligner.class
usr/share/java/bbmap/current/aligner/IndelFreeAligner.java
usr/share/java/bbmap/current/aligner/IntIndex.class
usr/share/java/bbmap/current/aligner/IntIndex.java
usr/share/java/bbmap/current/aligner/IntListAligner.class
usr/share/java/bbmap/current/aligner/IntListAligner.java
usr/share/java/bbmap/current/aligner/Ksw2gg$Cell.class
usr/share/java/bbmap/current/aligner/Ksw2gg.class
usr/share/java/bbmap/current/aligner/Ksw2gg.java
usr/share/java/bbmap/current/aligner/KswGgJava.class
usr/share/java/bbmap/current/aligner/KswGgJava.java
usr/share/java/bbmap/current/aligner/MSAViz.class
usr/share/java/bbmap/current/aligner/MSAViz.java
usr/share/java/bbmap/current/aligner/MicroAligner.class
usr/share/java/bbmap/current/aligner/MicroAligner.java
usr/share/java/bbmap/current/aligner/MicroAligner2.class
usr/share/java/bbmap/current/aligner/MicroAligner2.java
usr/share/java/bbmap/current/aligner/MicroAligner3.class
usr/share/java/bbmap/current/aligner/MicroAligner3.java
usr/share/java/bbmap/current/aligner/MicroIndex3.class
usr/share/java/bbmap/current/aligner/MicroIndex3.java
usr/share/java/bbmap/current/aligner/MicroWrapper$ProcessThread.class
usr/share/java/bbmap/current/aligner/MicroWrapper.class
usr/share/java/bbmap/current/aligner/MicroWrapper.java
usr/share/java/bbmap/current/aligner/MinHitsCalculator.class
usr/share/java/bbmap/current/aligner/MinHitsCalculator.java
usr/share/java/bbmap/current/aligner/MinHitsCalculator2.class
usr/share/java/bbmap/current/aligner/MinHitsCalculator2.java
usr/share/java/bbmap/current/aligner/MinHitsCalculatorOld.class
usr/share/java/bbmap/current/aligner/MinHitsCalculatorOld.java
usr/share/java/bbmap/current/aligner/MultiStateAligner9PacBioAdapter.class
usr/share/java/bbmap/current/aligner/MultiStateAligner9PacBioAdapter.java
usr/share/java/bbmap/current/aligner/MultiStateAligner9PacBioAdapter2.class
usr/share/java/bbmap/current/aligner/MultiStateAligner9PacBioAdapter2.java
usr/share/java/bbmap/current/aligner/MultiStateAligner9PacBioAdapter3.class
usr/share/java/bbmap/current/aligner/MultiStateAligner9PacBioAdapter3.java
usr/share/java/bbmap/current/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.class
usr/share/java/bbmap/current/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.java
usr/share/java/bbmap/current/aligner/Parallelogram.class
usr/share/java/bbmap/current/aligner/Parallelogram.java
usr/share/java/bbmap/current/aligner/QuabbleAligner.class
usr/share/java/bbmap/current/aligner/QuabbleAligner.java
usr/share/java/bbmap/current/aligner/QuantumAligner.class
usr/share/java/bbmap/current/aligner/QuantumAligner.java
usr/share/java/bbmap/current/aligner/QuantumAlignerConcise.class
usr/share/java/bbmap/current/aligner/QuantumAlignerConcise.java
usr/share/java/bbmap/current/aligner/QuantumAlignerConcise2.class
usr/share/java/bbmap/current/aligner/QuantumAlignerConcise2.java
usr/share/java/bbmap/current/aligner/QuantumAlignerM.class
usr/share/java/bbmap/current/aligner/QuantumAlignerM.java
usr/share/java/bbmap/current/aligner/QuantumAlignerQC.class
usr/share/java/bbmap/current/aligner/QuantumAlignerQC.java
usr/share/java/bbmap/current/aligner/QuantumPlusAligner.class
usr/share/java/bbmap/current/aligner/QuantumPlusAligner.java
usr/share/java/bbmap/current/aligner/QuantumPlusAligner2.class
usr/share/java/bbmap/current/aligner/QuantumPlusAligner2.java
usr/share/java/bbmap/current/aligner/QuantumPlusAligner3.class
usr/share/java/bbmap/current/aligner/QuantumPlusAligner3.java
usr/share/java/bbmap/current/aligner/QuantumPlusAligner4.class
usr/share/java/bbmap/current/aligner/QuantumPlusAligner4.java
usr/share/java/bbmap/current/aligner/Query.class
usr/share/java/bbmap/current/aligner/Query.java
usr/share/java/bbmap/current/aligner/README.md
usr/share/java/bbmap/current/aligner/RelativeAligner.class
usr/share/java/bbmap/current/aligner/RelativeAligner.java
usr/share/java/bbmap/current/aligner/ScrabbleAligner.class
usr/share/java/bbmap/current/aligner/ScrabbleAligner.java
usr/share/java/bbmap/current/aligner/SideChannel3.class
usr/share/java/bbmap/current/aligner/SideChannel3.java
usr/share/java/bbmap/current/aligner/SingleStateAlignerFlat.class
usr/share/java/bbmap/current/aligner/SingleStateAlignerFlat.java
usr/share/java/bbmap/current/aligner/SingleStateAlignerFlat2.class
usr/share/java/bbmap/current/aligner/SingleStateAlignerFlat2.java
usr/share/java/bbmap/current/aligner/SingleStateAlignerFlat2Amino.class
usr/share/java/bbmap/current/aligner/SingleStateAlignerFlat2Amino.java
usr/share/java/bbmap/current/aligner/SingleStateAlignerFlat2_1D.class
usr/share/java/bbmap/current/aligner/SingleStateAlignerFlat2_1D.java
usr/share/java/bbmap/current/aligner/SingleStateAlignerFlat3.class
usr/share/java/bbmap/current/aligner/SingleStateAlignerFlat3.java
usr/share/java/bbmap/current/aligner/SingleStateAlignerFlatFloat.class
usr/share/java/bbmap/current/aligner/SingleStateAlignerFlatFloat.java
usr/share/java/bbmap/current/aligner/SingleStateAlignerPacBioAdapter.class
usr/share/java/bbmap/current/aligner/SingleStateAlignerPacBioAdapter.java
usr/share/java/bbmap/current/aligner/SmithWaterman.class
usr/share/java/bbmap/current/aligner/SmithWaterman.java
usr/share/java/bbmap/current/aligner/Test$Runner.class
usr/share/java/bbmap/current/aligner/Test.class
usr/share/java/bbmap/current/aligner/Test.java
usr/share/java/bbmap/current/aligner/TestAlignerSuite$Job.class
usr/share/java/bbmap/current/aligner/TestAlignerSuite$Worker.class
usr/share/java/bbmap/current/aligner/TestAlignerSuite.class
usr/share/java/bbmap/current/aligner/TestAlignerSuite.java
usr/share/java/bbmap/current/aligner/Tracer.class
usr/share/java/bbmap/current/aligner/Tracer.java
usr/share/java/bbmap/current/aligner/VisualizationConverter.class
usr/share/java/bbmap/current/aligner/VisualizationConverter.java
usr/share/java/bbmap/current/aligner/Visualizer.class
usr/share/java/bbmap/current/aligner/Visualizer.java
usr/share/java/bbmap/current/aligner/WaveFrontAligner.class
usr/share/java/bbmap/current/aligner/WaveFrontAligner.java
usr/share/java/bbmap/current/aligner/WaveFrontAligner2.class
usr/share/java/bbmap/current/aligner/WaveFrontAligner2.java
usr/share/java/bbmap/current/aligner/WaveFrontAlignerViz.class
usr/share/java/bbmap/current/aligner/WaveFrontAlignerViz.java
usr/share/java/bbmap/current/aligner/WobbleAligner.class
usr/share/java/bbmap/current/aligner/WobbleAligner.java
usr/share/java/bbmap/current/aligner/WobbleAlignerConcise.class
usr/share/java/bbmap/current/aligner/WobbleAlignerConcise.java
usr/share/java/bbmap/current/aligner/WobblePlusAligner.class
usr/share/java/bbmap/current/aligner/WobblePlusAligner.java
usr/share/java/bbmap/current/aligner/WobblePlusAligner2.class
usr/share/java/bbmap/current/aligner/WobblePlusAligner2.java
usr/share/java/bbmap/current/aligner/WobblePlusAligner3.class
usr/share/java/bbmap/current/aligner/WobblePlusAligner3.java
usr/share/java/bbmap/current/aligner/WobblePlusAligner4.class
usr/share/java/bbmap/current/aligner/WobblePlusAligner4.java
usr/share/java/bbmap/current/aligner/WobblePlusAligner5.class
usr/share/java/bbmap/current/aligner/WobblePlusAligner5.java
usr/share/java/bbmap/current/aligner/XDropHAligner.class
usr/share/java/bbmap/current/aligner/XDropHAligner.java
usr/share/java/bbmap/current/assemble/
usr/share/java/bbmap/current/assemble/AbstractBuildThread.class
usr/share/java/bbmap/current/assemble/AbstractBuildThread.java
usr/share/java/bbmap/current/assemble/AbstractExploreThread.class
usr/share/java/bbmap/current/assemble/AbstractExploreThread.java
usr/share/java/bbmap/current/assemble/AbstractProcessContigThread.class
usr/share/java/bbmap/current/assemble/AbstractProcessContigThread.java
usr/share/java/bbmap/current/assemble/AbstractRemoveThread$RemoveThread1.class
usr/share/java/bbmap/current/assemble/AbstractRemoveThread$RemoveThread2.class
usr/share/java/bbmap/current/assemble/AbstractRemoveThread.class
usr/share/java/bbmap/current/assemble/AbstractRemoveThread.java
usr/share/java/bbmap/current/assemble/AbstractShaveThread.class
usr/share/java/bbmap/current/assemble/AbstractShaveThread.java
usr/share/java/bbmap/current/assemble/BubblePopper.class
usr/share/java/bbmap/current/assemble/BubblePopper.java
usr/share/java/bbmap/current/assemble/Contig.class
usr/share/java/bbmap/current/assemble/Contig.java
usr/share/java/bbmap/current/assemble/Edge.class
usr/share/java/bbmap/current/assemble/Edge.java
usr/share/java/bbmap/current/assemble/ErrorTracker.class
usr/share/java/bbmap/current/assemble/ErrorTracker.java
usr/share/java/bbmap/current/assemble/KmerCompressor$BuildThread.class
usr/share/java/bbmap/current/assemble/KmerCompressor.class
usr/share/java/bbmap/current/assemble/KmerCompressor.java
usr/share/java/bbmap/current/assemble/Postfilter.class
usr/share/java/bbmap/current/assemble/Postfilter.java
usr/share/java/bbmap/current/assemble/README.md
usr/share/java/bbmap/current/assemble/Rollback.class
usr/share/java/bbmap/current/assemble/Rollback.java
usr/share/java/bbmap/current/assemble/ShaveObject.class
usr/share/java/bbmap/current/assemble/ShaveObject.java
usr/share/java/bbmap/current/assemble/Shaver.class
usr/share/java/bbmap/current/assemble/Shaver.java
usr/share/java/bbmap/current/assemble/Shaver1$ExploreThread.class
usr/share/java/bbmap/current/assemble/Shaver1$ShaveThread.class
usr/share/java/bbmap/current/assemble/Shaver1.class
usr/share/java/bbmap/current/assemble/Shaver1.java
usr/share/java/bbmap/current/assemble/Shaver2$ExploreThread.class
usr/share/java/bbmap/current/assemble/Shaver2$ShaveThread.class
usr/share/java/bbmap/current/assemble/Shaver2.class
usr/share/java/bbmap/current/assemble/Shaver2.java
usr/share/java/bbmap/current/assemble/TadPipe.class
usr/share/java/bbmap/current/assemble/TadPipe.java
usr/share/java/bbmap/current/assemble/Tadpole$DumpKmersThread.class
usr/share/java/bbmap/current/assemble/Tadpole$ExtendThread.class
usr/share/java/bbmap/current/assemble/Tadpole$MakeKhistThread.class
usr/share/java/bbmap/current/assemble/Tadpole.class
usr/share/java/bbmap/current/assemble/Tadpole.java
usr/share/java/bbmap/current/assemble/Tadpole1$BuildThread.class
usr/share/java/bbmap/current/assemble/Tadpole1$ProcessContigThread.class
usr/share/java/bbmap/current/assemble/Tadpole1.class
usr/share/java/bbmap/current/assemble/Tadpole1.java
usr/share/java/bbmap/current/assemble/Tadpole2$BuildThread.class
usr/share/java/bbmap/current/assemble/Tadpole2$ProcessContigThread.class
usr/share/java/bbmap/current/assemble/Tadpole2.class
usr/share/java/bbmap/current/assemble/Tadpole2.java
usr/share/java/bbmap/current/assemble/TadpoleWrapper$1.class
usr/share/java/bbmap/current/assemble/TadpoleWrapper$Record.class
usr/share/java/bbmap/current/assemble/TadpoleWrapper.class
usr/share/java/bbmap/current/assemble/TadpoleWrapper.java
usr/share/java/bbmap/current/barcode/
usr/share/java/bbmap/current/barcode/AnalyzeBarcodes.class
usr/share/java/bbmap/current/barcode/AnalyzeBarcodes.java
usr/share/java/bbmap/current/barcode/Barcode.class
usr/share/java/bbmap/current/barcode/Barcode.java
usr/share/java/bbmap/current/barcode/BarcodeCounter.class
usr/share/java/bbmap/current/barcode/BarcodeCounter.java
usr/share/java/bbmap/current/barcode/BarcodeMappingStats.class
usr/share/java/bbmap/current/barcode/BarcodeMappingStats.java
usr/share/java/bbmap/current/barcode/BarcodeStats.class
usr/share/java/bbmap/current/barcode/BarcodeStats.java
usr/share/java/bbmap/current/barcode/CompareLabels$Label.class
usr/share/java/bbmap/current/barcode/CompareLabels.class
usr/share/java/bbmap/current/barcode/CompareLabels.java
usr/share/java/bbmap/current/barcode/CorrelateBarcodes.class
usr/share/java/bbmap/current/barcode/CorrelateBarcodes.java
usr/share/java/bbmap/current/barcode/CountBarcodes.class
usr/share/java/bbmap/current/barcode/CountBarcodes.java
usr/share/java/bbmap/current/barcode/CountBarcodes2.class
usr/share/java/bbmap/current/barcode/CountBarcodes2.java
usr/share/java/bbmap/current/barcode/DemuxClient.class
usr/share/java/bbmap/current/barcode/DemuxClient.java
usr/share/java/bbmap/current/barcode/DemuxData.class
usr/share/java/bbmap/current/barcode/DemuxData.java
usr/share/java/bbmap/current/barcode/DemuxServer$BaseHandler.class
usr/share/java/bbmap/current/barcode/DemuxServer$DemuxHandler.class
usr/share/java/bbmap/current/barcode/DemuxServer$IconHandler.class
usr/share/java/bbmap/current/barcode/DemuxServer$KillHandler.class
usr/share/java/bbmap/current/barcode/DemuxServer$Pair.class
usr/share/java/bbmap/current/barcode/DemuxServer$StatsHandler.class
usr/share/java/bbmap/current/barcode/DemuxServer.class
usr/share/java/bbmap/current/barcode/DemuxServer.java
usr/share/java/bbmap/current/barcode/LegacyFileWriter$QTag.class
usr/share/java/bbmap/current/barcode/LegacyFileWriter.class
usr/share/java/bbmap/current/barcode/LegacyFileWriter.java
usr/share/java/bbmap/current/barcode/NovaDemux.class
usr/share/java/bbmap/current/barcode/NovaDemux.java
usr/share/java/bbmap/current/barcode/PCRMatrix$MapLine.class
usr/share/java/bbmap/current/barcode/PCRMatrix.class
usr/share/java/bbmap/current/barcode/PCRMatrix.java
usr/share/java/bbmap/current/barcode/PCRMatrixHDist$PopThread.class
usr/share/java/bbmap/current/barcode/PCRMatrixHDist.class
usr/share/java/bbmap/current/barcode/PCRMatrixHDist.java
usr/share/java/bbmap/current/barcode/README.md
usr/share/java/bbmap/current/barcode/TagAndMerge.class
usr/share/java/bbmap/current/barcode/TagAndMerge.java
usr/share/java/bbmap/current/barcode/Transition.class
usr/share/java/bbmap/current/barcode/Transition.java
usr/share/java/bbmap/current/barcode/stub/
usr/share/java/bbmap/current/barcode/stub/PCRMatrixProb.class
usr/share/java/bbmap/current/barcode/stub/PCRMatrixProb.java
usr/share/java/bbmap/current/barcode/stub/PCRMatrixProbAbstract.class
usr/share/java/bbmap/current/barcode/stub/PCRMatrixProbAbstract.java
usr/share/java/bbmap/current/barcode/stub/PCRMatrixTile.class
usr/share/java/bbmap/current/barcode/stub/PCRMatrixTile.java
usr/share/java/bbmap/current/bbduk/
usr/share/java/bbmap/current/bbduk/Allocator$AllocThread.class
usr/share/java/bbmap/current/bbduk/Allocator.class
usr/share/java/bbmap/current/bbduk/Allocator.java
usr/share/java/bbmap/current/bbduk/BBDuk2$LoadThread.class
usr/share/java/bbmap/current/bbduk/BBDuk2$ProcessThread.class
usr/share/java/bbmap/current/bbduk/BBDuk2.class
usr/share/java/bbmap/current/bbduk/BBDuk2.java
usr/share/java/bbmap/current/bbduk/BBDuk3$ProcessThread.class
usr/share/java/bbmap/current/bbduk/BBDuk3.class
usr/share/java/bbmap/current/bbduk/BBDuk3.java
usr/share/java/bbmap/current/bbduk/BBDuk4$ProcessThread.class
usr/share/java/bbmap/current/bbduk/BBDuk4.class
usr/share/java/bbmap/current/bbduk/BBDuk4.java
usr/share/java/bbmap/current/bbduk/BBDuk5$ProcessThread.class
usr/share/java/bbmap/current/bbduk/BBDuk5.class
usr/share/java/bbmap/current/bbduk/BBDuk5.java
usr/share/java/bbmap/current/bbduk/BBDuk6$ProcessThread.class
usr/share/java/bbmap/current/bbduk/BBDuk6.class
usr/share/java/bbmap/current/bbduk/BBDuk6.java
usr/share/java/bbmap/current/bbduk/BBDukIndex.class
usr/share/java/bbmap/current/bbduk/BBDukIndex.java
usr/share/java/bbmap/current/bbduk/BBDukIndexAbstract.class
usr/share/java/bbmap/current/bbduk/BBDukIndexAbstract.java
usr/share/java/bbmap/current/bbduk/BBDukIndexAndLoader$LoadThread.class
usr/share/java/bbmap/current/bbduk/BBDukIndexAndLoader.class
usr/share/java/bbmap/current/bbduk/BBDukIndexAndLoader.java
usr/share/java/bbmap/current/bbduk/BBDukIndexMask.class
usr/share/java/bbmap/current/bbduk/BBDukIndexMask.java
usr/share/java/bbmap/current/bbduk/BBDukIndexMask2.class
usr/share/java/bbmap/current/bbduk/BBDukIndexMask2.java
usr/share/java/bbmap/current/bbduk/BBDukIndexMod.class
usr/share/java/bbmap/current/bbduk/BBDukIndexMod.java
usr/share/java/bbmap/current/bbduk/BBDukIndex_clean$LoadThread.class
usr/share/java/bbmap/current/bbduk/BBDukIndex_clean.class
usr/share/java/bbmap/current/bbduk/BBDukIndex_clean.java
usr/share/java/bbmap/current/bbduk/BBDukLoader$LoadThread.class
usr/share/java/bbmap/current/bbduk/BBDukLoader.class
usr/share/java/bbmap/current/bbduk/BBDukLoader.java
usr/share/java/bbmap/current/bbduk/BBDukParser.class
usr/share/java/bbmap/current/bbduk/BBDukParser.java
usr/share/java/bbmap/current/bbduk/BBDukProcessor.class
usr/share/java/bbmap/current/bbduk/BBDukProcessor.java
usr/share/java/bbmap/current/bbduk/BBDukProcessor2.class
usr/share/java/bbmap/current/bbduk/BBDukProcessor2.java
usr/share/java/bbmap/current/bbduk/BBDukProcessorS.class
usr/share/java/bbmap/current/bbduk/BBDukProcessorS.java
usr/share/java/bbmap/current/bbduk/BBDukS$ProcessThread.class
usr/share/java/bbmap/current/bbduk/BBDukS.class
usr/share/java/bbmap/current/bbduk/BBDukS.java
usr/share/java/bbmap/current/bbmin/
usr/share/java/bbmap/current/bbmin/Minimizer.class
usr/share/java/bbmap/current/bbmin/Minimizer.java
usr/share/java/bbmap/current/bbmin/README.md
usr/share/java/bbmap/current/bin/
usr/share/java/bbmap/current/bin/AbstractRefiner$EnsembleRefinerParams.class
usr/share/java/bbmap/current/bin/AbstractRefiner$EvidenceRefinerParams.class
usr/share/java/bbmap/current/bin/AbstractRefiner$GraphRefinerParams.class
usr/share/java/bbmap/current/bin/AbstractRefiner$RefinerParams.class
usr/share/java/bbmap/current/bin/AbstractRefiner.class
usr/share/java/bbmap/current/bin/AbstractRefiner.java
usr/share/java/bbmap/current/bin/AdjustEntropy.class
usr/share/java/bbmap/current/bin/AdjustEntropy.java
usr/share/java/bbmap/current/bin/AllToAllVectorMaker.class
usr/share/java/bbmap/current/bin/AllToAllVectorMaker.java
usr/share/java/bbmap/current/bin/Bin.class
usr/share/java/bbmap/current/bin/Bin.java
usr/share/java/bbmap/current/bin/BinComparator.class
usr/share/java/bbmap/current/bin/BinComparator.java
usr/share/java/bbmap/current/bin/BinMap.class
usr/share/java/bbmap/current/bin/BinMap.java
usr/share/java/bbmap/current/bin/BinObject.class
usr/share/java/bbmap/current/bin/BinObject.java
usr/share/java/bbmap/current/bin/BinSketcher$ProcessThread.class
usr/share/java/bbmap/current/bin/BinSketcher.class
usr/share/java/bbmap/current/bin/BinSketcher.java
usr/share/java/bbmap/current/bin/BinStats.class
usr/share/java/bbmap/current/bin/BinStats.java
usr/share/java/bbmap/current/bin/BinStatsComparator.class
usr/share/java/bbmap/current/bin/BinStatsComparator.java
usr/share/java/bbmap/current/bin/Binner$CompareThread.class
usr/share/java/bbmap/current/bin/Binner.class
usr/share/java/bbmap/current/bin/Binner.java
usr/share/java/bbmap/current/bin/ChartMaker.class
usr/share/java/bbmap/current/bin/ChartMaker.java
usr/share/java/bbmap/current/bin/Cluster.class
usr/share/java/bbmap/current/bin/Cluster.java
usr/share/java/bbmap/current/bin/ClusterWriter.class
usr/share/java/bbmap/current/bin/ClusterWriter.java
usr/share/java/bbmap/current/bin/ClusterWriter2$WriteThread.class
usr/share/java/bbmap/current/bin/ClusterWriter2.class
usr/share/java/bbmap/current/bin/ClusterWriter2.java
usr/share/java/bbmap/current/bin/ConservationModel.class
usr/share/java/bbmap/current/bin/ConservationModel.java
usr/share/java/bbmap/current/bin/Contig$ContigIterator.class
usr/share/java/bbmap/current/bin/Contig.class
usr/share/java/bbmap/current/bin/Contig.java
usr/share/java/bbmap/current/bin/ContigRenamer$ProcessThread.class
usr/share/java/bbmap/current/bin/ContigRenamer$Scaf.class
usr/share/java/bbmap/current/bin/ContigRenamer.class
usr/share/java/bbmap/current/bin/ContigRenamer.java
usr/share/java/bbmap/current/bin/CrystalChamber$Centroid.class
usr/share/java/bbmap/current/bin/CrystalChamber.class
usr/share/java/bbmap/current/bin/CrystalChamber.java
usr/share/java/bbmap/current/bin/CrystalChamber2$Centroid.class
usr/share/java/bbmap/current/bin/CrystalChamber2.class
usr/share/java/bbmap/current/bin/CrystalChamber2.java
usr/share/java/bbmap/current/bin/DataLoader.class
usr/share/java/bbmap/current/bin/DataLoader.java
usr/share/java/bbmap/current/bin/EnsembleRefiner$ConsensusResult.class
usr/share/java/bbmap/current/bin/EnsembleRefiner$RefinerResult.class
usr/share/java/bbmap/current/bin/EnsembleRefiner.class
usr/share/java/bbmap/current/bin/EnsembleRefiner.java
usr/share/java/bbmap/current/bin/EvidenceRefiner$ContigStatus.class
usr/share/java/bbmap/current/bin/EvidenceRefiner$DBSCANResult.class
usr/share/java/bbmap/current/bin/EvidenceRefiner.class
usr/share/java/bbmap/current/bin/EvidenceRefiner.java
usr/share/java/bbmap/current/bin/FileRenamer.class
usr/share/java/bbmap/current/bin/FileRenamer.java
usr/share/java/bbmap/current/bin/GTDBLine.class
usr/share/java/bbmap/current/bin/GTDBLine.java
usr/share/java/bbmap/current/bin/GeneTools.class
usr/share/java/bbmap/current/bin/GeneTools.java
usr/share/java/bbmap/current/bin/GradeBins$CCLine.class
usr/share/java/bbmap/current/bin/GradeBins$PTAccumulator.class
usr/share/java/bbmap/current/bin/GradeBins$ProcessThread.class
usr/share/java/bbmap/current/bin/GradeBins.class
usr/share/java/bbmap/current/bin/GradeBins.java
usr/share/java/bbmap/current/bin/GraphRefiner$SimilarityGraph$Edge.class
usr/share/java/bbmap/current/bin/GraphRefiner$SimilarityGraph.class
usr/share/java/bbmap/current/bin/GraphRefiner.class
usr/share/java/bbmap/current/bin/GraphRefiner.java
usr/share/java/bbmap/current/bin/IDComparator.class
usr/share/java/bbmap/current/bin/IDComparator.java
usr/share/java/bbmap/current/bin/Key.class
usr/share/java/bbmap/current/bin/Key.java
usr/share/java/bbmap/current/bin/KeyValue.class
usr/share/java/bbmap/current/bin/KeyValue.java
usr/share/java/bbmap/current/bin/KmerProb.class
usr/share/java/bbmap/current/bin/KmerProb.java
usr/share/java/bbmap/current/bin/Oracle.class
usr/share/java/bbmap/current/bin/Oracle.java
usr/share/java/bbmap/current/bin/QuickBin$ProcessThread.class
usr/share/java/bbmap/current/bin/QuickBin.class
usr/share/java/bbmap/current/bin/QuickBin.java
usr/share/java/bbmap/current/bin/README.md
usr/share/java/bbmap/current/bin/SamLoader$LoadThread.class
usr/share/java/bbmap/current/bin/SamLoader.class
usr/share/java/bbmap/current/bin/SamLoader.java
usr/share/java/bbmap/current/bin/SamLoader2$ParallelWorker.class
usr/share/java/bbmap/current/bin/SamLoader2$QueueWorker.class
usr/share/java/bbmap/current/bin/SamLoader2$Worker.class
usr/share/java/bbmap/current/bin/SamLoader2.class
usr/share/java/bbmap/current/bin/SamLoader2.java
usr/share/java/bbmap/current/bin/SamLoader3$ParallelWorker.class
usr/share/java/bbmap/current/bin/SamLoader3$QueueWorker.class
usr/share/java/bbmap/current/bin/SamLoader3$Worker.class
usr/share/java/bbmap/current/bin/SamLoader3.class
usr/share/java/bbmap/current/bin/SamLoader3.java
usr/share/java/bbmap/current/bin/ScoreComparator.class
usr/share/java/bbmap/current/bin/ScoreComparator.java
usr/share/java/bbmap/current/bin/SimilarityMeasures.class
usr/share/java/bbmap/current/bin/SimilarityMeasures.java
usr/share/java/bbmap/current/bin/SketchRecord.class
usr/share/java/bbmap/current/bin/SketchRecord.java
usr/share/java/bbmap/current/bin/Sketchable.class
usr/share/java/bbmap/current/bin/Sketchable.java
usr/share/java/bbmap/current/bin/SpectraCounter$LoadThread.class
usr/share/java/bbmap/current/bin/SpectraCounter.class
usr/share/java/bbmap/current/bin/SpectraCounter.java
usr/share/java/bbmap/current/bloom/
usr/share/java/bbmap/current/bloom/BloomFilter.class
usr/share/java/bbmap/current/bloom/BloomFilter.java
usr/share/java/bbmap/current/bloom/BloomFilterCorrector.class
usr/share/java/bbmap/current/bloom/BloomFilterCorrector.java
usr/share/java/bbmap/current/bloom/BloomFilterCorrectorWrapper$ProcessThread.class
usr/share/java/bbmap/current/bloom/BloomFilterCorrectorWrapper.class
usr/share/java/bbmap/current/bloom/BloomFilterCorrectorWrapper.java
usr/share/java/bbmap/current/bloom/BloomFilterWrapper$ProcessThread.class
usr/share/java/bbmap/current/bloom/BloomFilterWrapper.class
usr/share/java/bbmap/current/bloom/BloomFilterWrapper.java
usr/share/java/bbmap/current/bloom/ErrorCorrect$1.class
usr/share/java/bbmap/current/bloom/ErrorCorrect.class
usr/share/java/bbmap/current/bloom/ErrorCorrect.java
usr/share/java/bbmap/current/bloom/IndexCounter$CountThread.class
usr/share/java/bbmap/current/bloom/IndexCounter.class
usr/share/java/bbmap/current/bloom/IndexCounter.java
usr/share/java/bbmap/current/bloom/KCountArray$AllocThread.class
usr/share/java/bbmap/current/bloom/KCountArray.class
usr/share/java/bbmap/current/bloom/KCountArray.java
usr/share/java/bbmap/current/bloom/KCountArray2.class
usr/share/java/bbmap/current/bloom/KCountArray2.java
usr/share/java/bbmap/current/bloom/KCountArray3.class
usr/share/java/bbmap/current/bloom/KCountArray3.java
usr/share/java/bbmap/current/bloom/KCountArray4.class
usr/share/java/bbmap/current/bloom/KCountArray4.java
usr/share/java/bbmap/current/bloom/KCountArray4MT$WriteThread.class
usr/share/java/bbmap/current/bloom/KCountArray4MT.class
usr/share/java/bbmap/current/bloom/KCountArray4MT.java
usr/share/java/bbmap/current/bloom/KCountArray5MT$WriteThread.class
usr/share/java/bbmap/current/bloom/KCountArray5MT.class
usr/share/java/bbmap/current/bloom/KCountArray5MT.java
usr/share/java/bbmap/current/bloom/KCountArray6MT$WriteThread.class
usr/share/java/bbmap/current/bloom/KCountArray6MT.class
usr/share/java/bbmap/current/bloom/KCountArray6MT.java
usr/share/java/bbmap/current/bloom/KCountArray7MT$WriteThread.class
usr/share/java/bbmap/current/bloom/KCountArray7MT.class
usr/share/java/bbmap/current/bloom/KCountArray7MT.java
usr/share/java/bbmap/current/bloom/KCountArray7MTA$CountUsedThread.class
usr/share/java/bbmap/current/bloom/KCountArray7MTA.class
usr/share/java/bbmap/current/bloom/KCountArray7MTA.java
usr/share/java/bbmap/current/bloom/KCountArray8MT$WriteThread.class
usr/share/java/bbmap/current/bloom/KCountArray8MT.class
usr/share/java/bbmap/current/bloom/KCountArray8MT.java
usr/share/java/bbmap/current/bloom/KmerCount3.class
usr/share/java/bbmap/current/bloom/KmerCount3.java
usr/share/java/bbmap/current/bloom/KmerCount4.class
usr/share/java/bbmap/current/bloom/KmerCount4.java
usr/share/java/bbmap/current/bloom/KmerCount5.class
usr/share/java/bbmap/current/bloom/KmerCount5.java
usr/share/java/bbmap/current/bloom/KmerCount6.class
usr/share/java/bbmap/current/bloom/KmerCount6.java
usr/share/java/bbmap/current/bloom/KmerCountAbstract.class
usr/share/java/bbmap/current/bloom/KmerCountAbstract.java
usr/share/java/bbmap/current/bloom/LargeKmerCount.class
usr/share/java/bbmap/current/bloom/LargeKmerCount.java
usr/share/java/bbmap/current/bloom/LargeKmerCount2.class
usr/share/java/bbmap/current/bloom/LargeKmerCount2.java
usr/share/java/bbmap/current/bloom/ParseBloomFilter.class
usr/share/java/bbmap/current/bloom/ParseBloomFilter.java
usr/share/java/bbmap/current/bloom/PolyFilter$ProcessThread.class
usr/share/java/bbmap/current/bloom/PolyFilter.class
usr/share/java/bbmap/current/bloom/PolyFilter.java
usr/share/java/bbmap/current/bloom/README.md
usr/share/java/bbmap/current/bloom/ReadCounter$1.class
usr/share/java/bbmap/current/bloom/ReadCounter$CountThread.class
usr/share/java/bbmap/current/bloom/ReadCounter.class
usr/share/java/bbmap/current/bloom/ReadCounter.java
usr/share/java/bbmap/current/bloom/TestLargeKmer.class
usr/share/java/bbmap/current/bloom/TestLargeKmer.java
usr/share/java/bbmap/current/cardinality/
usr/share/java/bbmap/current/cardinality/BBLog.class
usr/share/java/bbmap/current/cardinality/BBLog.java
usr/share/java/bbmap/current/cardinality/BBLog_simple.class
usr/share/java/bbmap/current/cardinality/BBLog_simple.java
usr/share/java/bbmap/current/cardinality/CardinalityTracker.class
usr/share/java/bbmap/current/cardinality/CardinalityTracker.java
usr/share/java/bbmap/current/cardinality/LogLog.class
usr/share/java/bbmap/current/cardinality/LogLog.java
usr/share/java/bbmap/current/cardinality/LogLog16.class
usr/share/java/bbmap/current/cardinality/LogLog16.java
usr/share/java/bbmap/current/cardinality/LogLog2.class
usr/share/java/bbmap/current/cardinality/LogLog2.java
usr/share/java/bbmap/current/cardinality/LogLog8.class
usr/share/java/bbmap/current/cardinality/LogLog8.java
usr/share/java/bbmap/current/cardinality/LogLog8_simple.class
usr/share/java/bbmap/current/cardinality/LogLog8_simple.java
usr/share/java/bbmap/current/cardinality/LogLogWrapper$LogLogThread.class
usr/share/java/bbmap/current/cardinality/LogLogWrapper.class
usr/share/java/bbmap/current/cardinality/LogLogWrapper.java
usr/share/java/bbmap/current/cardinality/LogLog_old$LogLogWrapper$LogLogThread.class
usr/share/java/bbmap/current/cardinality/LogLog_old$LogLogWrapper.class
usr/share/java/bbmap/current/cardinality/LogLog_old.class
usr/share/java/bbmap/current/cardinality/LogLog_old.java
usr/share/java/bbmap/current/cardinality/MultiLogLog.class
usr/share/java/bbmap/current/cardinality/MultiLogLog.java
usr/share/java/bbmap/current/cardinality/README.md
usr/share/java/bbmap/current/clade/
usr/share/java/bbmap/current/clade/Clade.class
usr/share/java/bbmap/current/clade/Clade.java
usr/share/java/bbmap/current/clade/CladeContext.class
usr/share/java/bbmap/current/clade/CladeContext.java
usr/share/java/bbmap/current/clade/CladeIndex.class
usr/share/java/bbmap/current/clade/CladeIndex.java
usr/share/java/bbmap/current/clade/CladeLoader$ProcessThread.class
usr/share/java/bbmap/current/clade/CladeLoader.class
usr/share/java/bbmap/current/clade/CladeLoader.java
usr/share/java/bbmap/current/clade/CladeLoaderMF$ProcessThread.class
usr/share/java/bbmap/current/clade/CladeLoaderMF.class
usr/share/java/bbmap/current/clade/CladeLoaderMF.java
usr/share/java/bbmap/current/clade/CladeObject.class
usr/share/java/bbmap/current/clade/CladeObject.java
usr/share/java/bbmap/current/clade/CladeSearcher$ProcessThread.class
usr/share/java/bbmap/current/clade/CladeSearcher.class
usr/share/java/bbmap/current/clade/CladeSearcher.java
usr/share/java/bbmap/current/clade/CladeServer$CladeClassificationHandler.class
usr/share/java/bbmap/current/clade/CladeServer$CompareSSUHandler.class
usr/share/java/bbmap/current/clade/CladeServer$FetchCladeHandler.class
usr/share/java/bbmap/current/clade/CladeServer$FetchSSUHandler.class
usr/share/java/bbmap/current/clade/CladeServer$IconHandler.class
usr/share/java/bbmap/current/clade/CladeServer$KillHandler.class
usr/share/java/bbmap/current/clade/CladeServer$StatsHandler.class
usr/share/java/bbmap/current/clade/CladeServer$UniversalHandler.class
usr/share/java/bbmap/current/clade/CladeServer.class
usr/share/java/bbmap/current/clade/CladeServer.java
usr/share/java/bbmap/current/clade/Comparison.class
usr/share/java/bbmap/current/clade/Comparison.java
usr/share/java/bbmap/current/clade/ComparisonHeap$WorstFirstComparator.class
usr/share/java/bbmap/current/clade/ComparisonHeap.class
usr/share/java/bbmap/current/clade/ComparisonHeap.java
usr/share/java/bbmap/current/clade/Organism.class
usr/share/java/bbmap/current/clade/Organism.java
usr/share/java/bbmap/current/clade/PreClade.class
usr/share/java/bbmap/current/clade/PreClade.java
usr/share/java/bbmap/current/clade/SendClade.class
usr/share/java/bbmap/current/clade/SendClade.java
usr/share/java/bbmap/current/clade/SeqIndex.class
usr/share/java/bbmap/current/clade/SeqIndex.java
usr/share/java/bbmap/current/clade/SeqIndexResult.class
usr/share/java/bbmap/current/clade/SeqIndexResult.java
usr/share/java/bbmap/current/clade/Sequence.class
usr/share/java/bbmap/current/clade/Sequence.java
usr/share/java/bbmap/current/clump/
usr/share/java/bbmap/current/clump/Clump.class
usr/share/java/bbmap/current/clump/Clump.java
usr/share/java/bbmap/current/clump/ClumpList$ClumpThread.class
usr/share/java/bbmap/current/clump/ClumpList$ProcessThread.class
usr/share/java/bbmap/current/clump/ClumpList.class
usr/share/java/bbmap/current/clump/ClumpList.java
usr/share/java/bbmap/current/clump/ClumpTools.class
usr/share/java/bbmap/current/clump/ClumpTools.java
usr/share/java/bbmap/current/clump/Clumpify.class
usr/share/java/bbmap/current/clump/Clumpify.java
usr/share/java/bbmap/current/clump/Hasher.class
usr/share/java/bbmap/current/clump/Hasher.java
usr/share/java/bbmap/current/clump/KmerComparator$HashThread.class
usr/share/java/bbmap/current/clump/KmerComparator.class
usr/share/java/bbmap/current/clump/KmerComparator.java
usr/share/java/bbmap/current/clump/KmerComparator2.class
usr/share/java/bbmap/current/clump/KmerComparator2.java
usr/share/java/bbmap/current/clump/KmerComparatorX.class
usr/share/java/bbmap/current/clump/KmerComparatorX.java
usr/share/java/bbmap/current/clump/KmerComparatorY.class
usr/share/java/bbmap/current/clump/KmerComparatorY.java
usr/share/java/bbmap/current/clump/KmerReduce$HashThread.class
usr/share/java/bbmap/current/clump/KmerReduce.class
usr/share/java/bbmap/current/clump/KmerReduce.java
usr/share/java/bbmap/current/clump/KmerSort$FetchThread1.class
usr/share/java/bbmap/current/clump/KmerSort$HashSplitThread.class
usr/share/java/bbmap/current/clump/KmerSort.class
usr/share/java/bbmap/current/clump/KmerSort.java
usr/share/java/bbmap/current/clump/KmerSort1.class
usr/share/java/bbmap/current/clump/KmerSort1.java
usr/share/java/bbmap/current/clump/KmerSort2.class
usr/share/java/bbmap/current/clump/KmerSort2.java
usr/share/java/bbmap/current/clump/KmerSort3$FetchThread3$FetchSubThread.class
usr/share/java/bbmap/current/clump/KmerSort3$FetchThread3.class
usr/share/java/bbmap/current/clump/KmerSort3.class
usr/share/java/bbmap/current/clump/KmerSort3.java
usr/share/java/bbmap/current/clump/KmerSplit$HashThread.class
usr/share/java/bbmap/current/clump/KmerSplit.class
usr/share/java/bbmap/current/clump/KmerSplit.java
usr/share/java/bbmap/current/clump/PivotSet$HashThread.class
usr/share/java/bbmap/current/clump/PivotSet.class
usr/share/java/bbmap/current/clump/PivotSet.java
usr/share/java/bbmap/current/clump/README.md
usr/share/java/bbmap/current/clump/ReadKey.class
usr/share/java/bbmap/current/clump/ReadKey.java
usr/share/java/bbmap/current/clump/Splitter.class
usr/share/java/bbmap/current/clump/Splitter.java
usr/share/java/bbmap/current/clump/StreamToOutput.class
usr/share/java/bbmap/current/clump/StreamToOutput.java
usr/share/java/bbmap/current/cluster/
usr/share/java/bbmap/current/cluster/Cluster.class
usr/share/java/bbmap/current/cluster/Cluster.java
usr/share/java/bbmap/current/cluster/ClusterTools.class
usr/share/java/bbmap/current/cluster/ClusterTools.java
usr/share/java/bbmap/current/cluster/MergeReadHeaders.class
usr/share/java/bbmap/current/cluster/MergeReadHeaders.java
usr/share/java/bbmap/current/cluster/README.md
usr/share/java/bbmap/current/cluster/ReadTag.class
usr/share/java/bbmap/current/cluster/ReadTag.java
usr/share/java/bbmap/current/cluster/ReclusterByKmer$ClusterThread.class
usr/share/java/bbmap/current/cluster/ReclusterByKmer.class
usr/share/java/bbmap/current/cluster/ReclusterByKmer.java
usr/share/java/bbmap/current/consensus/
usr/share/java/bbmap/current/consensus/BaseGraph.class
usr/share/java/bbmap/current/consensus/BaseGraph.java
usr/share/java/bbmap/current/consensus/BaseGraphPart.class
usr/share/java/bbmap/current/consensus/BaseGraphPart.java
usr/share/java/bbmap/current/consensus/BaseNode.class
usr/share/java/bbmap/current/consensus/BaseNode.java
usr/share/java/bbmap/current/consensus/ConsensusMaker$ProcessThread.class
usr/share/java/bbmap/current/consensus/ConsensusMaker.class
usr/share/java/bbmap/current/consensus/ConsensusMaker.java
usr/share/java/bbmap/current/consensus/ConsensusObject.class
usr/share/java/bbmap/current/consensus/ConsensusObject.java
usr/share/java/bbmap/current/consensus/FixScaffoldGaps$ProcessThread.class
usr/share/java/bbmap/current/consensus/FixScaffoldGaps$Scaffold.class
usr/share/java/bbmap/current/consensus/FixScaffoldGaps.class
usr/share/java/bbmap/current/consensus/FixScaffoldGaps.java
usr/share/java/bbmap/current/consensus/Lilypad$Contig.class
usr/share/java/bbmap/current/consensus/Lilypad$Edge.class
usr/share/java/bbmap/current/consensus/Lilypad$ProcessThread.class
usr/share/java/bbmap/current/consensus/Lilypad.class
usr/share/java/bbmap/current/consensus/Lilypad.java
usr/share/java/bbmap/current/consensus/README.md
usr/share/java/bbmap/current/covid/
usr/share/java/bbmap/current/covid/README.md
usr/share/java/bbmap/current/covid/SummarizeCoverage.class
usr/share/java/bbmap/current/covid/SummarizeCoverage.java
usr/share/java/bbmap/current/dna/
usr/share/java/bbmap/current/dna/AminoAcid.class
usr/share/java/bbmap/current/dna/AminoAcid.java
usr/share/java/bbmap/current/dna/ChromArrayMaker.class
usr/share/java/bbmap/current/dna/ChromArrayMaker.java
usr/share/java/bbmap/current/dna/ChromToFasta$1.class
usr/share/java/bbmap/current/dna/ChromToFasta.class
usr/share/java/bbmap/current/dna/ChromToFasta.java
usr/share/java/bbmap/current/dna/ChromosomeArray.class
usr/share/java/bbmap/current/dna/ChromosomeArray.java
usr/share/java/bbmap/current/dna/Data.class
usr/share/java/bbmap/current/dna/Data.java
usr/share/java/bbmap/current/dna/Exon.class
usr/share/java/bbmap/current/dna/Exon.java
usr/share/java/bbmap/current/dna/FastaToChromArrays2$1.class
usr/share/java/bbmap/current/dna/FastaToChromArrays2.class
usr/share/java/bbmap/current/dna/FastaToChromArrays2.java
usr/share/java/bbmap/current/dna/Gene.class
usr/share/java/bbmap/current/dna/Gene.java
usr/share/java/bbmap/current/dna/GeneSet.class
usr/share/java/bbmap/current/dna/GeneSet.java
usr/share/java/bbmap/current/dna/Matrix.class
usr/share/java/bbmap/current/dna/Matrix.java
usr/share/java/bbmap/current/dna/Motif.class
usr/share/java/bbmap/current/dna/Motif.java
usr/share/java/bbmap/current/dna/MotifMulti.class
usr/share/java/bbmap/current/dna/MotifMulti.java
usr/share/java/bbmap/current/dna/MotifProbsN.class
usr/share/java/bbmap/current/dna/MotifProbsN.java
usr/share/java/bbmap/current/dna/MotifSimple.class
usr/share/java/bbmap/current/dna/MotifSimple.java
usr/share/java/bbmap/current/dna/README.md
usr/share/java/bbmap/current/dna/ScafLoc.class
usr/share/java/bbmap/current/dna/ScafLoc.java
usr/share/java/bbmap/current/dna/Scaffold.class
usr/share/java/bbmap/current/dna/Scaffold.java
usr/share/java/bbmap/current/driver/
usr/share/java/bbmap/current/driver/BBVersion.class
usr/share/java/bbmap/current/driver/BBVersion.java
usr/share/java/bbmap/current/driver/ClearRam.class
usr/share/java/bbmap/current/driver/ClearRam.java
usr/share/java/bbmap/current/driver/CollateSpikeIn.class
usr/share/java/bbmap/current/driver/CollateSpikeIn.java
usr/share/java/bbmap/current/driver/CompareReferenceGenomes.class
usr/share/java/bbmap/current/driver/CompareReferenceGenomes.java
usr/share/java/bbmap/current/driver/CompareSequences.class
usr/share/java/bbmap/current/driver/CompareSequences.java
usr/share/java/bbmap/current/driver/ConcatenateFiles.class
usr/share/java/bbmap/current/driver/ConcatenateFiles.java
usr/share/java/bbmap/current/driver/ConcatenateTextFiles$1.class
usr/share/java/bbmap/current/driver/ConcatenateTextFiles$WriteThread.class
usr/share/java/bbmap/current/driver/ConcatenateTextFiles.class
usr/share/java/bbmap/current/driver/ConcatenateTextFiles.java
usr/share/java/bbmap/current/driver/Concatenator.class
usr/share/java/bbmap/current/driver/Concatenator.java
usr/share/java/bbmap/current/driver/ConvertSamToAln.class
usr/share/java/bbmap/current/driver/ConvertSamToAln.java
usr/share/java/bbmap/current/driver/CorrelateIdentity.class
usr/share/java/bbmap/current/driver/CorrelateIdentity.java
usr/share/java/bbmap/current/driver/CountRNAs.class
usr/share/java/bbmap/current/driver/CountRNAs.java
usr/share/java/bbmap/current/driver/CountSharedLines.class
usr/share/java/bbmap/current/driver/CountSharedLines.java
usr/share/java/bbmap/current/driver/EstherFilter.class
usr/share/java/bbmap/current/driver/EstherFilter.java
usr/share/java/bbmap/current/driver/FilterAssemblySummary.class
usr/share/java/bbmap/current/driver/FilterAssemblySummary.java
usr/share/java/bbmap/current/driver/FilterLines.class
usr/share/java/bbmap/current/driver/FilterLines.java
usr/share/java/bbmap/current/driver/FilterReadsByName.class
usr/share/java/bbmap/current/driver/FilterReadsByName.java
usr/share/java/bbmap/current/driver/FindMotifs.class
usr/share/java/bbmap/current/driver/FindMotifs.java
usr/share/java/bbmap/current/driver/FixChr.class
usr/share/java/bbmap/current/driver/FixChr.java
usr/share/java/bbmap/current/driver/FixDumbFile.class
usr/share/java/bbmap/current/driver/FixDumbFile.java
usr/share/java/bbmap/current/driver/GenerateNoCallsFromCoverage.class
usr/share/java/bbmap/current/driver/GenerateNoCallsFromCoverage.java
usr/share/java/bbmap/current/driver/GetSequence.class
usr/share/java/bbmap/current/driver/GetSequence.java
usr/share/java/bbmap/current/driver/GetUniquePrefixes.class
usr/share/java/bbmap/current/driver/GetUniquePrefixes.java
usr/share/java/bbmap/current/driver/Grep.class
usr/share/java/bbmap/current/driver/Grep.java
usr/share/java/bbmap/current/driver/Life.class
usr/share/java/bbmap/current/driver/Life.java
usr/share/java/bbmap/current/driver/LineCount.class
usr/share/java/bbmap/current/driver/LineCount.java
usr/share/java/bbmap/current/driver/LoadReads.class
usr/share/java/bbmap/current/driver/LoadReads.java
usr/share/java/bbmap/current/driver/LookAtID.class
usr/share/java/bbmap/current/driver/LookAtID.java
usr/share/java/bbmap/current/driver/MakeTestScript.class
usr/share/java/bbmap/current/driver/MakeTestScript.java
usr/share/java/bbmap/current/driver/MakeTestScriptScoreOnly.class
usr/share/java/bbmap/current/driver/MakeTestScriptScoreOnly.java
usr/share/java/bbmap/current/driver/MeasureGene.class
usr/share/java/bbmap/current/driver/MeasureGene.java
usr/share/java/bbmap/current/driver/MergeBigelow.class
usr/share/java/bbmap/current/driver/MergeBigelow.java
usr/share/java/bbmap/current/driver/MergeCoverageOTU.class
usr/share/java/bbmap/current/driver/MergeCoverageOTU.java
usr/share/java/bbmap/current/driver/MergeTextFiles.class
usr/share/java/bbmap/current/driver/MergeTextFiles.java
usr/share/java/bbmap/current/driver/MergeTextFiles2.class
usr/share/java/bbmap/current/driver/MergeTextFiles2.java
usr/share/java/bbmap/current/driver/MoveFiles.class
usr/share/java/bbmap/current/driver/MoveFiles.java
usr/share/java/bbmap/current/driver/ParseCrossblockResults$ResultsLine.class
usr/share/java/bbmap/current/driver/ParseCrossblockResults.class
usr/share/java/bbmap/current/driver/ParseCrossblockResults.java
usr/share/java/bbmap/current/driver/PlotGC.class
usr/share/java/bbmap/current/driver/PlotGC.java
usr/share/java/bbmap/current/driver/PrintEnv.class
usr/share/java/bbmap/current/driver/PrintEnv.java
usr/share/java/bbmap/current/driver/ProcessFragMerging.class
usr/share/java/bbmap/current/driver/ProcessFragMerging.java
usr/share/java/bbmap/current/driver/ProcessSpeed.class
usr/share/java/bbmap/current/driver/ProcessSpeed.java
usr/share/java/bbmap/current/driver/ProcessSpeed2.class
usr/share/java/bbmap/current/driver/ProcessSpeed2.java
usr/share/java/bbmap/current/driver/ProcessWebcheck.class
usr/share/java/bbmap/current/driver/ProcessWebcheck.java
usr/share/java/bbmap/current/driver/README.md
usr/share/java/bbmap/current/driver/ReduceSilva.class
usr/share/java/bbmap/current/driver/ReduceSilva.java
usr/share/java/bbmap/current/driver/RenameAndMux$MuxThread.class
usr/share/java/bbmap/current/driver/RenameAndMux.class
usr/share/java/bbmap/current/driver/RenameAndMux.java
usr/share/java/bbmap/current/driver/RenameByHeader.class
usr/share/java/bbmap/current/driver/RenameByHeader.java
usr/share/java/bbmap/current/driver/RenameNcbiToTid.class
usr/share/java/bbmap/current/driver/RenameNcbiToTid.java
usr/share/java/bbmap/current/driver/RenameRefseqFiles.class
usr/share/java/bbmap/current/driver/RenameRefseqFiles.java
usr/share/java/bbmap/current/driver/Sample.class
usr/share/java/bbmap/current/driver/Sample.java
usr/share/java/bbmap/current/driver/Search.class
usr/share/java/bbmap/current/driver/Search.java
usr/share/java/bbmap/current/driver/SelectReads.class
usr/share/java/bbmap/current/driver/SelectReads.java
usr/share/java/bbmap/current/driver/SniffSplices.class
usr/share/java/bbmap/current/driver/SniffSplices.java
usr/share/java/bbmap/current/driver/SummarizeContamReport$ComparatorA.class
usr/share/java/bbmap/current/driver/SummarizeContamReport$ComparatorB.class
usr/share/java/bbmap/current/driver/SummarizeContamReport$StringLongLong.class
usr/share/java/bbmap/current/driver/SummarizeContamReport.class
usr/share/java/bbmap/current/driver/SummarizeContamReport.java
usr/share/java/bbmap/current/driver/SummarizeCoverage.class
usr/share/java/bbmap/current/driver/SummarizeCoverage.java
usr/share/java/bbmap/current/driver/SummarizeCrossblock.class
usr/share/java/bbmap/current/driver/SummarizeCrossblock.java
usr/share/java/bbmap/current/driver/SummarizeMSDIN.class
usr/share/java/bbmap/current/driver/SummarizeMSDIN.java
usr/share/java/bbmap/current/driver/SummarizeQuast$Entry.class
usr/share/java/bbmap/current/driver/SummarizeQuast$QuastSummary.class
usr/share/java/bbmap/current/driver/SummarizeQuast.class
usr/share/java/bbmap/current/driver/SummarizeQuast.java
usr/share/java/bbmap/current/driver/SummarizeSealCrosstalk$Result.class
usr/share/java/bbmap/current/driver/SummarizeSealCrosstalk.class
usr/share/java/bbmap/current/driver/SummarizeSealCrosstalk.java
usr/share/java/bbmap/current/driver/SummarizeSealStats$SealSummary.class
usr/share/java/bbmap/current/driver/SummarizeSealStats.class
usr/share/java/bbmap/current/driver/SummarizeSealStats.java
usr/share/java/bbmap/current/driver/TestCompressionSpeed.class
usr/share/java/bbmap/current/driver/TestCompressionSpeed.java
usr/share/java/bbmap/current/driver/TestLockSpeed$1.class
usr/share/java/bbmap/current/driver/TestLockSpeed$AtomBox.class
usr/share/java/bbmap/current/driver/TestLockSpeed$CountBox.class
usr/share/java/bbmap/current/driver/TestLockSpeed$CountThread.class
usr/share/java/bbmap/current/driver/TestLockSpeed$LockBox.class
usr/share/java/bbmap/current/driver/TestLockSpeed$VolatileBox.class
usr/share/java/bbmap/current/driver/TestLockSpeed.class
usr/share/java/bbmap/current/driver/TestLockSpeed.java
usr/share/java/bbmap/current/driver/Translator.class
usr/share/java/bbmap/current/driver/Translator.java
usr/share/java/bbmap/current/driver/Translator2.class
usr/share/java/bbmap/current/driver/Translator2.java
usr/share/java/bbmap/current/driver/TransposeTextFile.class
usr/share/java/bbmap/current/driver/TransposeTextFile.java
usr/share/java/bbmap/current/driver/TrimSamFile.class
usr/share/java/bbmap/current/driver/TrimSamFile.java
usr/share/java/bbmap/current/fileIO/
usr/share/java/bbmap/current/fileIO/ArrayFile.class
usr/share/java/bbmap/current/fileIO/ArrayFile.java
usr/share/java/bbmap/current/fileIO/ByteFile.class
usr/share/java/bbmap/current/fileIO/ByteFile.java
usr/share/java/bbmap/current/fileIO/ByteFile1.class
usr/share/java/bbmap/current/fileIO/ByteFile1.java
usr/share/java/bbmap/current/fileIO/ByteFile1F.class
usr/share/java/bbmap/current/fileIO/ByteFile1F.java
usr/share/java/bbmap/current/fileIO/ByteFile1Fc.class
usr/share/java/bbmap/current/fileIO/ByteFile1Fc.java
usr/share/java/bbmap/current/fileIO/ByteFile1old.class
usr/share/java/bbmap/current/fileIO/ByteFile1old.java
usr/share/java/bbmap/current/fileIO/ByteFile2$BF1Thread.class
usr/share/java/bbmap/current/fileIO/ByteFile2.class
usr/share/java/bbmap/current/fileIO/ByteFile2.java
usr/share/java/bbmap/current/fileIO/ByteFile3$BufferJob.class
usr/share/java/bbmap/current/fileIO/ByteFile3$ProcessThread.class
usr/share/java/bbmap/current/fileIO/ByteFile3.class
usr/share/java/bbmap/current/fileIO/ByteFile3.java
usr/share/java/bbmap/current/fileIO/ByteFile4$BufferJob.class
usr/share/java/bbmap/current/fileIO/ByteFile4$ProcessThread.class
usr/share/java/bbmap/current/fileIO/ByteFile4.class
usr/share/java/bbmap/current/fileIO/ByteFile4.java
usr/share/java/bbmap/current/fileIO/ByteStreamWriter.class
usr/share/java/bbmap/current/fileIO/ByteStreamWriter.java
usr/share/java/bbmap/current/fileIO/ChainBlock.class
usr/share/java/bbmap/current/fileIO/ChainBlock.java
usr/share/java/bbmap/current/fileIO/ChainLine.class
usr/share/java/bbmap/current/fileIO/ChainLine.java
usr/share/java/bbmap/current/fileIO/CompressFiles.class
usr/share/java/bbmap/current/fileIO/CompressFiles.java
usr/share/java/bbmap/current/fileIO/Concatenate.class
usr/share/java/bbmap/current/fileIO/Concatenate.java
usr/share/java/bbmap/current/fileIO/Concatenate2.class
usr/share/java/bbmap/current/fileIO/Concatenate2.java
usr/share/java/bbmap/current/fileIO/CopyFile$1.class
usr/share/java/bbmap/current/fileIO/CopyFile.class
usr/share/java/bbmap/current/fileIO/CopyFile.java
usr/share/java/bbmap/current/fileIO/CopyFiles.class
usr/share/java/bbmap/current/fileIO/CopyFiles.java
usr/share/java/bbmap/current/fileIO/CopyFiles2.class
usr/share/java/bbmap/current/fileIO/CopyFiles2.java
usr/share/java/bbmap/current/fileIO/FileFormat.class
usr/share/java/bbmap/current/fileIO/FileFormat.java
usr/share/java/bbmap/current/fileIO/FindFiles.class
usr/share/java/bbmap/current/fileIO/FindFiles.java
usr/share/java/bbmap/current/fileIO/GenericTextFile.class
usr/share/java/bbmap/current/fileIO/GenericTextFile.java
usr/share/java/bbmap/current/fileIO/LoadThread.class
usr/share/java/bbmap/current/fileIO/LoadThread.java
usr/share/java/bbmap/current/fileIO/MatrixFile.class
usr/share/java/bbmap/current/fileIO/MatrixFile.java
usr/share/java/bbmap/current/fileIO/OpenFile.class
usr/share/java/bbmap/current/fileIO/OpenFile.java
usr/share/java/bbmap/current/fileIO/PipeThread.class
usr/share/java/bbmap/current/fileIO/PipeThread.java
usr/share/java/bbmap/current/fileIO/QuickFile.class
usr/share/java/bbmap/current/fileIO/QuickFile.java
usr/share/java/bbmap/current/fileIO/README.md
usr/share/java/bbmap/current/fileIO/ReadWrite$1.class
usr/share/java/bbmap/current/fileIO/ReadWrite$WriteObjectThread.class
usr/share/java/bbmap/current/fileIO/ReadWrite$WriteStringThread.class
usr/share/java/bbmap/current/fileIO/ReadWrite.class
usr/share/java/bbmap/current/fileIO/ReadWrite.java
usr/share/java/bbmap/current/fileIO/SummaryFile$1.class
usr/share/java/bbmap/current/fileIO/SummaryFile.class
usr/share/java/bbmap/current/fileIO/SummaryFile.java
usr/share/java/bbmap/current/fileIO/TextFile.class
usr/share/java/bbmap/current/fileIO/TextFile.java
usr/share/java/bbmap/current/fileIO/TextStreamWriter.class
usr/share/java/bbmap/current/fileIO/TextStreamWriter.java
usr/share/java/bbmap/current/fun/
usr/share/java/bbmap/current/fun/BenchIntAppend2.class
usr/share/java/bbmap/current/fun/BenchIntAppend2.java
usr/share/java/bbmap/current/fun/BenchLongAppend.class
usr/share/java/bbmap/current/fun/BenchLongAppend.java
usr/share/java/bbmap/current/fun/BenchStringAppend.class
usr/share/java/bbmap/current/fun/BenchStringAppend.java
usr/share/java/bbmap/current/fun/BenchStringAppend2.class
usr/share/java/bbmap/current/fun/BenchStringAppend2.java
usr/share/java/bbmap/current/fun/BenchmarkA48.class
usr/share/java/bbmap/current/fun/BenchmarkA48.java
usr/share/java/bbmap/current/fun/BenchmarkIntAppend.class
usr/share/java/bbmap/current/fun/BenchmarkIntAppend.java
usr/share/java/bbmap/current/fun/BenchmarkReverse.class
usr/share/java/bbmap/current/fun/BenchmarkReverse.java
usr/share/java/bbmap/current/fun/ByteVectorBench.class
usr/share/java/bbmap/current/fun/ByteVectorBench.java
usr/share/java/bbmap/current/fun/Calc.class
usr/share/java/bbmap/current/fun/Calc.java
usr/share/java/bbmap/current/fun/Chance.class
usr/share/java/bbmap/current/fun/Chance.java
usr/share/java/bbmap/current/fun/Crunch.class
usr/share/java/bbmap/current/fun/Crunch.java
usr/share/java/bbmap/current/fun/DiskBench$ReadThread.class
usr/share/java/bbmap/current/fun/DiskBench$WriteThread.class
usr/share/java/bbmap/current/fun/DiskBench.class
usr/share/java/bbmap/current/fun/DiskBench.java
usr/share/java/bbmap/current/fun/DiskSpaceAnalyzer$1.class
usr/share/java/bbmap/current/fun/DiskSpaceAnalyzer$2.class
usr/share/java/bbmap/current/fun/DiskSpaceAnalyzer$DirSize.class
usr/share/java/bbmap/current/fun/DiskSpaceAnalyzer.class
usr/share/java/bbmap/current/fun/DiskSpaceAnalyzer.java
usr/share/java/bbmap/current/fun/Dongle.class
usr/share/java/bbmap/current/fun/Dongle.java
usr/share/java/bbmap/current/fun/FindPath$Edge.class
usr/share/java/bbmap/current/fun/FindPath$Node.class
usr/share/java/bbmap/current/fun/FindPath$Path.class
usr/share/java/bbmap/current/fun/FindPath.class
usr/share/java/bbmap/current/fun/FindPath.java
usr/share/java/bbmap/current/fun/Foo.class
usr/share/java/bbmap/current/fun/Foo.java
usr/share/java/bbmap/current/fun/Foo2.class
usr/share/java/bbmap/current/fun/Foo2.java
usr/share/java/bbmap/current/fun/Foo3$LongList.class
usr/share/java/bbmap/current/fun/Foo3$Pair.class
usr/share/java/bbmap/current/fun/Foo3.class
usr/share/java/bbmap/current/fun/Foo3.java
usr/share/java/bbmap/current/fun/Foo4$Pair.class
usr/share/java/bbmap/current/fun/Foo4.class
usr/share/java/bbmap/current/fun/Foo4.java
usr/share/java/bbmap/current/fun/Foo5$LongList.class
usr/share/java/bbmap/current/fun/Foo5.class
usr/share/java/bbmap/current/fun/Foo5.java
usr/share/java/bbmap/current/fun/Foo6.class
usr/share/java/bbmap/current/fun/Foo6.java
usr/share/java/bbmap/current/fun/Foo7.class
usr/share/java/bbmap/current/fun/Foo7.java
usr/share/java/bbmap/current/fun/Genetic$Bug.class
usr/share/java/bbmap/current/fun/Genetic.class
usr/share/java/bbmap/current/fun/Genetic.java
usr/share/java/bbmap/current/fun/Life.class
usr/share/java/bbmap/current/fun/Life.java
usr/share/java/bbmap/current/fun/MakeAdjacencyList$1.class
usr/share/java/bbmap/current/fun/MakeAdjacencyList.class
usr/share/java/bbmap/current/fun/MakeAdjacencyList.java
usr/share/java/bbmap/current/fun/Merced$Person.class
usr/share/java/bbmap/current/fun/Merced.class
usr/share/java/bbmap/current/fun/Merced.java
usr/share/java/bbmap/current/fun/PalSim.class
usr/share/java/bbmap/current/fun/PalSim.java
usr/share/java/bbmap/current/fun/Palindrome.class
usr/share/java/bbmap/current/fun/Palindrome.java
usr/share/java/bbmap/current/fun/Palindrome2$Drome.class
usr/share/java/bbmap/current/fun/Palindrome2.class
usr/share/java/bbmap/current/fun/Palindrome2.java
usr/share/java/bbmap/current/fun/ParseDouble.class
usr/share/java/bbmap/current/fun/ParseDouble.java
usr/share/java/bbmap/current/fun/ProbShared.class
usr/share/java/bbmap/current/fun/ProbShared.java
usr/share/java/bbmap/current/fun/ProbShared2.class
usr/share/java/bbmap/current/fun/ProbShared2.java
usr/share/java/bbmap/current/fun/ProbShared3.class
usr/share/java/bbmap/current/fun/ProbShared3.java
usr/share/java/bbmap/current/fun/README.md
usr/share/java/bbmap/current/gff/
usr/share/java/bbmap/current/gff/CompareGff.class
usr/share/java/bbmap/current/gff/CompareGff.java
usr/share/java/bbmap/current/gff/CutGff$ProcessThread.class
usr/share/java/bbmap/current/gff/CutGff.class
usr/share/java/bbmap/current/gff/CutGff.java
usr/share/java/bbmap/current/gff/CutGff_ST.class
usr/share/java/bbmap/current/gff/CutGff_ST.java
usr/share/java/bbmap/current/gff/GbffFeature.class
usr/share/java/bbmap/current/gff/GbffFeature.java
usr/share/java/bbmap/current/gff/GbffFile.class
usr/share/java/bbmap/current/gff/GbffFile.java
usr/share/java/bbmap/current/gff/GbffLocus.class
usr/share/java/bbmap/current/gff/GbffLocus.java
usr/share/java/bbmap/current/gff/GffLine.class
usr/share/java/bbmap/current/gff/GffLine.java
usr/share/java/bbmap/current/gff/GtfLine.class
usr/share/java/bbmap/current/gff/GtfLine.java
usr/share/java/bbmap/current/gff/ParseCrispr.class
usr/share/java/bbmap/current/gff/ParseCrispr.java
usr/share/java/bbmap/current/gff/README.md
usr/share/java/bbmap/current/gff/VcfToGff$1.class
usr/share/java/bbmap/current/gff/VcfToGff.class
usr/share/java/bbmap/current/gff/VcfToGff.java
usr/share/java/bbmap/current/hiseq/
usr/share/java/bbmap/current/hiseq/AnalyzeFlowCell$ProcessThread.class
usr/share/java/bbmap/current/hiseq/AnalyzeFlowCell.class
usr/share/java/bbmap/current/hiseq/AnalyzeFlowCell.java
usr/share/java/bbmap/current/hiseq/BGI2Illumina.class
usr/share/java/bbmap/current/hiseq/BGI2Illumina.java
usr/share/java/bbmap/current/hiseq/BGIHeaderParser.class
usr/share/java/bbmap/current/hiseq/BGIHeaderParser.java
usr/share/java/bbmap/current/hiseq/BGIHeaderParser2.class
usr/share/java/bbmap/current/hiseq/BGIHeaderParser2.java
usr/share/java/bbmap/current/hiseq/CycleTracker.class
usr/share/java/bbmap/current/hiseq/CycleTracker.java
usr/share/java/bbmap/current/hiseq/FlowCell.class
usr/share/java/bbmap/current/hiseq/FlowCell.java
usr/share/java/bbmap/current/hiseq/FlowcellCoordinate.class
usr/share/java/bbmap/current/hiseq/FlowcellCoordinate.java
usr/share/java/bbmap/current/hiseq/IlluminaHeaderParser1.class
usr/share/java/bbmap/current/hiseq/IlluminaHeaderParser1.java
usr/share/java/bbmap/current/hiseq/IlluminaHeaderParser2.class
usr/share/java/bbmap/current/hiseq/IlluminaHeaderParser2.java
usr/share/java/bbmap/current/hiseq/Lane$TileIterator.class
usr/share/java/bbmap/current/hiseq/Lane.class
usr/share/java/bbmap/current/hiseq/Lane.java
usr/share/java/bbmap/current/hiseq/MicroTile.class
usr/share/java/bbmap/current/hiseq/MicroTile.java
usr/share/java/bbmap/current/hiseq/PlotFlowCell$WorkerThread.class
usr/share/java/bbmap/current/hiseq/PlotFlowCell.class
usr/share/java/bbmap/current/hiseq/PlotFlowCell.java
usr/share/java/bbmap/current/hiseq/PlotHist.class
usr/share/java/bbmap/current/hiseq/PlotHist.java
usr/share/java/bbmap/current/hiseq/PlotReadPosition.class
usr/share/java/bbmap/current/hiseq/PlotReadPosition.java
usr/share/java/bbmap/current/hiseq/README.md
usr/share/java/bbmap/current/hiseq/ReadHeaderParser.class
usr/share/java/bbmap/current/hiseq/ReadHeaderParser.java
usr/share/java/bbmap/current/hiseq/Tile.class
usr/share/java/bbmap/current/hiseq/Tile.java
usr/share/java/bbmap/current/hiseq/TileDump.class
usr/share/java/bbmap/current/hiseq/TileDump.java
usr/share/java/bbmap/current/hmm/
usr/share/java/bbmap/current/hmm/HMMSearchLine.class
usr/share/java/bbmap/current/hmm/HMMSearchLine.java
usr/share/java/bbmap/current/hmm/HMMSearchReport.class
usr/share/java/bbmap/current/hmm/HMMSearchReport.java
usr/share/java/bbmap/current/hmm/ProteinSummary.class
usr/share/java/bbmap/current/hmm/ProteinSummary.java
usr/share/java/bbmap/current/hmm/README.md
usr/share/java/bbmap/current/icecream/
usr/share/java/bbmap/current/icecream/IceCreamAligner.class
usr/share/java/bbmap/current/icecream/IceCreamAligner.java
usr/share/java/bbmap/current/icecream/IceCreamAlignerJNI.class
usr/share/java/bbmap/current/icecream/IceCreamAlignerJNI.java
usr/share/java/bbmap/current/icecream/IceCreamAlignerJava.class
usr/share/java/bbmap/current/icecream/IceCreamAlignerJava.java
usr/share/java/bbmap/current/icecream/IceCreamFinder$ProcessThread.class
usr/share/java/bbmap/current/icecream/IceCreamFinder.class
usr/share/java/bbmap/current/icecream/IceCreamFinder.java
usr/share/java/bbmap/current/icecream/IceCreamGrader.class
usr/share/java/bbmap/current/icecream/IceCreamGrader.java
usr/share/java/bbmap/current/icecream/IceCreamMaker$ProcessThread.class
usr/share/java/bbmap/current/icecream/IceCreamMaker.class
usr/share/java/bbmap/current/icecream/IceCreamMaker.java
usr/share/java/bbmap/current/icecream/PBHeader.class
usr/share/java/bbmap/current/icecream/PBHeader.java
usr/share/java/bbmap/current/icecream/PolymerTrimmer.class
usr/share/java/bbmap/current/icecream/PolymerTrimmer.java
usr/share/java/bbmap/current/icecream/README.md
usr/share/java/bbmap/current/icecream/ReadBuilder.class
usr/share/java/bbmap/current/icecream/ReadBuilder.java
usr/share/java/bbmap/current/icecream/ReformatPacBio$ProcessThread.class
usr/share/java/bbmap/current/icecream/ReformatPacBio.class
usr/share/java/bbmap/current/icecream/ReformatPacBio.java
usr/share/java/bbmap/current/icecream/ZMW.class
usr/share/java/bbmap/current/icecream/ZMW.java
usr/share/java/bbmap/current/icecream/ZMWStreamer.class
usr/share/java/bbmap/current/icecream/ZMWStreamer.java
usr/share/java/bbmap/current/illumina/
usr/share/java/bbmap/current/illumina/Cbcl2Text.class
usr/share/java/bbmap/current/illumina/Cbcl2Text.java
usr/share/java/bbmap/current/illumina/CbclDecoder.class
usr/share/java/bbmap/current/illumina/CbclDecoder.java
usr/share/java/bbmap/current/illumina/CbclHeader.class
usr/share/java/bbmap/current/illumina/CbclHeader.java
usr/share/java/bbmap/current/illumina/CbclInspector.class
usr/share/java/bbmap/current/illumina/CbclInspector.java
usr/share/java/bbmap/current/illumina/ClusterData.class
usr/share/java/bbmap/current/illumina/ClusterData.java
usr/share/java/bbmap/current/illumina/FilterReader.class
usr/share/java/bbmap/current/illumina/FilterReader.java
usr/share/java/bbmap/current/illumina/LocsReader.class
usr/share/java/bbmap/current/illumina/LocsReader.java
usr/share/java/bbmap/current/illumina/RunInfoParser.class
usr/share/java/bbmap/current/illumina/RunInfoParser.java
usr/share/java/bbmap/current/jasper/
usr/share/java/bbmap/current/jasper/KmerPosition.class
usr/share/java/bbmap/current/jasper/KmerPosition.java
usr/share/java/bbmap/current/jasper/KmerPosition3.class
usr/share/java/bbmap/current/jasper/KmerPosition3.java
usr/share/java/bbmap/current/jasper/README.md
usr/share/java/bbmap/current/jgi/
usr/share/java/bbmap/current/jgi/AddAdapters.class
usr/share/java/bbmap/current/jgi/AddAdapters.java
usr/share/java/bbmap/current/jgi/AdjustHomopolymers.class
usr/share/java/bbmap/current/jgi/AdjustHomopolymers.java
usr/share/java/bbmap/current/jgi/Assembly.class
usr/share/java/bbmap/current/jgi/Assembly.java
usr/share/java/bbmap/current/jgi/AssemblyStats2$Triple.class
usr/share/java/bbmap/current/jgi/AssemblyStats2.class
usr/share/java/bbmap/current/jgi/AssemblyStats2.java
usr/share/java/bbmap/current/jgi/AssemblyStats3.class
usr/share/java/bbmap/current/jgi/AssemblyStats3.java
usr/share/java/bbmap/current/jgi/AssemblyStatsWrapper.class
usr/share/java/bbmap/current/jgi/AssemblyStatsWrapper.java
usr/share/java/bbmap/current/jgi/BBDuk$LoadThread.class
usr/share/java/bbmap/current/jgi/BBDuk$ProcessThread.class
usr/share/java/bbmap/current/jgi/BBDuk.class
usr/share/java/bbmap/current/jgi/BBDuk.java
usr/share/java/bbmap/current/jgi/BBMask$MaskLowEntropyThread.class
usr/share/java/bbmap/current/jgi/BBMask$MaskRepeatThread.class
usr/share/java/bbmap/current/jgi/BBMask$MaskSamThread.class
usr/share/java/bbmap/current/jgi/BBMask.class
usr/share/java/bbmap/current/jgi/BBMask.java
usr/share/java/bbmap/current/jgi/BBMerge$MateThread.class
usr/share/java/bbmap/current/jgi/BBMerge.class
usr/share/java/bbmap/current/jgi/BBMerge.java
usr/share/java/bbmap/current/jgi/BBMergeOverlapper.class
usr/share/java/bbmap/current/jgi/BBMergeOverlapper.java
usr/share/java/bbmap/current/jgi/BBQC.class
usr/share/java/bbmap/current/jgi/BBQC.java
usr/share/java/bbmap/current/jgi/CalcTrueQuality$CountMatrixSet.class
usr/share/java/bbmap/current/jgi/CalcTrueQuality$GBMatrixSet.class
usr/share/java/bbmap/current/jgi/CalcTrueQuality$Worker.class
usr/share/java/bbmap/current/jgi/CalcTrueQuality.class
usr/share/java/bbmap/current/jgi/CalcTrueQuality.java
usr/share/java/bbmap/current/jgi/CalcUniqueness$Counter.class
usr/share/java/bbmap/current/jgi/CalcUniqueness.class
usr/share/java/bbmap/current/jgi/CalcUniqueness.java
usr/share/java/bbmap/current/jgi/CallPeaks$Peak.class
usr/share/java/bbmap/current/jgi/CallPeaks.class
usr/share/java/bbmap/current/jgi/CallPeaks.java
usr/share/java/bbmap/current/jgi/CheckStrand.class
usr/share/java/bbmap/current/jgi/CheckStrand.java
usr/share/java/bbmap/current/jgi/CheckStrand2$ProcessThread.class
usr/share/java/bbmap/current/jgi/CheckStrand2$Seq.class
usr/share/java/bbmap/current/jgi/CheckStrand2.class
usr/share/java/bbmap/current/jgi/CheckStrand2.java
usr/share/java/bbmap/current/jgi/CheckStrand3$ProcessThread.class
usr/share/java/bbmap/current/jgi/CheckStrand3$Seq.class
usr/share/java/bbmap/current/jgi/CheckStrand3.class
usr/share/java/bbmap/current/jgi/CheckStrand3.java
usr/share/java/bbmap/current/jgi/Consect.class
usr/share/java/bbmap/current/jgi/Consect.java
usr/share/java/bbmap/current/jgi/CountDuplicates$ProcessThread.class
usr/share/java/bbmap/current/jgi/CountDuplicates.class
usr/share/java/bbmap/current/jgi/CountDuplicates.java
usr/share/java/bbmap/current/jgi/CountDuplicatesBuffered$ProcessThread.class
usr/share/java/bbmap/current/jgi/CountDuplicatesBuffered.class
usr/share/java/bbmap/current/jgi/CountDuplicatesBuffered.java
usr/share/java/bbmap/current/jgi/CountGC$1.class
usr/share/java/bbmap/current/jgi/CountGC.class
usr/share/java/bbmap/current/jgi/CountGC.java
usr/share/java/bbmap/current/jgi/CountUniqueness.class
usr/share/java/bbmap/current/jgi/CountUniqueness.java
usr/share/java/bbmap/current/jgi/CovStatsLine.class
usr/share/java/bbmap/current/jgi/CovStatsLine.java
usr/share/java/bbmap/current/jgi/CoveragePileup.class
usr/share/java/bbmap/current/jgi/CoveragePileup.java
usr/share/java/bbmap/current/jgi/CoveragePileupMT$LoadThread.class
usr/share/java/bbmap/current/jgi/CoveragePileupMT.class
usr/share/java/bbmap/current/jgi/CoveragePileupMT.java
usr/share/java/bbmap/current/jgi/CrisprFinder$1.class
usr/share/java/bbmap/current/jgi/CrisprFinder$Alignment.class
usr/share/java/bbmap/current/jgi/CrisprFinder$ProcessThread.class
usr/share/java/bbmap/current/jgi/CrisprFinder.class
usr/share/java/bbmap/current/jgi/CrisprFinder.java
usr/share/java/bbmap/current/jgi/CutPrimers.class
usr/share/java/bbmap/current/jgi/CutPrimers.java
usr/share/java/bbmap/current/jgi/DecontaminateByNormalization.class
usr/share/java/bbmap/current/jgi/DecontaminateByNormalization.java
usr/share/java/bbmap/current/jgi/Dedupe$ClusterLengthComparator.class
usr/share/java/bbmap/current/jgi/Dedupe$ClusterThread.class
usr/share/java/bbmap/current/jgi/Dedupe$HashThread.class
usr/share/java/bbmap/current/jgi/Dedupe$MstThread.class
usr/share/java/bbmap/current/jgi/Dedupe$Overlap.class
usr/share/java/bbmap/current/jgi/Dedupe$Unit.class
usr/share/java/bbmap/current/jgi/Dedupe$UnitOffsetComparator.class
usr/share/java/bbmap/current/jgi/Dedupe.class
usr/share/java/bbmap/current/jgi/Dedupe.java
usr/share/java/bbmap/current/jgi/Dedupe2$ClusterLengthComparator.class
usr/share/java/bbmap/current/jgi/Dedupe2$ClusterThread.class
usr/share/java/bbmap/current/jgi/Dedupe2$HashThread.class
usr/share/java/bbmap/current/jgi/Dedupe2$MstThread.class
usr/share/java/bbmap/current/jgi/Dedupe2$Overlap.class
usr/share/java/bbmap/current/jgi/Dedupe2$Unit.class
usr/share/java/bbmap/current/jgi/Dedupe2$UnitOffsetComparator.class
usr/share/java/bbmap/current/jgi/Dedupe2.class
usr/share/java/bbmap/current/jgi/Dedupe2.java
usr/share/java/bbmap/current/jgi/DedupeByMapping$Quad.class
usr/share/java/bbmap/current/jgi/DedupeByMapping.class
usr/share/java/bbmap/current/jgi/DedupeByMapping.java
usr/share/java/bbmap/current/jgi/DedupeProtein$ClusterLengthComparator.class
usr/share/java/bbmap/current/jgi/DedupeProtein$ClusterThread.class
usr/share/java/bbmap/current/jgi/DedupeProtein$HashThread.class
usr/share/java/bbmap/current/jgi/DedupeProtein$MstThread.class
usr/share/java/bbmap/current/jgi/DedupeProtein$Overlap.class
usr/share/java/bbmap/current/jgi/DedupeProtein$Unit.class
usr/share/java/bbmap/current/jgi/DedupeProtein$UnitOffsetComparator.class
usr/share/java/bbmap/current/jgi/DedupeProtein.class
usr/share/java/bbmap/current/jgi/DedupeProtein.java
usr/share/java/bbmap/current/jgi/DemuxByName.class
usr/share/java/bbmap/current/jgi/DemuxByName.java
usr/share/java/bbmap/current/jgi/DemuxByName2.class
usr/share/java/bbmap/current/jgi/DemuxByName2.java
usr/share/java/bbmap/current/jgi/Difference.class
usr/share/java/bbmap/current/jgi/Difference.java
usr/share/java/bbmap/current/jgi/FilterByCoverage.class
usr/share/java/bbmap/current/jgi/FilterByCoverage.java
usr/share/java/bbmap/current/jgi/FilterBySequence$Code.class
usr/share/java/bbmap/current/jgi/FilterBySequence$LoadThread.class
usr/share/java/bbmap/current/jgi/FilterBySequence$ProcessThread.class
usr/share/java/bbmap/current/jgi/FilterBySequence.class
usr/share/java/bbmap/current/jgi/FilterBySequence.java
usr/share/java/bbmap/current/jgi/FilterReadsWithSubs.class
usr/share/java/bbmap/current/jgi/FilterReadsWithSubs.java
usr/share/java/bbmap/current/jgi/FindHiCJunctions.class
usr/share/java/bbmap/current/jgi/FindHiCJunctions.java
usr/share/java/bbmap/current/jgi/FindPrimers$ProcessThread.class
usr/share/java/bbmap/current/jgi/FindPrimers.class
usr/share/java/bbmap/current/jgi/FindPrimers.java
usr/share/java/bbmap/current/jgi/FindString.class
usr/share/java/bbmap/current/jgi/FindString.java
usr/share/java/bbmap/current/jgi/FungalRelease.class
usr/share/java/bbmap/current/jgi/FungalRelease.java
usr/share/java/bbmap/current/jgi/GatherKapaStats$KapaEntry.class
usr/share/java/bbmap/current/jgi/GatherKapaStats$Plate.class
usr/share/java/bbmap/current/jgi/GatherKapaStats$TagData.class
usr/share/java/bbmap/current/jgi/GatherKapaStats$Well.class
usr/share/java/bbmap/current/jgi/GatherKapaStats.class
usr/share/java/bbmap/current/jgi/GatherKapaStats.java
usr/share/java/bbmap/current/jgi/GetReads.class
usr/share/java/bbmap/current/jgi/GetReads.java
usr/share/java/bbmap/current/jgi/GradeMergedReads.class
usr/share/java/bbmap/current/jgi/GradeMergedReads.java
usr/share/java/bbmap/current/jgi/GreedyBarCodeFinder.class
usr/share/java/bbmap/current/jgi/GreedyBarCodeFinder.java
usr/share/java/bbmap/current/jgi/IdentityMatrix$ProcessThread.class
usr/share/java/bbmap/current/jgi/IdentityMatrix.class
usr/share/java/bbmap/current/jgi/IdentityMatrix.java
usr/share/java/bbmap/current/jgi/Info.class
usr/share/java/bbmap/current/jgi/Info.java
usr/share/java/bbmap/current/jgi/KExpand.class
usr/share/java/bbmap/current/jgi/KExpand.java
usr/share/java/bbmap/current/jgi/KeepBestCopy.class
usr/share/java/bbmap/current/jgi/KeepBestCopy.java
usr/share/java/bbmap/current/jgi/KmerCountExact$DumpKmersThread.class
usr/share/java/bbmap/current/jgi/KmerCountExact$MakeKhistThread.class
usr/share/java/bbmap/current/jgi/KmerCountExact.class
usr/share/java/bbmap/current/jgi/KmerCountExact.java
usr/share/java/bbmap/current/jgi/KmerCountMulti$ProcessThread.class
usr/share/java/bbmap/current/jgi/KmerCountMulti.class
usr/share/java/bbmap/current/jgi/KmerCountMulti.java
usr/share/java/bbmap/current/jgi/KmerCountShort$ProcessThread.class
usr/share/java/bbmap/current/jgi/KmerCountShort.class
usr/share/java/bbmap/current/jgi/KmerCountShort.java
usr/share/java/bbmap/current/jgi/KmerCoverage$1.class
usr/share/java/bbmap/current/jgi/KmerCoverage$ProcessThread.class
usr/share/java/bbmap/current/jgi/KmerCoverage.class
usr/share/java/bbmap/current/jgi/KmerCoverage.java
usr/share/java/bbmap/current/jgi/KmerFilterSetMaker.class
usr/share/java/bbmap/current/jgi/KmerFilterSetMaker.java
usr/share/java/bbmap/current/jgi/KmerNormalize$1.class
usr/share/java/bbmap/current/jgi/KmerNormalize$ProcessThread.class
usr/share/java/bbmap/current/jgi/KmerNormalize.class
usr/share/java/bbmap/current/jgi/KmerNormalize.java
usr/share/java/bbmap/current/jgi/KmerSample.class
usr/share/java/bbmap/current/jgi/KmerSample.java
usr/share/java/bbmap/current/jgi/MakeLengthHistogram$1.class
usr/share/java/bbmap/current/jgi/MakeLengthHistogram.class
usr/share/java/bbmap/current/jgi/MakeLengthHistogram.java
usr/share/java/bbmap/current/jgi/MakePolymers.class
usr/share/java/bbmap/current/jgi/MakePolymers.java
usr/share/java/bbmap/current/jgi/MergeBarcodes.class
usr/share/java/bbmap/current/jgi/MergeBarcodes.java
usr/share/java/bbmap/current/jgi/MergeSam.class
usr/share/java/bbmap/current/jgi/MergeSam.java
usr/share/java/bbmap/current/jgi/Orf.class
usr/share/java/bbmap/current/jgi/Orf.java
usr/share/java/bbmap/current/jgi/PartitionReads$Partition.class
usr/share/java/bbmap/current/jgi/PartitionReads.class
usr/share/java/bbmap/current/jgi/PartitionReads.java
usr/share/java/bbmap/current/jgi/PhylipToFasta.class
usr/share/java/bbmap/current/jgi/PhylipToFasta.java
usr/share/java/bbmap/current/jgi/PickSubset$Edge.class
usr/share/java/bbmap/current/jgi/PickSubset$Node.class
usr/share/java/bbmap/current/jgi/PickSubset.class
usr/share/java/bbmap/current/jgi/PickSubset.java
usr/share/java/bbmap/current/jgi/README.md
usr/share/java/bbmap/current/jgi/RQCFilter2.class
usr/share/java/bbmap/current/jgi/RQCFilter2.java
usr/share/java/bbmap/current/jgi/RQCFilter3.class
usr/share/java/bbmap/current/jgi/RQCFilter3.java
usr/share/java/bbmap/current/jgi/RQCFilterStats.class
usr/share/java/bbmap/current/jgi/RQCFilterStats.java
usr/share/java/bbmap/current/jgi/ReadKmerDepthDistribution$1.class
usr/share/java/bbmap/current/jgi/ReadKmerDepthDistribution$ProcessThread.class
usr/share/java/bbmap/current/jgi/ReadKmerDepthDistribution.class
usr/share/java/bbmap/current/jgi/ReadKmerDepthDistribution.java
usr/share/java/bbmap/current/jgi/RedirectTest.class
usr/share/java/bbmap/current/jgi/RedirectTest.java
usr/share/java/bbmap/current/jgi/RefRenamer.class
usr/share/java/bbmap/current/jgi/RefRenamer.java
usr/share/java/bbmap/current/jgi/Reformat2$ProcessThread.class
usr/share/java/bbmap/current/jgi/Reformat2.class
usr/share/java/bbmap/current/jgi/Reformat2.java
usr/share/java/bbmap/current/jgi/ReformatReads.class
usr/share/java/bbmap/current/jgi/ReformatReads.java
usr/share/java/bbmap/current/jgi/ReformatReadsOld.class
usr/share/java/bbmap/current/jgi/ReformatReadsOld.java
usr/share/java/bbmap/current/jgi/ReformatStreamer$ProcessThread.class
usr/share/java/bbmap/current/jgi/ReformatStreamer.class
usr/share/java/bbmap/current/jgi/ReformatStreamer.java
usr/share/java/bbmap/current/jgi/RemapQuality.class
usr/share/java/bbmap/current/jgi/RemapQuality.java
usr/share/java/bbmap/current/jgi/RemoveBadBarcodes.class
usr/share/java/bbmap/current/jgi/RemoveBadBarcodes.java
usr/share/java/bbmap/current/jgi/RenameReads.class
usr/share/java/bbmap/current/jgi/RenameReads.java
usr/share/java/bbmap/current/jgi/ReplaceHeaders.class
usr/share/java/bbmap/current/jgi/ReplaceHeaders.java
usr/share/java/bbmap/current/jgi/RepresentativeSet$Edge.class
usr/share/java/bbmap/current/jgi/RepresentativeSet$Node.class
usr/share/java/bbmap/current/jgi/RepresentativeSet.class
usr/share/java/bbmap/current/jgi/RepresentativeSet.java
usr/share/java/bbmap/current/jgi/SamToEst$1.class
usr/share/java/bbmap/current/jgi/SamToEst$EST.class
usr/share/java/bbmap/current/jgi/SamToEst.class
usr/share/java/bbmap/current/jgi/SamToEst.java
usr/share/java/bbmap/current/jgi/Seal$LoadThread.class
usr/share/java/bbmap/current/jgi/Seal$ProcessThread.class
usr/share/java/bbmap/current/jgi/Seal.class
usr/share/java/bbmap/current/jgi/Seal.java
usr/share/java/bbmap/current/jgi/SealRefInfo.class
usr/share/java/bbmap/current/jgi/SealRefInfo.java
usr/share/java/bbmap/current/jgi/SmallKmerFrequency$CountComparator.class
usr/share/java/bbmap/current/jgi/SmallKmerFrequency$Kmer.class
usr/share/java/bbmap/current/jgi/SmallKmerFrequency$NumComparator.class
usr/share/java/bbmap/current/jgi/SmallKmerFrequency.class
usr/share/java/bbmap/current/jgi/SmallKmerFrequency.java
usr/share/java/bbmap/current/jgi/SplitNexteraLMP.class
usr/share/java/bbmap/current/jgi/SplitNexteraLMP.java
usr/share/java/bbmap/current/jgi/SplitPairsAndSingles.class
usr/share/java/bbmap/current/jgi/SplitPairsAndSingles.java
usr/share/java/bbmap/current/jgi/SplitSam4Way.class
usr/share/java/bbmap/current/jgi/SplitSam4Way.java
usr/share/java/bbmap/current/jgi/SplitSam6Way.class
usr/share/java/bbmap/current/jgi/SplitSam6Way.java
usr/share/java/bbmap/current/jgi/SplitSamFile.class
usr/share/java/bbmap/current/jgi/SplitSamFile.java
usr/share/java/bbmap/current/jgi/TestFilesystem$WriteThread.class
usr/share/java/bbmap/current/jgi/TestFilesystem.class
usr/share/java/bbmap/current/jgi/TestFilesystem.java
usr/share/java/bbmap/current/jgi/TestFormat$TestThread.class
usr/share/java/bbmap/current/jgi/TestFormat.class
usr/share/java/bbmap/current/jgi/TestFormat.java
usr/share/java/bbmap/current/jgi/TetramerFrequencies$Line.class
usr/share/java/bbmap/current/jgi/TetramerFrequencies$PrintThread.class
usr/share/java/bbmap/current/jgi/TetramerFrequencies.class
usr/share/java/bbmap/current/jgi/TetramerFrequencies.java
usr/share/java/bbmap/current/jgi/TranslateSixFrames.class
usr/share/java/bbmap/current/jgi/TranslateSixFrames.java
usr/share/java/bbmap/current/jgi/TrimContigs$Range.class
usr/share/java/bbmap/current/jgi/TrimContigs.class
usr/share/java/bbmap/current/jgi/TrimContigs.java
usr/share/java/bbmap/current/jgi/UnicodeToAscii.class
usr/share/java/bbmap/current/jgi/UnicodeToAscii.java
usr/share/java/bbmap/current/jgi/Unzip.class
usr/share/java/bbmap/current/jgi/Unzip.java
usr/share/java/bbmap/current/json/
usr/share/java/bbmap/current/json/JsonLiteral.class
usr/share/java/bbmap/current/json/JsonLiteral.java
usr/share/java/bbmap/current/json/JsonObject.class
usr/share/java/bbmap/current/json/JsonObject.java
usr/share/java/bbmap/current/json/JsonParser.class
usr/share/java/bbmap/current/json/JsonParser.java
usr/share/java/bbmap/current/json/README.md
usr/share/java/bbmap/current/kmer/
usr/share/java/bbmap/current/kmer/AbstractKmerTable$AllocThread.class
usr/share/java/bbmap/current/kmer/AbstractKmerTable.class
usr/share/java/bbmap/current/kmer/AbstractKmerTable.java
usr/share/java/bbmap/current/kmer/AbstractKmerTableSet.class
usr/share/java/bbmap/current/kmer/AbstractKmerTableSet.java
usr/share/java/bbmap/current/kmer/DumpThread.class
usr/share/java/bbmap/current/kmer/DumpThread.java
usr/share/java/bbmap/current/kmer/HashArray.class
usr/share/java/bbmap/current/kmer/HashArray.java
usr/share/java/bbmap/current/kmer/HashArray1D$Walker1D.class
usr/share/java/bbmap/current/kmer/HashArray1D.class
usr/share/java/bbmap/current/kmer/HashArray1D.java
usr/share/java/bbmap/current/kmer/HashArray2D.class
usr/share/java/bbmap/current/kmer/HashArray2D.java
usr/share/java/bbmap/current/kmer/HashArrayHybrid.class
usr/share/java/bbmap/current/kmer/HashArrayHybrid.java
usr/share/java/bbmap/current/kmer/HashArrayHybridFast.class
usr/share/java/bbmap/current/kmer/HashArrayHybridFast.java
usr/share/java/bbmap/current/kmer/HashBuffer.class
usr/share/java/bbmap/current/kmer/HashBuffer.java
usr/share/java/bbmap/current/kmer/HashForest.class
usr/share/java/bbmap/current/kmer/HashForest.java
usr/share/java/bbmap/current/kmer/HistogramMaker$FillThread.class
usr/share/java/bbmap/current/kmer/HistogramMaker.class
usr/share/java/bbmap/current/kmer/HistogramMaker.java
usr/share/java/bbmap/current/kmer/KmerBuffer.class
usr/share/java/bbmap/current/kmer/KmerBuffer.java
usr/share/java/bbmap/current/kmer/KmerLink.class
usr/share/java/bbmap/current/kmer/KmerLink.java
usr/share/java/bbmap/current/kmer/KmerNode.class
usr/share/java/bbmap/current/kmer/KmerNode.java
usr/share/java/bbmap/current/kmer/KmerNode1D.class
usr/share/java/bbmap/current/kmer/KmerNode1D.java
usr/share/java/bbmap/current/kmer/KmerNode2D.class
usr/share/java/bbmap/current/kmer/KmerNode2D.java
usr/share/java/bbmap/current/kmer/KmerTable.class
usr/share/java/bbmap/current/kmer/KmerTable.java
usr/share/java/bbmap/current/kmer/KmerTableSet$LoadThread.class
usr/share/java/bbmap/current/kmer/KmerTableSet$WalkerKST.class
usr/share/java/bbmap/current/kmer/KmerTableSet.class
usr/share/java/bbmap/current/kmer/KmerTableSet.java
usr/share/java/bbmap/current/kmer/OwnershipThread.class
usr/share/java/bbmap/current/kmer/OwnershipThread.java
usr/share/java/bbmap/current/kmer/README.md
usr/share/java/bbmap/current/kmer/ScheduleMaker.class
usr/share/java/bbmap/current/kmer/ScheduleMaker.java
usr/share/java/bbmap/current/kmer/SimpleKmerTable.class
usr/share/java/bbmap/current/kmer/SimpleKmerTable.java
usr/share/java/bbmap/current/kmer/TableLoaderLockFree$LoadThread.class
usr/share/java/bbmap/current/kmer/TableLoaderLockFree.class
usr/share/java/bbmap/current/kmer/TableLoaderLockFree.java
usr/share/java/bbmap/current/kmer/TableReader.class
usr/share/java/bbmap/current/kmer/TableReader.java
usr/share/java/bbmap/current/kmer/Walker.class
usr/share/java/bbmap/current/kmer/Walker.java
usr/share/java/bbmap/current/map/
usr/share/java/bbmap/current/map/IntHashMap2.class
usr/share/java/bbmap/current/map/IntHashMap2.java
usr/share/java/bbmap/current/map/IntHashMap3.class
usr/share/java/bbmap/current/map/IntHashMap3.java
usr/share/java/bbmap/current/map/IntObjectMap.class
usr/share/java/bbmap/current/map/IntObjectMap.java
usr/share/java/bbmap/current/map/LongIntMap.class
usr/share/java/bbmap/current/map/LongIntMap.java
usr/share/java/bbmap/current/map/LongIntMapX.class
usr/share/java/bbmap/current/map/LongIntMapX.java
usr/share/java/bbmap/current/map/LongLongHashMap2.class
usr/share/java/bbmap/current/map/LongLongHashMap2.java
usr/share/java/bbmap/current/map/LongObjectMap.class
usr/share/java/bbmap/current/map/LongObjectMap.java
usr/share/java/bbmap/current/map/ObjectIntMap.class
usr/share/java/bbmap/current/map/ObjectIntMap.java
usr/share/java/bbmap/current/map/ObjectMap.class
usr/share/java/bbmap/current/map/ObjectMap.java
usr/share/java/bbmap/current/ml/
usr/share/java/bbmap/current/ml/Bell.class
usr/share/java/bbmap/current/ml/Bell.java
usr/share/java/bbmap/current/ml/Cell.class
usr/share/java/bbmap/current/ml/Cell.java
usr/share/java/bbmap/current/ml/CellNet.class
usr/share/java/bbmap/current/ml/CellNet.java
usr/share/java/bbmap/current/ml/CellNetParser.class
usr/share/java/bbmap/current/ml/CellNetParser.java
usr/share/java/bbmap/current/ml/CellNetReverseComparator.class
usr/share/java/bbmap/current/ml/CellNetReverseComparator.java
usr/share/java/bbmap/current/ml/DataLoader$Triple.class
usr/share/java/bbmap/current/ml/DataLoader.class
usr/share/java/bbmap/current/ml/DataLoader.java
usr/share/java/bbmap/current/ml/ExtendedMSig.class
usr/share/java/bbmap/current/ml/ExtendedMSig.java
usr/share/java/bbmap/current/ml/ExtendedSigmoid.class
usr/share/java/bbmap/current/ml/ExtendedSigmoid.java
usr/share/java/bbmap/current/ml/Function.class
usr/share/java/bbmap/current/ml/Function.java
usr/share/java/bbmap/current/ml/Functions.class
usr/share/java/bbmap/current/ml/Functions.java
usr/share/java/bbmap/current/ml/JobData.class
usr/share/java/bbmap/current/ml/JobData.java
usr/share/java/bbmap/current/ml/JobResults.class
usr/share/java/bbmap/current/ml/JobResults.java
usr/share/java/bbmap/current/ml/MSig.class
usr/share/java/bbmap/current/ml/MSig.java
usr/share/java/bbmap/current/ml/Matrix.class
usr/share/java/bbmap/current/ml/Matrix.java
usr/share/java/bbmap/current/ml/NetFilter$ProcessThread.class
usr/share/java/bbmap/current/ml/NetFilter.class
usr/share/java/bbmap/current/ml/NetFilter.java
usr/share/java/bbmap/current/ml/ProcessBBMergeHeaders$Header.class
usr/share/java/bbmap/current/ml/ProcessBBMergeHeaders.class
usr/share/java/bbmap/current/ml/ProcessBBMergeHeaders.java
usr/share/java/bbmap/current/ml/Profiler.class
usr/share/java/bbmap/current/ml/Profiler.java
usr/share/java/bbmap/current/ml/README.md
usr/share/java/bbmap/current/ml/RSLog.class
usr/share/java/bbmap/current/ml/RSLog.java
usr/share/java/bbmap/current/ml/ReduceColumns.class
usr/share/java/bbmap/current/ml/ReduceColumns.java
usr/share/java/bbmap/current/ml/Sample.class
usr/share/java/bbmap/current/ml/Sample.java
usr/share/java/bbmap/current/ml/SampleErrorComparator.class
usr/share/java/bbmap/current/ml/SampleErrorComparator.java
usr/share/java/bbmap/current/ml/SampleSet.class
usr/share/java/bbmap/current/ml/SampleSet.java
usr/share/java/bbmap/current/ml/SampleValueComparator.class
usr/share/java/bbmap/current/ml/SampleValueComparator.java
usr/share/java/bbmap/current/ml/ScannerThread$LaunchThread.class
usr/share/java/bbmap/current/ml/ScannerThread.class
usr/share/java/bbmap/current/ml/ScannerThread.java
usr/share/java/bbmap/current/ml/ScoreSequence.class
usr/share/java/bbmap/current/ml/ScoreSequence.java
usr/share/java/bbmap/current/ml/Seed.class
usr/share/java/bbmap/current/ml/Seed.java
usr/share/java/bbmap/current/ml/SequenceToVector$1.class
usr/share/java/bbmap/current/ml/SequenceToVector.class
usr/share/java/bbmap/current/ml/SequenceToVector.java
usr/share/java/bbmap/current/ml/Sigmoid.class
usr/share/java/bbmap/current/ml/Sigmoid.java
usr/share/java/bbmap/current/ml/Source.class
usr/share/java/bbmap/current/ml/Source.java
usr/share/java/bbmap/current/ml/Status.class
usr/share/java/bbmap/current/ml/Status.java
usr/share/java/bbmap/current/ml/Subset.class
usr/share/java/bbmap/current/ml/Subset.java
usr/share/java/bbmap/current/ml/Swish.class
usr/share/java/bbmap/current/ml/Swish.java
usr/share/java/bbmap/current/ml/Tanh.class
usr/share/java/bbmap/current/ml/Tanh.java
usr/share/java/bbmap/current/ml/Trainer.class
usr/share/java/bbmap/current/ml/Trainer.java
usr/share/java/bbmap/current/ml/TrainerThread$LaunchThread.class
usr/share/java/bbmap/current/ml/TrainerThread.class
usr/share/java/bbmap/current/ml/TrainerThread.java
usr/share/java/bbmap/current/ml/WorkerThread.class
usr/share/java/bbmap/current/ml/WorkerThread.java
usr/share/java/bbmap/current/pacbio/
usr/share/java/bbmap/current/pacbio/CalcCoverageFromSites$1.class
usr/share/java/bbmap/current/pacbio/CalcCoverageFromSites.class
usr/share/java/bbmap/current/pacbio/CalcCoverageFromSites.java
usr/share/java/bbmap/current/pacbio/GenerateMultiChrom.class
usr/share/java/bbmap/current/pacbio/GenerateMultiChrom.java
usr/share/java/bbmap/current/pacbio/MakePacBioScript.class
usr/share/java/bbmap/current/pacbio/MakePacBioScript.java
usr/share/java/bbmap/current/pacbio/MergeFastaContigs$1.class
usr/share/java/bbmap/current/pacbio/MergeFastaContigs.class
usr/share/java/bbmap/current/pacbio/MergeFastaContigs.java
usr/share/java/bbmap/current/pacbio/MergeReadsAndGenome$1.class
usr/share/java/bbmap/current/pacbio/MergeReadsAndGenome.class
usr/share/java/bbmap/current/pacbio/MergeReadsAndGenome.java
usr/share/java/bbmap/current/pacbio/PartitionFastaFile.class
usr/share/java/bbmap/current/pacbio/PartitionFastaFile.java
usr/share/java/bbmap/current/pacbio/PartitionReads$1.class
usr/share/java/bbmap/current/pacbio/PartitionReads.class
usr/share/java/bbmap/current/pacbio/PartitionReads.java
usr/share/java/bbmap/current/pacbio/ProcessStackedSitesNormalized$1.class
usr/share/java/bbmap/current/pacbio/ProcessStackedSitesNormalized$Buffer.class
usr/share/java/bbmap/current/pacbio/ProcessStackedSitesNormalized$Ssra.class
usr/share/java/bbmap/current/pacbio/ProcessStackedSitesNormalized.class
usr/share/java/bbmap/current/pacbio/ProcessStackedSitesNormalized.java
usr/share/java/bbmap/current/pacbio/README.md
usr/share/java/bbmap/current/pacbio/RemoveAdapters2$1.class
usr/share/java/bbmap/current/pacbio/RemoveAdapters2$ProcessThread.class
usr/share/java/bbmap/current/pacbio/RemoveAdapters2.class
usr/share/java/bbmap/current/pacbio/RemoveAdapters2.java
usr/share/java/bbmap/current/pacbio/RemoveAdapters3$ProcessThread.class
usr/share/java/bbmap/current/pacbio/RemoveAdapters3.class
usr/share/java/bbmap/current/pacbio/RemoveAdapters3.java
usr/share/java/bbmap/current/pacbio/SiteR.class
usr/share/java/bbmap/current/pacbio/SiteR.java
usr/share/java/bbmap/current/pacbio/SortSites$1.class
usr/share/java/bbmap/current/pacbio/SortSites.class
usr/share/java/bbmap/current/pacbio/SortSites.java
usr/share/java/bbmap/current/pacbio/SplitOffPerfectContigs$1.class
usr/share/java/bbmap/current/pacbio/SplitOffPerfectContigs.class
usr/share/java/bbmap/current/pacbio/SplitOffPerfectContigs.java
usr/share/java/bbmap/current/pacbio/StackSites$1.class
usr/share/java/bbmap/current/pacbio/StackSites$Glob.class
usr/share/java/bbmap/current/pacbio/StackSites.class
usr/share/java/bbmap/current/pacbio/StackSites.java
usr/share/java/bbmap/current/pacbio/StackSites2$1.class
usr/share/java/bbmap/current/pacbio/StackSites2$Glob.class
usr/share/java/bbmap/current/pacbio/StackSites2.class
usr/share/java/bbmap/current/pacbio/StackSites2.java
usr/share/java/bbmap/current/processor/
usr/share/java/bbmap/current/processor/Processor.class
usr/share/java/bbmap/current/processor/Processor.java
usr/share/java/bbmap/current/processor/ReformatProcessor.class
usr/share/java/bbmap/current/processor/ReformatProcessor.java
usr/share/java/bbmap/current/prok/
usr/share/java/bbmap/current/prok/AnalyzeGenes$FileThread.class
usr/share/java/bbmap/current/prok/AnalyzeGenes.class
usr/share/java/bbmap/current/prok/AnalyzeGenes.java
usr/share/java/bbmap/current/prok/CallGenes$ProcessThread.class
usr/share/java/bbmap/current/prok/CallGenes.class
usr/share/java/bbmap/current/prok/CallGenes.java
usr/share/java/bbmap/current/prok/FetchProks$ProcessThread.class
usr/share/java/bbmap/current/prok/FetchProks$Stats.class
usr/share/java/bbmap/current/prok/FetchProks.class
usr/share/java/bbmap/current/prok/FetchProks.java
usr/share/java/bbmap/current/prok/FilterSilva.class
usr/share/java/bbmap/current/prok/FilterSilva.java
usr/share/java/bbmap/current/prok/FrameStats.class
usr/share/java/bbmap/current/prok/FrameStats.java
usr/share/java/bbmap/current/prok/GeneCaller.class
usr/share/java/bbmap/current/prok/GeneCaller.java
usr/share/java/bbmap/current/prok/GeneModel.class
usr/share/java/bbmap/current/prok/GeneModel.java
usr/share/java/bbmap/current/prok/GeneModelParser.class
usr/share/java/bbmap/current/prok/GeneModelParser.java
usr/share/java/bbmap/current/prok/MergeRibo$ListComparator.class
usr/share/java/bbmap/current/prok/MergeRibo$ProcessThread.class
usr/share/java/bbmap/current/prok/MergeRibo$Ribo.class
usr/share/java/bbmap/current/prok/MergeRibo.class
usr/share/java/bbmap/current/prok/MergeRibo.java
usr/share/java/bbmap/current/prok/MergeRibo_Fast$ProcessThread.class
usr/share/java/bbmap/current/prok/MergeRibo_Fast$Ribo.class
usr/share/java/bbmap/current/prok/MergeRibo_Fast.class
usr/share/java/bbmap/current/prok/MergeRibo_Fast.java
usr/share/java/bbmap/current/prok/Orf.class
usr/share/java/bbmap/current/prok/Orf.java
usr/share/java/bbmap/current/prok/PFeature$FeatureComparatorScore.class
usr/share/java/bbmap/current/prok/PFeature.class
usr/share/java/bbmap/current/prok/PFeature.java
usr/share/java/bbmap/current/prok/PGMTools$1.class
usr/share/java/bbmap/current/prok/PGMTools.class
usr/share/java/bbmap/current/prok/PGMTools.java
usr/share/java/bbmap/current/prok/ProkObject.class
usr/share/java/bbmap/current/prok/ProkObject.java
usr/share/java/bbmap/current/prok/README.md
usr/share/java/bbmap/current/prok/RiboMaker$ProcessThread.class
usr/share/java/bbmap/current/prok/RiboMaker.class
usr/share/java/bbmap/current/prok/RiboMaker.java
usr/share/java/bbmap/current/prok/ScafData.class
usr/share/java/bbmap/current/prok/ScafData.java
usr/share/java/bbmap/current/prok/ScoreTracker.class
usr/share/java/bbmap/current/prok/ScoreTracker.java
usr/share/java/bbmap/current/prok/SplitRibo$ProcessThread.class
usr/share/java/bbmap/current/prok/SplitRibo.class
usr/share/java/bbmap/current/prok/SplitRibo.java
usr/share/java/bbmap/current/prok/StatsContainer.class
usr/share/java/bbmap/current/prok/StatsContainer.java
usr/share/java/bbmap/current/repeat/
usr/share/java/bbmap/current/repeat/Palindrome.class
usr/share/java/bbmap/current/repeat/Palindrome.java
usr/share/java/bbmap/current/repeat/PalindromeFinder.class
usr/share/java/bbmap/current/repeat/PalindromeFinder.java
usr/share/java/bbmap/current/repeat/Repeat$PosComparator.class
usr/share/java/bbmap/current/repeat/Repeat$PosComparator2.class
usr/share/java/bbmap/current/repeat/Repeat.class
usr/share/java/bbmap/current/repeat/Repeat.java
usr/share/java/bbmap/current/repeat/RepeatFinder$ProcessThread.class
usr/share/java/bbmap/current/repeat/RepeatFinder.class
usr/share/java/bbmap/current/repeat/RepeatFinder.java
usr/share/java/bbmap/current/repeat/RepeatSet.class
usr/share/java/bbmap/current/repeat/RepeatSet.java
usr/share/java/bbmap/current/scalar/
usr/share/java/bbmap/current/scalar/CloudPlot.class
usr/share/java/bbmap/current/scalar/CloudPlot.java
usr/share/java/bbmap/current/scalar/ScalarData.class
usr/share/java/bbmap/current/scalar/ScalarData.java
usr/share/java/bbmap/current/scalar/ScalarIntervals$ProcessThread.class
usr/share/java/bbmap/current/scalar/ScalarIntervals$SDAccumulator.class
usr/share/java/bbmap/current/scalar/ScalarIntervals.class
usr/share/java/bbmap/current/scalar/ScalarIntervals.java
usr/share/java/bbmap/current/scalar/Scalars.class
usr/share/java/bbmap/current/scalar/Scalars.java
usr/share/java/bbmap/current/server/
usr/share/java/bbmap/current/server/PercentEncoding.class
usr/share/java/bbmap/current/server/PercentEncoding.java
usr/share/java/bbmap/current/server/README.md
usr/share/java/bbmap/current/server/ServerTools$1.class
usr/share/java/bbmap/current/server/ServerTools.class
usr/share/java/bbmap/current/server/ServerTools.java
usr/share/java/bbmap/current/server/SimpleHttpServer$GetHandler.class
usr/share/java/bbmap/current/server/SimpleHttpServer.class
usr/share/java/bbmap/current/server/SimpleHttpServer.java
usr/share/java/bbmap/current/server/StressTest.class
usr/share/java/bbmap/current/server/StressTest.java
usr/share/java/bbmap/current/server/StressTest2$1.class
usr/share/java/bbmap/current/server/StressTest2.class
usr/share/java/bbmap/current/server/StressTest2.java
usr/share/java/bbmap/current/server/StressTest3.class
usr/share/java/bbmap/current/server/StressTest3.java
usr/share/java/bbmap/current/shared/
usr/share/java/bbmap/current/shared/Colors.class
usr/share/java/bbmap/current/shared/Colors.java
usr/share/java/bbmap/current/shared/FastRandom.class
usr/share/java/bbmap/current/shared/FastRandom.java
usr/share/java/bbmap/current/shared/FastRandomAES.class
usr/share/java/bbmap/current/shared/FastRandomAES.java
usr/share/java/bbmap/current/shared/FastRandomSIMD.class
usr/share/java/bbmap/current/shared/FastRandomSIMD.java
usr/share/java/bbmap/current/shared/FastRandomXoshiro.class
usr/share/java/bbmap/current/shared/FastRandomXoshiro.java
usr/share/java/bbmap/current/shared/KillSwitch.class
usr/share/java/bbmap/current/shared/KillSwitch.java
usr/share/java/bbmap/current/shared/LineParser.class
usr/share/java/bbmap/current/shared/LineParser.java
usr/share/java/bbmap/current/shared/LineParser1.class
usr/share/java/bbmap/current/shared/LineParser1.java
usr/share/java/bbmap/current/shared/LineParser2.class
usr/share/java/bbmap/current/shared/LineParser2.java
usr/share/java/bbmap/current/shared/LineParser4.class
usr/share/java/bbmap/current/shared/LineParser4.java
usr/share/java/bbmap/current/shared/LineParserS.class
usr/share/java/bbmap/current/shared/LineParserS.java
usr/share/java/bbmap/current/shared/LineParserS1.class
usr/share/java/bbmap/current/shared/LineParserS1.java
usr/share/java/bbmap/current/shared/LineParserS2.class
usr/share/java/bbmap/current/shared/LineParserS2.java
usr/share/java/bbmap/current/shared/LineParserS3.class
usr/share/java/bbmap/current/shared/LineParserS3.java
usr/share/java/bbmap/current/shared/LineParserS4.class
usr/share/java/bbmap/current/shared/LineParserS4.java
usr/share/java/bbmap/current/shared/LineParserS4Reverse.class
usr/share/java/bbmap/current/shared/LineParserS4Reverse.java
usr/share/java/bbmap/current/shared/LineParserSimple.class
usr/share/java/bbmap/current/shared/LineParserSimple.java
usr/share/java/bbmap/current/shared/MetadataWriter.class
usr/share/java/bbmap/current/shared/MetadataWriter.java
usr/share/java/bbmap/current/shared/Parse.class
usr/share/java/bbmap/current/shared/Parse.java
usr/share/java/bbmap/current/shared/Parser.class
usr/share/java/bbmap/current/shared/Parser.java
usr/share/java/bbmap/current/shared/PreParser.class
usr/share/java/bbmap/current/shared/PreParser.java
usr/share/java/bbmap/current/shared/Primes.class
usr/share/java/bbmap/current/shared/Primes.java
usr/share/java/bbmap/current/shared/README.md
usr/share/java/bbmap/current/shared/SIMD.class
usr/share/java/bbmap/current/shared/SIMD.java
usr/share/java/bbmap/current/shared/SIMDAlign.class
usr/share/java/bbmap/current/shared/SIMDAlign.java
usr/share/java/bbmap/current/shared/SIMDAlignByte.class
usr/share/java/bbmap/current/shared/SIMDAlignByte.java
usr/share/java/bbmap/current/shared/SIMDByte256.class
usr/share/java/bbmap/current/shared/SIMDByte256.java
usr/share/java/bbmap/current/shared/SIMDByte256_only.class
usr/share/java/bbmap/current/shared/SIMDByte256_only.java
usr/share/java/bbmap/current/shared/Shared.class
usr/share/java/bbmap/current/shared/Shared.java
usr/share/java/bbmap/current/shared/SyncHeart.class
usr/share/java/bbmap/current/shared/SyncHeart.java
usr/share/java/bbmap/current/shared/Timer.class
usr/share/java/bbmap/current/shared/Timer.java
usr/share/java/bbmap/current/shared/Tools$1.class
usr/share/java/bbmap/current/shared/Tools.class
usr/share/java/bbmap/current/shared/Tools.java
usr/share/java/bbmap/current/shared/TrimRead.class
usr/share/java/bbmap/current/shared/TrimRead.java
usr/share/java/bbmap/current/shared/VarHandler.class
usr/share/java/bbmap/current/shared/VarHandler.java
usr/share/java/bbmap/current/shared/Vector.class
usr/share/java/bbmap/current/shared/Vector.java
usr/share/java/bbmap/current/simd/
usr/share/java/bbmap/current/simd/SIMD128.class
usr/share/java/bbmap/current/simd/SIMD128.java
usr/share/java/bbmap/current/simd/SIMDAlign128.class
usr/share/java/bbmap/current/simd/SIMDAlign128.java
usr/share/java/bbmap/current/simd/SIMDAlignByte128.class
usr/share/java/bbmap/current/simd/SIMDAlignByte128.java
usr/share/java/bbmap/current/simd/SIMDByte128.class
usr/share/java/bbmap/current/simd/SIMDByte128.java
usr/share/java/bbmap/current/sketch/
usr/share/java/bbmap/current/sketch/AddSSU$SketchHeader.class
usr/share/java/bbmap/current/sketch/AddSSU.class
usr/share/java/bbmap/current/sketch/AddSSU.java
usr/share/java/bbmap/current/sketch/AlignmentJob.class
usr/share/java/bbmap/current/sketch/AlignmentJob.java
usr/share/java/bbmap/current/sketch/AlignmentThreadPool$AlignmentThread.class
usr/share/java/bbmap/current/sketch/AlignmentThreadPool.class
usr/share/java/bbmap/current/sketch/AlignmentThreadPool.java
usr/share/java/bbmap/current/sketch/AnalyzeSketchResults$SSUThread.class
usr/share/java/bbmap/current/sketch/AnalyzeSketchResults.class
usr/share/java/bbmap/current/sketch/AnalyzeSketchResults.java
usr/share/java/bbmap/current/sketch/Blacklist.class
usr/share/java/bbmap/current/sketch/Blacklist.java
usr/share/java/bbmap/current/sketch/BlacklistMaker$ProcessThread.class
usr/share/java/bbmap/current/sketch/BlacklistMaker.class
usr/share/java/bbmap/current/sketch/BlacklistMaker.java
usr/share/java/bbmap/current/sketch/BlacklistMaker2$KeyPair.class
usr/share/java/bbmap/current/sketch/BlacklistMaker2$ProcessThread.class
usr/share/java/bbmap/current/sketch/BlacklistMaker2.class
usr/share/java/bbmap/current/sketch/BlacklistMaker2.java
usr/share/java/bbmap/current/sketch/CompareBuffer.class
usr/share/java/bbmap/current/sketch/CompareBuffer.java
usr/share/java/bbmap/current/sketch/CompareSSU$ProcessThread.class
usr/share/java/bbmap/current/sketch/CompareSSU.class
usr/share/java/bbmap/current/sketch/CompareSSU.java
usr/share/java/bbmap/current/sketch/CompareSketch$CompareThread.class
usr/share/java/bbmap/current/sketch/CompareSketch.class
usr/share/java/bbmap/current/sketch/CompareSketch.java
usr/share/java/bbmap/current/sketch/Comparison$Depth2Comparator.class
usr/share/java/bbmap/current/sketch/Comparison$DepthComparator.class
usr/share/java/bbmap/current/sketch/Comparison$HitsComparator.class
usr/share/java/bbmap/current/sketch/Comparison$KIDComparator.class
usr/share/java/bbmap/current/sketch/Comparison$SSUComparator.class
usr/share/java/bbmap/current/sketch/Comparison$ScoreComparator.class
usr/share/java/bbmap/current/sketch/Comparison$VolumeComparator.class
usr/share/java/bbmap/current/sketch/Comparison$WKIDComparator.class
usr/share/java/bbmap/current/sketch/Comparison.class
usr/share/java/bbmap/current/sketch/Comparison.java
usr/share/java/bbmap/current/sketch/DisplayParams.class
usr/share/java/bbmap/current/sketch/DisplayParams.java
usr/share/java/bbmap/current/sketch/InvertKey.class
usr/share/java/bbmap/current/sketch/InvertKey.java
usr/share/java/bbmap/current/sketch/KmerLimit$ProcessThread.class
usr/share/java/bbmap/current/sketch/KmerLimit.class
usr/share/java/bbmap/current/sketch/KmerLimit.java
usr/share/java/bbmap/current/sketch/KmerLimit2$ProcessThread.class
usr/share/java/bbmap/current/sketch/KmerLimit2.class
usr/share/java/bbmap/current/sketch/KmerLimit2.java
usr/share/java/bbmap/current/sketch/MergeSketch.class
usr/share/java/bbmap/current/sketch/MergeSketch.java
usr/share/java/bbmap/current/sketch/README.md
usr/share/java/bbmap/current/sketch/Record.class
usr/share/java/bbmap/current/sketch/Record.java
usr/share/java/bbmap/current/sketch/RecordSet.class
usr/share/java/bbmap/current/sketch/RecordSet.java
usr/share/java/bbmap/current/sketch/ResultLineParser.class
usr/share/java/bbmap/current/sketch/ResultLineParser.java
usr/share/java/bbmap/current/sketch/SSUMap.class
usr/share/java/bbmap/current/sketch/SSUMap.java
usr/share/java/bbmap/current/sketch/SendSketch.class
usr/share/java/bbmap/current/sketch/SendSketch.java
usr/share/java/bbmap/current/sketch/Sketch.class
usr/share/java/bbmap/current/sketch/Sketch.java
usr/share/java/bbmap/current/sketch/SketchHeap.class
usr/share/java/bbmap/current/sketch/SketchHeap.java
usr/share/java/bbmap/current/sketch/SketchIdComparator.class
usr/share/java/bbmap/current/sketch/SketchIdComparator.java
usr/share/java/bbmap/current/sketch/SketchIndex$IndexThread.class
usr/share/java/bbmap/current/sketch/SketchIndex.class
usr/share/java/bbmap/current/sketch/SketchIndex.java
usr/share/java/bbmap/current/sketch/SketchMaker$ProcessThread.class
usr/share/java/bbmap/current/sketch/SketchMaker$WriteThread.class
usr/share/java/bbmap/current/sketch/SketchMaker.class
usr/share/java/bbmap/current/sketch/SketchMaker.java
usr/share/java/bbmap/current/sketch/SketchMakerMini.class
usr/share/java/bbmap/current/sketch/SketchMakerMini.java
usr/share/java/bbmap/current/sketch/SketchObject.class
usr/share/java/bbmap/current/sketch/SketchObject.java
usr/share/java/bbmap/current/sketch/SketchResults.class
usr/share/java/bbmap/current/sketch/SketchResults.java
usr/share/java/bbmap/current/sketch/SketchSearcher$CompareThread.class
usr/share/java/bbmap/current/sketch/SketchSearcher.class
usr/share/java/bbmap/current/sketch/SketchSearcher.java
usr/share/java/bbmap/current/sketch/SketchTool$LoadThread.class
usr/share/java/bbmap/current/sketch/SketchTool$LoadThread2.class
usr/share/java/bbmap/current/sketch/SketchTool$SketchThread.class
usr/share/java/bbmap/current/sketch/SketchTool.class
usr/share/java/bbmap/current/sketch/SketchTool.java
usr/share/java/bbmap/current/sketch/SubSketch.class
usr/share/java/bbmap/current/sketch/SubSketch.java
usr/share/java/bbmap/current/sketch/SummarizeSketchStats$SketchResultsLine.class
usr/share/java/bbmap/current/sketch/SummarizeSketchStats$SketchResultsSummary.class
usr/share/java/bbmap/current/sketch/SummarizeSketchStats.class
usr/share/java/bbmap/current/sketch/SummarizeSketchStats.java
usr/share/java/bbmap/current/sketch/Whitelist.class
usr/share/java/bbmap/current/sketch/Whitelist.java
usr/share/java/bbmap/current/sort/
usr/share/java/bbmap/current/sort/ContigLengthComparator.class
usr/share/java/bbmap/current/sort/ContigLengthComparator.java
usr/share/java/bbmap/current/sort/MergeSorted.class
usr/share/java/bbmap/current/sort/MergeSorted.java
usr/share/java/bbmap/current/sort/README.md
usr/share/java/bbmap/current/sort/ReadComparator.class
usr/share/java/bbmap/current/sort/ReadComparator.java
usr/share/java/bbmap/current/sort/ReadComparatorClump.class
usr/share/java/bbmap/current/sort/ReadComparatorClump.java
usr/share/java/bbmap/current/sort/ReadComparatorCrispr.class
usr/share/java/bbmap/current/sort/ReadComparatorCrispr.java
usr/share/java/bbmap/current/sort/ReadComparatorFlowcell.class
usr/share/java/bbmap/current/sort/ReadComparatorFlowcell.java
usr/share/java/bbmap/current/sort/ReadComparatorID.class
usr/share/java/bbmap/current/sort/ReadComparatorID.java
usr/share/java/bbmap/current/sort/ReadComparatorList.class
usr/share/java/bbmap/current/sort/ReadComparatorList.java
usr/share/java/bbmap/current/sort/ReadComparatorMapping.class
usr/share/java/bbmap/current/sort/ReadComparatorMapping.java
usr/share/java/bbmap/current/sort/ReadComparatorName.class
usr/share/java/bbmap/current/sort/ReadComparatorName.java
usr/share/java/bbmap/current/sort/ReadComparatorPosition.class
usr/share/java/bbmap/current/sort/ReadComparatorPosition.java
usr/share/java/bbmap/current/sort/ReadComparatorRandom.class
usr/share/java/bbmap/current/sort/ReadComparatorRandom.java
usr/share/java/bbmap/current/sort/ReadComparatorTaxa.class
usr/share/java/bbmap/current/sort/ReadComparatorTaxa.java
usr/share/java/bbmap/current/sort/ReadComparatorTopological.class
usr/share/java/bbmap/current/sort/ReadComparatorTopological.java
usr/share/java/bbmap/current/sort/ReadComparatorTopological5Bit.class
usr/share/java/bbmap/current/sort/ReadComparatorTopological5Bit.java
usr/share/java/bbmap/current/sort/ReadErrorComparator.class
usr/share/java/bbmap/current/sort/ReadErrorComparator.java
usr/share/java/bbmap/current/sort/ReadLengthComparator.class
usr/share/java/bbmap/current/sort/ReadLengthComparator.java
usr/share/java/bbmap/current/sort/ReadQualityComparator.class
usr/share/java/bbmap/current/sort/ReadQualityComparator.java
usr/share/java/bbmap/current/sort/Shuffle$ShuffleThread.class
usr/share/java/bbmap/current/sort/Shuffle.class
usr/share/java/bbmap/current/sort/Shuffle.java
usr/share/java/bbmap/current/sort/Shuffle2$WriteThread.class
usr/share/java/bbmap/current/sort/Shuffle2.class
usr/share/java/bbmap/current/sort/Shuffle2.java
usr/share/java/bbmap/current/sort/SortByName$WriteThread.class
usr/share/java/bbmap/current/sort/SortByName.class
usr/share/java/bbmap/current/sort/SortByName.java
usr/share/java/bbmap/current/sort/SortReadsByID$1.class
usr/share/java/bbmap/current/sort/SortReadsByID$Block.class
usr/share/java/bbmap/current/sort/SortReadsByID.class
usr/share/java/bbmap/current/sort/SortReadsByID.java
usr/share/java/bbmap/current/stream/
usr/share/java/bbmap/current/stream/ArrayListSet$Pack.class
usr/share/java/bbmap/current/stream/ArrayListSet.class
usr/share/java/bbmap/current/stream/ArrayListSet.java
usr/share/java/bbmap/current/stream/BamStreamer$ProcessThread.class
usr/share/java/bbmap/current/stream/BamStreamer.class
usr/share/java/bbmap/current/stream/BamStreamer.java
usr/share/java/bbmap/current/stream/BamWriter$ProcessThread.class
usr/share/java/bbmap/current/stream/BamWriter$SamWriterInputJob.class
usr/share/java/bbmap/current/stream/BamWriter$SamWriterOutputJob.class
usr/share/java/bbmap/current/stream/BamWriter.class
usr/share/java/bbmap/current/stream/BamWriter.java
usr/share/java/bbmap/current/stream/BufferedMultiCros.class
usr/share/java/bbmap/current/stream/BufferedMultiCros.java
usr/share/java/bbmap/current/stream/ConcurrentCollectionReadInputStream.class
usr/share/java/bbmap/current/stream/ConcurrentCollectionReadInputStream.java
usr/share/java/bbmap/current/stream/ConcurrentDepot.class
usr/share/java/bbmap/current/stream/ConcurrentDepot.java
usr/share/java/bbmap/current/stream/ConcurrentGenericReadInputStream$1.class
usr/share/java/bbmap/current/stream/ConcurrentGenericReadInputStream$ReadThread.class
usr/share/java/bbmap/current/stream/ConcurrentGenericReadInputStream.class
usr/share/java/bbmap/current/stream/ConcurrentGenericReadInputStream.java
usr/share/java/bbmap/current/stream/ConcurrentGenericReadOutputStream.class
usr/share/java/bbmap/current/stream/ConcurrentGenericReadOutputStream.java
usr/share/java/bbmap/current/stream/ConcurrentLegacyReadInputStream.class
usr/share/java/bbmap/current/stream/ConcurrentLegacyReadInputStream.java
usr/share/java/bbmap/current/stream/ConcurrentReadInputStream.class
usr/share/java/bbmap/current/stream/ConcurrentReadInputStream.java
usr/share/java/bbmap/current/stream/ConcurrentReadInputStreamD.class
usr/share/java/bbmap/current/stream/ConcurrentReadInputStreamD.java
usr/share/java/bbmap/current/stream/ConcurrentReadListDepot.class
usr/share/java/bbmap/current/stream/ConcurrentReadListDepot.java
usr/share/java/bbmap/current/stream/ConcurrentReadOutputStream.class
usr/share/java/bbmap/current/stream/ConcurrentReadOutputStream.java
usr/share/java/bbmap/current/stream/ConcurrentReadOutputStreamD$ListenThread.class
usr/share/java/bbmap/current/stream/ConcurrentReadOutputStreamD.class
usr/share/java/bbmap/current/stream/ConcurrentReadOutputStreamD.java
usr/share/java/bbmap/current/stream/ConcurrentReadStreamInterface.class
usr/share/java/bbmap/current/stream/ConcurrentReadStreamInterface.java
usr/share/java/bbmap/current/stream/CrisContainer.class
usr/share/java/bbmap/current/stream/CrisContainer.java
usr/share/java/bbmap/current/stream/CrisWrapper.class
usr/share/java/bbmap/current/stream/CrisWrapper.java
usr/share/java/bbmap/current/stream/CustomHeader.class
usr/share/java/bbmap/current/stream/CustomHeader.java
usr/share/java/bbmap/current/stream/DualCris.class
usr/share/java/bbmap/current/stream/DualCris.java
usr/share/java/bbmap/current/stream/EmblReadInputStream.class
usr/share/java/bbmap/current/stream/EmblReadInputStream.java
usr/share/java/bbmap/current/stream/FASTQ.class
usr/share/java/bbmap/current/stream/FASTQ.java
usr/share/java/bbmap/current/stream/FastaQualReadInputStream.class
usr/share/java/bbmap/current/stream/FastaQualReadInputStream.java
usr/share/java/bbmap/current/stream/FastaQualStreamer$ProcessThread.class
usr/share/java/bbmap/current/stream/FastaQualStreamer.class
usr/share/java/bbmap/current/stream/FastaQualStreamer.java
usr/share/java/bbmap/current/stream/FastaQualStreamerZT.class
usr/share/java/bbmap/current/stream/FastaQualStreamerZT.java
usr/share/java/bbmap/current/stream/FastaQualWriterST$WriterRunnable.class
usr/share/java/bbmap/current/stream/FastaQualWriterST.class
usr/share/java/bbmap/current/stream/FastaQualWriterST.java
usr/share/java/bbmap/current/stream/FastaQualWriterZT.class
usr/share/java/bbmap/current/stream/FastaQualWriterZT.java
usr/share/java/bbmap/current/stream/FastaReadInputStream.class
usr/share/java/bbmap/current/stream/FastaReadInputStream.java
usr/share/java/bbmap/current/stream/FastaShredInputStream.class
usr/share/java/bbmap/current/stream/FastaShredInputStream.java
usr/share/java/bbmap/current/stream/FastaStreamer$ProcessThread.class
usr/share/java/bbmap/current/stream/FastaStreamer.class
usr/share/java/bbmap/current/stream/FastaStreamer.java
usr/share/java/bbmap/current/stream/FastaStreamer2ST$ProcessThread.class
usr/share/java/bbmap/current/stream/FastaStreamer2ST.class
usr/share/java/bbmap/current/stream/FastaStreamer2ST.java
usr/share/java/bbmap/current/stream/FastaStreamer2ZT.class
usr/share/java/bbmap/current/stream/FastaStreamer2ZT.java
usr/share/java/bbmap/current/stream/FastaStreamerST$ProcessThread.class
usr/share/java/bbmap/current/stream/FastaStreamerST.class
usr/share/java/bbmap/current/stream/FastaStreamerST.java
usr/share/java/bbmap/current/stream/FastaStreamerZT.class
usr/share/java/bbmap/current/stream/FastaStreamerZT.java
usr/share/java/bbmap/current/stream/FastqReadInputStream.class
usr/share/java/bbmap/current/stream/FastqReadInputStream.java
usr/share/java/bbmap/current/stream/FastqScan.class
usr/share/java/bbmap/current/stream/FastqScan.java
usr/share/java/bbmap/current/stream/FastqScanFC.class
usr/share/java/bbmap/current/stream/FastqScanFC.java
usr/share/java/bbmap/current/stream/FastqScanMT$ScanThread.class
usr/share/java/bbmap/current/stream/FastqScanMT.class
usr/share/java/bbmap/current/stream/FastqScanMT.java
usr/share/java/bbmap/current/stream/FastqScanStreamer$ReaderRunnable.class
usr/share/java/bbmap/current/stream/FastqScanStreamer.class
usr/share/java/bbmap/current/stream/FastqScanStreamer.java
usr/share/java/bbmap/current/stream/FastqStreamer$ProcessThread.class
usr/share/java/bbmap/current/stream/FastqStreamer.class
usr/share/java/bbmap/current/stream/FastqStreamer.java
usr/share/java/bbmap/current/stream/FastqStreamerST$ProcessThread.class
usr/share/java/bbmap/current/stream/FastqStreamerST.class
usr/share/java/bbmap/current/stream/FastqStreamerST.java
usr/share/java/bbmap/current/stream/FastqWriter$FastqWriterInputJob.class
usr/share/java/bbmap/current/stream/FastqWriter$FastqWriterOutputJob.class
usr/share/java/bbmap/current/stream/FastqWriter$ProcessThread.class
usr/share/java/bbmap/current/stream/FastqWriter.class
usr/share/java/bbmap/current/stream/FastqWriter.java
usr/share/java/bbmap/current/stream/FastqWriterST.class
usr/share/java/bbmap/current/stream/FastqWriterST.java
usr/share/java/bbmap/current/stream/FastqWriterST2$WriterRunnable.class
usr/share/java/bbmap/current/stream/FastqWriterST2.class
usr/share/java/bbmap/current/stream/FastqWriterST2.java
usr/share/java/bbmap/current/stream/FileScanMT$ScanThread.class
usr/share/java/bbmap/current/stream/FileScanMT.class
usr/share/java/bbmap/current/stream/FileScanMT.java
usr/share/java/bbmap/current/stream/GbkReadInputStream.class
usr/share/java/bbmap/current/stream/GbkReadInputStream.java
usr/share/java/bbmap/current/stream/GfaReadInputStream.class
usr/share/java/bbmap/current/stream/GfaReadInputStream.java
usr/share/java/bbmap/current/stream/GfaStreamerST$ProcessThread.class
usr/share/java/bbmap/current/stream/GfaStreamerST.class
usr/share/java/bbmap/current/stream/GfaStreamerST.java
usr/share/java/bbmap/current/stream/HasID.class
usr/share/java/bbmap/current/stream/HasID.java
usr/share/java/bbmap/current/stream/HeaderInputStream.class
usr/share/java/bbmap/current/stream/HeaderInputStream.java
usr/share/java/bbmap/current/stream/JobQueue$HasIDComparator.class
usr/share/java/bbmap/current/stream/JobQueue.class
usr/share/java/bbmap/current/stream/JobQueue.java
usr/share/java/bbmap/current/stream/MDWalker.class
usr/share/java/bbmap/current/stream/MDWalker.java
usr/share/java/bbmap/current/stream/MDWalker2.class
usr/share/java/bbmap/current/stream/MDWalker2.java
usr/share/java/bbmap/current/stream/MultiCros.class
usr/share/java/bbmap/current/stream/MultiCros.java
usr/share/java/bbmap/current/stream/MultiCros2$Buffer.class
usr/share/java/bbmap/current/stream/MultiCros2.class
usr/share/java/bbmap/current/stream/MultiCros2.java
usr/share/java/bbmap/current/stream/MultiCros3$Buffer.class
usr/share/java/bbmap/current/stream/MultiCros3.class
usr/share/java/bbmap/current/stream/MultiCros3.java
usr/share/java/bbmap/current/stream/MultiCros4$Buffer.class
usr/share/java/bbmap/current/stream/MultiCros4$RetireThread.class
usr/share/java/bbmap/current/stream/MultiCros4$Token.class
usr/share/java/bbmap/current/stream/MultiCros4.class
usr/share/java/bbmap/current/stream/MultiCros4.java
usr/share/java/bbmap/current/stream/MultiCros5$Buffer.class
usr/share/java/bbmap/current/stream/MultiCros5.class
usr/share/java/bbmap/current/stream/MultiCros5.java
usr/share/java/bbmap/current/stream/MultiCros6$Buffer.class
usr/share/java/bbmap/current/stream/MultiCros6$TimestampComparator.class
usr/share/java/bbmap/current/stream/MultiCros6.class
usr/share/java/bbmap/current/stream/MultiCros6.java
usr/share/java/bbmap/current/stream/NullOutputStream.class
usr/share/java/bbmap/current/stream/NullOutputStream.java
usr/share/java/bbmap/current/stream/OnelineReadInputStream.class
usr/share/java/bbmap/current/stream/OnelineReadInputStream.java
usr/share/java/bbmap/current/stream/OrderedQueueSystem.class
usr/share/java/bbmap/current/stream/OrderedQueueSystem.java
usr/share/java/bbmap/current/stream/OrderedQueueSystem2.class
usr/share/java/bbmap/current/stream/OrderedQueueSystem2.java
usr/share/java/bbmap/current/stream/PairStreamer.class
usr/share/java/bbmap/current/stream/PairStreamer.java
usr/share/java/bbmap/current/stream/PairedWriter.class
usr/share/java/bbmap/current/stream/PairedWriter.java
usr/share/java/bbmap/current/stream/RTextInputStream.class
usr/share/java/bbmap/current/stream/RTextInputStream.java
usr/share/java/bbmap/current/stream/RandomReadInputStream3.class
usr/share/java/bbmap/current/stream/RandomReadInputStream3.java
usr/share/java/bbmap/current/stream/Read.class
usr/share/java/bbmap/current/stream/Read.java
usr/share/java/bbmap/current/stream/ReadInputStream.class
usr/share/java/bbmap/current/stream/ReadInputStream.java
usr/share/java/bbmap/current/stream/ReadStreamByteWriter.class
usr/share/java/bbmap/current/stream/ReadStreamByteWriter.java
usr/share/java/bbmap/current/stream/ReadStreamSamWriter.class
usr/share/java/bbmap/current/stream/ReadStreamSamWriter.java
usr/share/java/bbmap/current/stream/ReadStreamWriter$Job.class
usr/share/java/bbmap/current/stream/ReadStreamWriter.class
usr/share/java/bbmap/current/stream/ReadStreamWriter.java
usr/share/java/bbmap/current/stream/SamHeader.class
usr/share/java/bbmap/current/stream/SamHeader.java
usr/share/java/bbmap/current/stream/SamHeaderWriter$WriterThread.class
usr/share/java/bbmap/current/stream/SamHeaderWriter.class
usr/share/java/bbmap/current/stream/SamHeaderWriter.java
usr/share/java/bbmap/current/stream/SamLine.class
usr/share/java/bbmap/current/stream/SamLine.java
usr/share/java/bbmap/current/stream/SamReadInputStream.class
usr/share/java/bbmap/current/stream/SamReadInputStream.java
usr/share/java/bbmap/current/stream/SamStreamer$ProcessThread.class
usr/share/java/bbmap/current/stream/SamStreamer.class
usr/share/java/bbmap/current/stream/SamStreamer.java
usr/share/java/bbmap/current/stream/SamStreamerMF.class
usr/share/java/bbmap/current/stream/SamStreamerMF.java
usr/share/java/bbmap/current/stream/SamStreamerST$ProcessThread.class
usr/share/java/bbmap/current/stream/SamStreamerST.class
usr/share/java/bbmap/current/stream/SamStreamerST.java
usr/share/java/bbmap/current/stream/SamStreamerWrapper.class
usr/share/java/bbmap/current/stream/SamStreamerWrapper.java
usr/share/java/bbmap/current/stream/SamWriter$ProcessThread.class
usr/share/java/bbmap/current/stream/SamWriter$SamWriterInputJob.class
usr/share/java/bbmap/current/stream/SamWriter$SamWriterOutputJob.class
usr/share/java/bbmap/current/stream/SamWriter.class
usr/share/java/bbmap/current/stream/SamWriter.java
usr/share/java/bbmap/current/stream/SamWriterST.class
usr/share/java/bbmap/current/stream/SamWriterST.java
usr/share/java/bbmap/current/stream/SamWriterST2$WriterRunnable.class
usr/share/java/bbmap/current/stream/SamWriterST2.class
usr/share/java/bbmap/current/stream/SamWriterST2.java
usr/share/java/bbmap/current/stream/ScaffoldCoordinates.class
usr/share/java/bbmap/current/stream/ScaffoldCoordinates.java
usr/share/java/bbmap/current/stream/ScarfReadInputStream.class
usr/share/java/bbmap/current/stream/ScarfReadInputStream.java
usr/share/java/bbmap/current/stream/ScarfStreamer$ProcessThread.class
usr/share/java/bbmap/current/stream/ScarfStreamer.class
usr/share/java/bbmap/current/stream/ScarfStreamer.java
usr/share/java/bbmap/current/stream/SequentialReadInputStream.class
usr/share/java/bbmap/current/stream/SequentialReadInputStream.java
usr/share/java/bbmap/current/stream/SiteScore$PositionComparator.class
usr/share/java/bbmap/current/stream/SiteScore.class
usr/share/java/bbmap/current/stream/SiteScore.java
usr/share/java/bbmap/current/stream/SiteScoreR$IDComparator.class
usr/share/java/bbmap/current/stream/SiteScoreR$NormalizedComparator.class
usr/share/java/bbmap/current/stream/SiteScoreR$PositionComparator.class
usr/share/java/bbmap/current/stream/SiteScoreR.class
usr/share/java/bbmap/current/stream/SiteScoreR.java
usr/share/java/bbmap/current/stream/Streamer.class
usr/share/java/bbmap/current/stream/Streamer.java
usr/share/java/bbmap/current/stream/StreamerFactory.class
usr/share/java/bbmap/current/stream/StreamerFactory.java
usr/share/java/bbmap/current/stream/StreamerWrapper.class
usr/share/java/bbmap/current/stream/StreamerWrapper.java
usr/share/java/bbmap/current/stream/TestMDWalker.class
usr/share/java/bbmap/current/stream/TestMDWalker.java
usr/share/java/bbmap/current/stream/Writer.class
usr/share/java/bbmap/current/stream/Writer.java
usr/share/java/bbmap/current/stream/WriterFactory.class
usr/share/java/bbmap/current/stream/WriterFactory.java
usr/share/java/bbmap/current/stream/bam/
usr/share/java/bbmap/current/stream/bam/BamIndexWriter$BinData.class
usr/share/java/bbmap/current/stream/bam/BamIndexWriter$ReferenceIndex.class
usr/share/java/bbmap/current/stream/bam/BamIndexWriter.class
usr/share/java/bbmap/current/stream/bam/BamIndexWriter.java
usr/share/java/bbmap/current/stream/bam/BamInputStream.class
usr/share/java/bbmap/current/stream/bam/BamInputStream.java
usr/share/java/bbmap/current/stream/bam/BamOutputStream.class
usr/share/java/bbmap/current/stream/bam/BamOutputStream.java
usr/share/java/bbmap/current/stream/bam/BamReadInputStream.class
usr/share/java/bbmap/current/stream/bam/BamReadInputStream.java
usr/share/java/bbmap/current/stream/bam/BamReadInputStreamST.class
usr/share/java/bbmap/current/stream/bam/BamReadInputStreamST.java
usr/share/java/bbmap/current/stream/bam/BamReader.class
usr/share/java/bbmap/current/stream/bam/BamReader.java
usr/share/java/bbmap/current/stream/bam/BamToSamConverter.class
usr/share/java/bbmap/current/stream/bam/BamToSamConverter.java
usr/share/java/bbmap/current/stream/bam/BamWriterHelper.class
usr/share/java/bbmap/current/stream/bam/BamWriterHelper.java
usr/share/java/bbmap/current/stream/bam/BgzfInputJob.class
usr/share/java/bbmap/current/stream/bam/BgzfInputJob.java
usr/share/java/bbmap/current/stream/bam/BgzfInputStream$PrefixedInputStream.class
usr/share/java/bbmap/current/stream/bam/BgzfInputStream.class
usr/share/java/bbmap/current/stream/bam/BgzfInputStream.java
usr/share/java/bbmap/current/stream/bam/BgzfInputStreamMT$1.class
usr/share/java/bbmap/current/stream/bam/BgzfInputStreamMT$2.class
usr/share/java/bbmap/current/stream/bam/BgzfInputStreamMT$PrefixedInputStream.class
usr/share/java/bbmap/current/stream/bam/BgzfInputStreamMT.class
usr/share/java/bbmap/current/stream/bam/BgzfInputStreamMT.java
usr/share/java/bbmap/current/stream/bam/BgzfInputStreamMT2$1.class
usr/share/java/bbmap/current/stream/bam/BgzfInputStreamMT2$2.class
usr/share/java/bbmap/current/stream/bam/BgzfInputStreamMT2$PrefixedInputStream.class
usr/share/java/bbmap/current/stream/bam/BgzfInputStreamMT2.class
usr/share/java/bbmap/current/stream/bam/BgzfInputStreamMT2.java
usr/share/java/bbmap/current/stream/bam/BgzfInputStreamMT3$1.class
usr/share/java/bbmap/current/stream/bam/BgzfInputStreamMT3$2.class
usr/share/java/bbmap/current/stream/bam/BgzfInputStreamMT3$PrefixedInputStream.class
usr/share/java/bbmap/current/stream/bam/BgzfInputStreamMT3.class
usr/share/java/bbmap/current/stream/bam/BgzfInputStreamMT3.java
usr/share/java/bbmap/current/stream/bam/BgzfJob.class
usr/share/java/bbmap/current/stream/bam/BgzfJob.java
usr/share/java/bbmap/current/stream/bam/BgzfOutputStream.class
usr/share/java/bbmap/current/stream/bam/BgzfOutputStream.java
usr/share/java/bbmap/current/stream/bam/BgzfOutputStreamMT$1.class
usr/share/java/bbmap/current/stream/bam/BgzfOutputStreamMT$2.class
usr/share/java/bbmap/current/stream/bam/BgzfOutputStreamMT.class
usr/share/java/bbmap/current/stream/bam/BgzfOutputStreamMT.java
usr/share/java/bbmap/current/stream/bam/BgzfOutputStreamMT2$ProcessThread.class
usr/share/java/bbmap/current/stream/bam/BgzfOutputStreamMT2.class
usr/share/java/bbmap/current/stream/bam/BgzfOutputStreamMT2.java
usr/share/java/bbmap/current/stream/bam/BgzfSettings.class
usr/share/java/bbmap/current/stream/bam/BgzfSettings.java
usr/share/java/bbmap/current/stream/bam/DebugBgzfRead.class
usr/share/java/bbmap/current/stream/bam/DebugBgzfRead.java
usr/share/java/bbmap/current/stream/bam/DebugBgzfWrite.class
usr/share/java/bbmap/current/stream/bam/DebugBgzfWrite.java
usr/share/java/bbmap/current/stream/bam/SamToBamConverter.class
usr/share/java/bbmap/current/stream/bam/SamToBamConverter.java
usr/share/java/bbmap/current/stream/bam/TestBamIndexWriter.class
usr/share/java/bbmap/current/stream/bam/TestBamIndexWriter.java
usr/share/java/bbmap/current/stream/bam/TestBamReader.class
usr/share/java/bbmap/current/stream/bam/TestBamReader.java
usr/share/java/bbmap/current/stream/bam/TestBgzfA80k.class
usr/share/java/bbmap/current/stream/bam/TestBgzfA80k.java
usr/share/java/bbmap/current/stream/bam/TestBgzfMultithreaded.class
usr/share/java/bbmap/current/stream/bam/TestBgzfMultithreaded.java
usr/share/java/bbmap/current/stream/bam/TestBgzfSimple.class
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usr/share/java/bbmap/current/stream/bam/TestSeqReverse.class
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usr/share/java/bbmap/current/stream/bam/TestSimpleBgzfRead.class
usr/share/java/bbmap/current/stream/bam/TestSimpleBgzfRead.java
usr/share/java/bbmap/current/structures/
usr/share/java/bbmap/current/structures/AbstractBitSet.class
usr/share/java/bbmap/current/structures/AbstractBitSet.java
usr/share/java/bbmap/current/structures/AbstractIntHashMap.class
usr/share/java/bbmap/current/structures/AbstractIntHashMap.java
usr/share/java/bbmap/current/structures/AtomicBitSet.class
usr/share/java/bbmap/current/structures/AtomicBitSet.java
usr/share/java/bbmap/current/structures/AtomicStringNum.class
usr/share/java/bbmap/current/structures/AtomicStringNum.java
usr/share/java/bbmap/current/structures/BinaryByteWrapperLE.class
usr/share/java/bbmap/current/structures/BinaryByteWrapperLE.java
usr/share/java/bbmap/current/structures/ByteBuilder.class
usr/share/java/bbmap/current/structures/ByteBuilder.java
usr/share/java/bbmap/current/structures/CRange.class
usr/share/java/bbmap/current/structures/CRange.java
usr/share/java/bbmap/current/structures/CoverageArray.class
usr/share/java/bbmap/current/structures/CoverageArray.java
usr/share/java/bbmap/current/structures/CoverageArray2.class
usr/share/java/bbmap/current/structures/CoverageArray2.java
usr/share/java/bbmap/current/structures/CoverageArray2A.class
usr/share/java/bbmap/current/structures/CoverageArray2A.java
usr/share/java/bbmap/current/structures/CoverageArray3.class
usr/share/java/bbmap/current/structures/CoverageArray3.java
usr/share/java/bbmap/current/structures/CoverageArray3A.class
usr/share/java/bbmap/current/structures/CoverageArray3A.java
usr/share/java/bbmap/current/structures/Crispr.class
usr/share/java/bbmap/current/structures/Crispr.java
usr/share/java/bbmap/current/structures/DoubleList.class
usr/share/java/bbmap/current/structures/DoubleList.java
usr/share/java/bbmap/current/structures/Feature.class
usr/share/java/bbmap/current/structures/Feature.java
usr/share/java/bbmap/current/structures/FloatList.class
usr/share/java/bbmap/current/structures/FloatList.java
usr/share/java/bbmap/current/structures/Heap$HeapIterator.class
usr/share/java/bbmap/current/structures/Heap.class
usr/share/java/bbmap/current/structures/Heap.java
usr/share/java/bbmap/current/structures/HeapLoc$HeapIterator.class
usr/share/java/bbmap/current/structures/HeapLoc.class
usr/share/java/bbmap/current/structures/HeapLoc.java
usr/share/java/bbmap/current/structures/IntHashMap.class
usr/share/java/bbmap/current/structures/IntHashMap.java
usr/share/java/bbmap/current/structures/IntHashMapBinary.class
usr/share/java/bbmap/current/structures/IntHashMapBinary.java
usr/share/java/bbmap/current/structures/IntHashSet.class
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usr/share/java/bbmap/current/structures/IntHashSetList.class
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usr/share/java/bbmap/current/structures/IntList2.java
usr/share/java/bbmap/current/structures/IntList3.class
usr/share/java/bbmap/current/structures/IntList3.java
usr/share/java/bbmap/current/structures/IntListCompressor.class
usr/share/java/bbmap/current/structures/IntListCompressor.java
usr/share/java/bbmap/current/structures/IntListHashMap.class
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usr/share/java/bbmap/current/structures/IntLongHashMap.class
usr/share/java/bbmap/current/structures/IntLongHashMap.java
usr/share/java/bbmap/current/structures/IntMap.class
usr/share/java/bbmap/current/structures/IntMap.java
usr/share/java/bbmap/current/structures/IntRingBuffer.class
usr/share/java/bbmap/current/structures/IntRingBuffer.java
usr/share/java/bbmap/current/structures/IntRingBufferCond.class
usr/share/java/bbmap/current/structures/IntRingBufferCond.java
usr/share/java/bbmap/current/structures/ListNum.class
usr/share/java/bbmap/current/structures/ListNum.java
usr/share/java/bbmap/current/structures/LongArrayListHashMap.class
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usr/share/java/bbmap/current/structures/LongHashMap.class
usr/share/java/bbmap/current/structures/LongHashMap.java
usr/share/java/bbmap/current/structures/LongHashSet.class
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usr/share/java/bbmap/current/structures/LongHeapSetInterface.class
usr/share/java/bbmap/current/structures/LongHeapSetInterface.java
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usr/share/java/bbmap/current/structures/LongList2.class
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usr/share/java/bbmap/current/structures/LongList3.class
usr/share/java/bbmap/current/structures/LongList3.java
usr/share/java/bbmap/current/structures/LongListSet$LongListSetIterator.class
usr/share/java/bbmap/current/structures/LongListSet.class
usr/share/java/bbmap/current/structures/LongListSet.java
usr/share/java/bbmap/current/structures/LongLongHashMap.class
usr/share/java/bbmap/current/structures/LongLongHashMap.java
usr/share/java/bbmap/current/structures/LongLongHashMapHybrid.class
usr/share/java/bbmap/current/structures/LongLongHashMapHybrid.java
usr/share/java/bbmap/current/structures/LongLongListHashMap.class
usr/share/java/bbmap/current/structures/LongLongListHashMap.java
usr/share/java/bbmap/current/structures/LongM.class
usr/share/java/bbmap/current/structures/LongM.java
usr/share/java/bbmap/current/structures/LongPair.class
usr/share/java/bbmap/current/structures/LongPair.java
usr/share/java/bbmap/current/structures/MultiBitSet.class
usr/share/java/bbmap/current/structures/MultiBitSet.java
usr/share/java/bbmap/current/structures/Point.class
usr/share/java/bbmap/current/structures/Point.java
usr/share/java/bbmap/current/structures/Quantizer.class
usr/share/java/bbmap/current/structures/Quantizer.java
usr/share/java/bbmap/current/structures/README.md
usr/share/java/bbmap/current/structures/Range.class
usr/share/java/bbmap/current/structures/Range.java
usr/share/java/bbmap/current/structures/RawBitSet.class
usr/share/java/bbmap/current/structures/RawBitSet.java
usr/share/java/bbmap/current/structures/RingBuffer.class
usr/share/java/bbmap/current/structures/RingBuffer.java
usr/share/java/bbmap/current/structures/RingBufferMask.class
usr/share/java/bbmap/current/structures/RingBufferMask.java
usr/share/java/bbmap/current/structures/RingBufferMod.class
usr/share/java/bbmap/current/structures/RingBufferMod.java
usr/share/java/bbmap/current/structures/SeqCount.class
usr/share/java/bbmap/current/structures/SeqCount.java
usr/share/java/bbmap/current/structures/SeqCountM.class
usr/share/java/bbmap/current/structures/SeqCountM.java
usr/share/java/bbmap/current/structures/SeqMap$1.class
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usr/share/java/bbmap/current/structures/SeqMap$3.class
usr/share/java/bbmap/current/structures/SeqMap.class
usr/share/java/bbmap/current/structures/SeqMap.java
usr/share/java/bbmap/current/structures/SeqPos.class
usr/share/java/bbmap/current/structures/SeqPos.java
usr/share/java/bbmap/current/structures/SeqPosM.class
usr/share/java/bbmap/current/structures/SeqPosM.java
usr/share/java/bbmap/current/structures/SetLoc.class
usr/share/java/bbmap/current/structures/SetLoc.java
usr/share/java/bbmap/current/structures/StandardDeviator$ProcessThread.class
usr/share/java/bbmap/current/structures/StandardDeviator.class
usr/share/java/bbmap/current/structures/StandardDeviator.java
usr/share/java/bbmap/current/structures/StringCount.class
usr/share/java/bbmap/current/structures/StringCount.java
usr/share/java/bbmap/current/structures/StringNum.class
usr/share/java/bbmap/current/structures/StringNum.java
usr/share/java/bbmap/current/structures/StringPair.class
usr/share/java/bbmap/current/structures/StringPair.java
usr/share/java/bbmap/current/structures/SuperLongList.class
usr/share/java/bbmap/current/structures/SuperLongList.java
usr/share/java/bbmap/current/structures/XNum.class
usr/share/java/bbmap/current/structures/XNum.java
usr/share/java/bbmap/current/synth/
usr/share/java/bbmap/current/synth/CoverageModel.class
usr/share/java/bbmap/current/synth/CoverageModel.java
usr/share/java/bbmap/current/synth/CrossContaminate$Vessel.class
usr/share/java/bbmap/current/synth/CrossContaminate.class
usr/share/java/bbmap/current/synth/CrossContaminate.java
usr/share/java/bbmap/current/synth/FakeReads.class
usr/share/java/bbmap/current/synth/FakeReads.java
usr/share/java/bbmap/current/synth/FuseSequence.class
usr/share/java/bbmap/current/synth/FuseSequence.java
usr/share/java/bbmap/current/synth/GCBias.class
usr/share/java/bbmap/current/synth/GCBias.java
usr/share/java/bbmap/current/synth/MakeChimeras.class
usr/share/java/bbmap/current/synth/MakeChimeras.java
usr/share/java/bbmap/current/synth/MakeContaminatedGenomes.class
usr/share/java/bbmap/current/synth/MakeContaminatedGenomes.java
usr/share/java/bbmap/current/synth/MutateGenome$SmallVar.class
usr/share/java/bbmap/current/synth/MutateGenome.class
usr/share/java/bbmap/current/synth/MutateGenome.java
usr/share/java/bbmap/current/synth/MutateGenome2$SmallVar.class
usr/share/java/bbmap/current/synth/MutateGenome2.class
usr/share/java/bbmap/current/synth/MutateGenome2.java
usr/share/java/bbmap/current/synth/RandomGenome.class
usr/share/java/bbmap/current/synth/RandomGenome.java
usr/share/java/bbmap/current/synth/RandomHexamer.class
usr/share/java/bbmap/current/synth/RandomHexamer.java
usr/share/java/bbmap/current/synth/RandomReads3$1.class
usr/share/java/bbmap/current/synth/RandomReads3.class
usr/share/java/bbmap/current/synth/RandomReads3.java
usr/share/java/bbmap/current/synth/RandomReadsMG$ProcessThread.class
usr/share/java/bbmap/current/synth/RandomReadsMG.class
usr/share/java/bbmap/current/synth/RandomReadsMG.java
usr/share/java/bbmap/current/synth/Shred.class
usr/share/java/bbmap/current/synth/Shred.java
usr/share/java/bbmap/current/synth/SynthMDA.class
usr/share/java/bbmap/current/synth/SynthMDA.java
usr/share/java/bbmap/current/tax/
usr/share/java/bbmap/current/tax/AccessionToTaxid$HashThread.class
usr/share/java/bbmap/current/tax/AccessionToTaxid.class
usr/share/java/bbmap/current/tax/AccessionToTaxid.java
usr/share/java/bbmap/current/tax/AnalyzeAccession$ProcessThread.class
usr/share/java/bbmap/current/tax/AnalyzeAccession.class
usr/share/java/bbmap/current/tax/AnalyzeAccession.java
usr/share/java/bbmap/current/tax/AnalyzeAccession_ST.class
usr/share/java/bbmap/current/tax/AnalyzeAccession_ST.java
usr/share/java/bbmap/current/tax/CanonicalLineage.class
usr/share/java/bbmap/current/tax/CanonicalLineage.java
usr/share/java/bbmap/current/tax/ExplodeTree.class
usr/share/java/bbmap/current/tax/ExplodeTree.java
usr/share/java/bbmap/current/tax/FilterByTaxa.class
usr/share/java/bbmap/current/tax/FilterByTaxa.java
usr/share/java/bbmap/current/tax/FindAncestor.class
usr/share/java/bbmap/current/tax/FindAncestor.java
usr/share/java/bbmap/current/tax/GiToTaxid.class
usr/share/java/bbmap/current/tax/GiToTaxid.java
usr/share/java/bbmap/current/tax/GiToTaxidInt.class
usr/share/java/bbmap/current/tax/GiToTaxidInt.java
usr/share/java/bbmap/current/tax/IDNode.class
usr/share/java/bbmap/current/tax/IDNode.java
usr/share/java/bbmap/current/tax/IDTree.class
usr/share/java/bbmap/current/tax/IDTree.java
usr/share/java/bbmap/current/tax/ImgRecord.class
usr/share/java/bbmap/current/tax/ImgRecord.java
usr/share/java/bbmap/current/tax/ImgRecord2.class
usr/share/java/bbmap/current/tax/ImgRecord2.java
usr/share/java/bbmap/current/tax/Lineage.class
usr/share/java/bbmap/current/tax/Lineage.java
usr/share/java/bbmap/current/tax/PrintTaxonomy.class
usr/share/java/bbmap/current/tax/PrintTaxonomy.java
usr/share/java/bbmap/current/tax/Query.class
usr/share/java/bbmap/current/tax/Query.java
usr/share/java/bbmap/current/tax/README.md
usr/share/java/bbmap/current/tax/RenameGiToTaxid.class
usr/share/java/bbmap/current/tax/RenameGiToTaxid.java
usr/share/java/bbmap/current/tax/RenameIMG.class
usr/share/java/bbmap/current/tax/RenameIMG.java
usr/share/java/bbmap/current/tax/ShrinkAccession.class
usr/share/java/bbmap/current/tax/ShrinkAccession.java
usr/share/java/bbmap/current/tax/SplitByTaxa.class
usr/share/java/bbmap/current/tax/SplitByTaxa.java
usr/share/java/bbmap/current/tax/TaxApp$1.class
usr/share/java/bbmap/current/tax/TaxApp.class
usr/share/java/bbmap/current/tax/TaxApp.java
usr/share/java/bbmap/current/tax/TaxClient.class
usr/share/java/bbmap/current/tax/TaxClient.java
usr/share/java/bbmap/current/tax/TaxFilter$1.class
usr/share/java/bbmap/current/tax/TaxFilter.class
usr/share/java/bbmap/current/tax/TaxFilter.java
usr/share/java/bbmap/current/tax/TaxNode$CountComparator.class
usr/share/java/bbmap/current/tax/TaxNode.class
usr/share/java/bbmap/current/tax/TaxNode.java
usr/share/java/bbmap/current/tax/TaxServer$CompareThread.class
usr/share/java/bbmap/current/tax/TaxServer$HelpHandler.class
usr/share/java/bbmap/current/tax/TaxServer$IconHandler.class
usr/share/java/bbmap/current/tax/TaxServer$KillHandler.class
usr/share/java/bbmap/current/tax/TaxServer$SketchHandler$SketchInstance.class
usr/share/java/bbmap/current/tax/TaxServer$SketchHandler.class
usr/share/java/bbmap/current/tax/TaxServer$StatsHandler.class
usr/share/java/bbmap/current/tax/TaxServer$TaxHandler.class
usr/share/java/bbmap/current/tax/TaxServer.class
usr/share/java/bbmap/current/tax/TaxServer.java
usr/share/java/bbmap/current/tax/TaxSize.class
usr/share/java/bbmap/current/tax/TaxSize.java
usr/share/java/bbmap/current/tax/TaxTree.class
usr/share/java/bbmap/current/tax/TaxTree.java
usr/share/java/bbmap/current/template/
usr/share/java/bbmap/current/template/A_Sample.class
usr/share/java/bbmap/current/template/A_Sample.java
usr/share/java/bbmap/current/template/A_Sample2.class
usr/share/java/bbmap/current/template/A_Sample2.java
usr/share/java/bbmap/current/template/A_SampleBasic.class
usr/share/java/bbmap/current/template/A_SampleBasic.java
usr/share/java/bbmap/current/template/A_SampleBasic2.class
usr/share/java/bbmap/current/template/A_SampleBasic2.java
usr/share/java/bbmap/current/template/A_SampleByteFile.class
usr/share/java/bbmap/current/template/A_SampleByteFile.java
usr/share/java/bbmap/current/template/A_SampleByteFileMT$ProcessThread.class
usr/share/java/bbmap/current/template/A_SampleByteFileMT.class
usr/share/java/bbmap/current/template/A_SampleByteFileMT.java
usr/share/java/bbmap/current/template/A_SampleD.class
usr/share/java/bbmap/current/template/A_SampleD.java
usr/share/java/bbmap/current/template/A_SampleMT$ProcessThread.class
usr/share/java/bbmap/current/template/A_SampleMT.class
usr/share/java/bbmap/current/template/A_SampleMT.java
usr/share/java/bbmap/current/template/A_SampleMultipleInput.class
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usr/share/java/bbmap/current/template/A_SampleSamStreamer$ProcessThread.class
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usr/share/java/bbmap/current/template/A_SampleSamStreamer.java
usr/share/java/bbmap/current/template/A_SampleStreamer.class
usr/share/java/bbmap/current/template/A_SampleStreamer.java
usr/share/java/bbmap/current/template/A_SampleSummary.class
usr/share/java/bbmap/current/template/A_SampleSummary.java
usr/share/java/bbmap/current/template/A_Sample_Generator$ProcessThread.class
usr/share/java/bbmap/current/template/A_Sample_Generator.class
usr/share/java/bbmap/current/template/A_Sample_Generator.java
usr/share/java/bbmap/current/template/A_Sample_Unpaired.class
usr/share/java/bbmap/current/template/A_Sample_Unpaired.java
usr/share/java/bbmap/current/template/Accumulator.class
usr/share/java/bbmap/current/template/Accumulator.java
usr/share/java/bbmap/current/template/BBTool_ST.class
usr/share/java/bbmap/current/template/BBTool_ST.java
usr/share/java/bbmap/current/template/DoWorker.class
usr/share/java/bbmap/current/template/DoWorker.java
usr/share/java/bbmap/current/template/README.md
usr/share/java/bbmap/current/template/ThreadPoolJob.class
usr/share/java/bbmap/current/template/ThreadPoolJob.java
usr/share/java/bbmap/current/template/ThreadWaiter.class
usr/share/java/bbmap/current/template/ThreadWaiter.java
usr/share/java/bbmap/current/tracker/
usr/share/java/bbmap/current/tracker/AdapterTracker.class
usr/share/java/bbmap/current/tracker/AdapterTracker.java
usr/share/java/bbmap/current/tracker/CrisprTracker.class
usr/share/java/bbmap/current/tracker/CrisprTracker.java
usr/share/java/bbmap/current/tracker/EntropyTracker.class
usr/share/java/bbmap/current/tracker/EntropyTracker.java
usr/share/java/bbmap/current/tracker/KmerTracker.class
usr/share/java/bbmap/current/tracker/KmerTracker.java
usr/share/java/bbmap/current/tracker/PalindromeTracker.class
usr/share/java/bbmap/current/tracker/PalindromeTracker.java
usr/share/java/bbmap/current/tracker/PolymerTracker.class
usr/share/java/bbmap/current/tracker/PolymerTracker.java
usr/share/java/bbmap/current/tracker/QualityTracker.class
usr/share/java/bbmap/current/tracker/QualityTracker.java
usr/share/java/bbmap/current/tracker/ReadStats.class
usr/share/java/bbmap/current/tracker/ReadStats.java
usr/share/java/bbmap/current/tracker/SealStats$SealStatsLine.class
usr/share/java/bbmap/current/tracker/SealStats.class
usr/share/java/bbmap/current/tracker/SealStats.java
usr/share/java/bbmap/current/ukmer/
usr/share/java/bbmap/current/ukmer/AbstractKmerTableU$AllocThread.class
usr/share/java/bbmap/current/ukmer/AbstractKmerTableU.class
usr/share/java/bbmap/current/ukmer/AbstractKmerTableU.java
usr/share/java/bbmap/current/ukmer/DumpThreadU.class
usr/share/java/bbmap/current/ukmer/DumpThreadU.java
usr/share/java/bbmap/current/ukmer/HashArrayU.class
usr/share/java/bbmap/current/ukmer/HashArrayU.java
usr/share/java/bbmap/current/ukmer/HashArrayU1D$WalkerU1D.class
usr/share/java/bbmap/current/ukmer/HashArrayU1D.class
usr/share/java/bbmap/current/ukmer/HashArrayU1D.java
usr/share/java/bbmap/current/ukmer/HashArrayU2D.class
usr/share/java/bbmap/current/ukmer/HashArrayU2D.java
usr/share/java/bbmap/current/ukmer/HashArrayUHybrid.class
usr/share/java/bbmap/current/ukmer/HashArrayUHybrid.java
usr/share/java/bbmap/current/ukmer/HashBufferU.class
usr/share/java/bbmap/current/ukmer/HashBufferU.java
usr/share/java/bbmap/current/ukmer/HashForestU.class
usr/share/java/bbmap/current/ukmer/HashForestU.java
usr/share/java/bbmap/current/ukmer/HistogramMakerU$FillThread.class
usr/share/java/bbmap/current/ukmer/HistogramMakerU.class
usr/share/java/bbmap/current/ukmer/HistogramMakerU.java
usr/share/java/bbmap/current/ukmer/Kmer.class
usr/share/java/bbmap/current/ukmer/Kmer.java
usr/share/java/bbmap/current/ukmer/KmerBufferU.class
usr/share/java/bbmap/current/ukmer/KmerBufferU.java
usr/share/java/bbmap/current/ukmer/KmerNodeU.class
usr/share/java/bbmap/current/ukmer/KmerNodeU.java
usr/share/java/bbmap/current/ukmer/KmerNodeU1D.class
usr/share/java/bbmap/current/ukmer/KmerNodeU1D.java
usr/share/java/bbmap/current/ukmer/KmerNodeU2D.class
usr/share/java/bbmap/current/ukmer/KmerNodeU2D.java
usr/share/java/bbmap/current/ukmer/KmerTableSetU$LoadThread.class
usr/share/java/bbmap/current/ukmer/KmerTableSetU$WalkerKSTU.class
usr/share/java/bbmap/current/ukmer/KmerTableSetU.class
usr/share/java/bbmap/current/ukmer/KmerTableSetU.java
usr/share/java/bbmap/current/ukmer/OwnershipThread.class
usr/share/java/bbmap/current/ukmer/OwnershipThread.java
usr/share/java/bbmap/current/ukmer/README.md
usr/share/java/bbmap/current/ukmer/WalkerU.class
usr/share/java/bbmap/current/ukmer/WalkerU.java
usr/share/java/bbmap/current/var/
usr/share/java/bbmap/current/var/ApplyVarsToReference$1.class
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usr/share/java/bbmap/current/var/ApplyVarsToReference.java
usr/share/java/bbmap/current/var/GenerateConsensusVariations$1.class
usr/share/java/bbmap/current/var/GenerateConsensusVariations.class
usr/share/java/bbmap/current/var/GenerateConsensusVariations.java
usr/share/java/bbmap/current/var/GenerateVarlets$ProcessThread.class
usr/share/java/bbmap/current/var/GenerateVarlets.class
usr/share/java/bbmap/current/var/GenerateVarlets.java
usr/share/java/bbmap/current/var/GenerateVarlets2$1.class
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usr/share/java/bbmap/current/var/GenerateVarlets3.java
usr/share/java/bbmap/current/var/README.md
usr/share/java/bbmap/current/var/StackVariations$1.class
usr/share/java/bbmap/current/var/StackVariations$SVThread.class
usr/share/java/bbmap/current/var/StackVariations.class
usr/share/java/bbmap/current/var/StackVariations.java
usr/share/java/bbmap/current/var/StackVariations2$1.class
usr/share/java/bbmap/current/var/StackVariations2$SVThread.class
usr/share/java/bbmap/current/var/StackVariations2.class
usr/share/java/bbmap/current/var/StackVariations2.java
usr/share/java/bbmap/current/var/VarLine.class
usr/share/java/bbmap/current/var/VarLine.java
usr/share/java/bbmap/current/var/Variation.class
usr/share/java/bbmap/current/var/Variation.java
usr/share/java/bbmap/current/var/Varlet.class
usr/share/java/bbmap/current/var/Varlet.java
usr/share/java/bbmap/current/var2/
usr/share/java/bbmap/current/var2/AnalyzeVars.class
usr/share/java/bbmap/current/var2/AnalyzeVars.java
usr/share/java/bbmap/current/var2/ApplyVariants.class
usr/share/java/bbmap/current/var2/ApplyVariants.java
usr/share/java/bbmap/current/var2/CVOutputWriter.class
usr/share/java/bbmap/current/var2/CVOutputWriter.java
usr/share/java/bbmap/current/var2/CallVariants$ProcessThread.class
usr/share/java/bbmap/current/var2/CallVariants.class
usr/share/java/bbmap/current/var2/CallVariants.java
usr/share/java/bbmap/current/var2/CallVariants2$Sample$ProcessThread.class
usr/share/java/bbmap/current/var2/CallVariants2$Sample.class
usr/share/java/bbmap/current/var2/CallVariants2.class
usr/share/java/bbmap/current/var2/CallVariants2.java
usr/share/java/bbmap/current/var2/CompareVCF.class
usr/share/java/bbmap/current/var2/CompareVCF.java
usr/share/java/bbmap/current/var2/FeatureVectorMaker.class
usr/share/java/bbmap/current/var2/FeatureVectorMaker.java
usr/share/java/bbmap/current/var2/FilterSam$ProcessThread.class
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usr/share/java/bbmap/current/var2/FilterSam.java
usr/share/java/bbmap/current/var2/FilterVCF$ProcessThread.class
usr/share/java/bbmap/current/var2/FilterVCF.class
usr/share/java/bbmap/current/var2/FilterVCF.java
usr/share/java/bbmap/current/var2/MergeSamples$MergeThread.class
usr/share/java/bbmap/current/var2/MergeSamples.class
usr/share/java/bbmap/current/var2/MergeSamples.java
usr/share/java/bbmap/current/var2/README.md
usr/share/java/bbmap/current/var2/Realign$ProcessThread.class
usr/share/java/bbmap/current/var2/Realign.class
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usr/share/java/bbmap/current/var2/ScafMap.class
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usr/share/java/bbmap/current/var2/Scaffold.class
usr/share/java/bbmap/current/var2/Scaffold.java
usr/share/java/bbmap/current/var2/SoftClipper.class
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usr/share/java/bbmap/current/var2/VCFFile$1.class
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usr/share/java/bbmap/current/var2/VCFFile.java
usr/share/java/bbmap/current/var2/VCFLine.class
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usr/share/java/bbmap/current/var2/Var.class
usr/share/java/bbmap/current/var2/Var.java
usr/share/java/bbmap/current/var2/VarFilter.class
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usr/share/java/bbmap/current/var2/VarHelper.class
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usr/share/java/bbmap/current/var2/VarKey.class
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usr/share/java/bbmap/current/var2/VarProb.class
usr/share/java/bbmap/current/var2/VarProb.java
usr/share/java/bbmap/current/var2/VcfLoader$ProcessThread.class
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usr/share/java/bbmap/current/var2/VcfLoader.java
usr/share/java/bbmap/current/var2/VcfToVar.class
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usr/share/java/bbmap/current/var2/VcfWriter$ProcessThread.class
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usr/share/java/bbmap/current/var2/VcfWriter.java
usr/share/java/bbmap/current/var2/VectorDonovan$QuantileTransformer.class
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usr/share/java/bbmap/current/var2/VectorDonovan.java
usr/share/java/bbmap/current/var2/VectorElba$ElbaMinMaxValues.class
usr/share/java/bbmap/current/var2/VectorElba.class
usr/share/java/bbmap/current/var2/VectorElba.java
usr/share/java/bbmap/jni/
usr/share/java/bbmap/jni/BBMergeOverlapper.c
usr/share/java/bbmap/jni/BBMergeOverlapper.o
usr/share/java/bbmap/jni/BandedAlignerJNI.c
usr/share/java/bbmap/jni/BandedAlignerJNI.o
usr/share/java/bbmap/jni/CMakeLists.txt
usr/share/java/bbmap/jni/IceCreamAlignerJNI.c
usr/share/java/bbmap/jni/IceCreamAlignerJNI.o
usr/share/java/bbmap/jni/MultiStateAligner11tsJNI.c
usr/share/java/bbmap/jni/MultiStateAligner11tsJNI.o
usr/share/java/bbmap/jni/README.txt
usr/share/java/bbmap/jni/align2_BandedAlignerJNI.h
usr/share/java/bbmap/jni/align2_MultiStateAligner11tsJNI.h
usr/share/java/bbmap/jni/icecream_IceCreamAlignerJNI.h
usr/share/java/bbmap/jni/jgi_BBMergeOverlapper.h
usr/share/java/bbmap/jni/libbbtoolsjni.dylib
usr/share/java/bbmap/jni/libbbtoolsjni.so
usr/share/java/bbmap/jni/makefile.linux
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usr/share/java/bbmap/jni/run.sh
usr/share/java/bbmap/pipelines/
usr/share/java/bbmap/pipelines/assembleMito_Illumina.sh
usr/share/java/bbmap/pipelines/assembleMito_PacBio.sh
usr/share/java/bbmap/pipelines/assemble_polyg_isolate_v1.sh
usr/share/java/bbmap/pipelines/assemble_polyg_meta_v1.sh
usr/share/java/bbmap/pipelines/assemblyPipeline.sh
usr/share/java/bbmap/pipelines/callInsertions.sh
usr/share/java/bbmap/pipelines/covid/
usr/share/java/bbmap/pipelines/covid/makeSummary.sh
usr/share/java/bbmap/pipelines/covid/processCorona.sh
usr/share/java/bbmap/pipelines/covid/processCoronaWrapper.sh
usr/share/java/bbmap/pipelines/covid/readme.txt
usr/share/java/bbmap/pipelines/covid/recal.sh
usr/share/java/bbmap/pipelines/crisprPipeline.sh
usr/share/java/bbmap/pipelines/cutRna.sh
usr/share/java/bbmap/pipelines/fetch/
usr/share/java/bbmap/pipelines/fetch/fetchMito.sh
usr/share/java/bbmap/pipelines/fetch/fetchNt.sh
usr/share/java/bbmap/pipelines/fetch/fetchNtOuter.sh
usr/share/java/bbmap/pipelines/fetch/fetchPlasmid.sh
usr/share/java/bbmap/pipelines/fetch/fetchPlastid.sh
usr/share/java/bbmap/pipelines/fetch/fetchProkByGenus.sh
usr/share/java/bbmap/pipelines/fetch/fetchRefSeq.sh
usr/share/java/bbmap/pipelines/fetch/fetchRefSeqClades.sh
usr/share/java/bbmap/pipelines/fetch/fetchRefSeqCladesOuter.sh
usr/share/java/bbmap/pipelines/fetch/fetchSilva.sh
usr/share/java/bbmap/pipelines/fetch/fetchTaxonomy.sh
usr/share/java/bbmap/pipelines/fetch/runRefSeqProtein.sh
usr/share/java/bbmap/pipelines/fetch/sketchRefSeq.sh
usr/share/java/bbmap/pipelines/makeRiboKmers.sh
usr/share/java/bbmap/pipelines/processIMG.sh
usr/share/java/bbmap/pipelines/process_lane_v007.sh
usr/share/java/bbmap/pipelines/server/
usr/share/java/bbmap/pipelines/server/startNtServerVM.sh
usr/share/java/bbmap/pipelines/server/startProteinServerVM.sh
usr/share/java/bbmap/pipelines/server/startRefseqServerVM.sh
usr/share/java/bbmap/pipelines/server/startSilvaServerVM.sh
usr/share/java/bbmap/pipelines/server/startTaxServerVM.sh
usr/share/java/bbmap/pipelines/silva/
usr/share/java/bbmap/pipelines/silva/fetchSilva.sh
usr/share/java/bbmap/pipelines/silva/make15mers.sh
usr/share/java/bbmap/pipelines/silva/makeCoveringSetLsu.sh
usr/share/java/bbmap/pipelines/silva/makeCoveringSetSsu.sh
usr/share/java/bbmap/pipelines/silva/makeRep.sh
usr/share/java/bbmap/pipelines/testPlatformQuality.sh
usr/share/java/bbmap/pipelines/testsketch.sh
usr/share/java/bbmap/pipelines/variantPipeline.sh
usr/share/java/bbmap/resources/
usr/share/java/bbmap/resources/16S_15mers.fa
usr/share/java/bbmap/resources/16S_consensus_sequence.fa
usr/share/java/bbmap/resources/18S_15mers.fa
usr/share/java/bbmap/resources/18S_consensus_sequence.fa
usr/share/java/bbmap/resources/23S_15mers.fa
usr/share/java/bbmap/resources/23S_consensus_sequence.fa
usr/share/java/bbmap/resources/5S_10mers.fa
usr/share/java/bbmap/resources/5S_11mers.fa
usr/share/java/bbmap/resources/5S_12mers.fa
usr/share/java/bbmap/resources/5S_15mers.fa
usr/share/java/bbmap/resources/5S_9mers.fa
usr/share/java/bbmap/resources/5S_consensus_sequence.fa
usr/share/java/bbmap/resources/Covid19_ref.fa
usr/share/java/bbmap/resources/ITS_animal_consensus_sequence.fq
usr/share/java/bbmap/resources/ITS_consensus_sequence.fq
usr/share/java/bbmap/resources/ITS_fungi_consensus_sequence.fq
usr/share/java/bbmap/resources/ITS_nonfungi_consensus_sequence.fq
usr/share/java/bbmap/resources/ITS_other_consensus_sequence.fq
usr/share/java/bbmap/resources/ITS_plant_consensus_sequence.fq
usr/share/java/bbmap/resources/ITS_universal_consensus_sequence.fq
usr/share/java/bbmap/resources/PacBioAdapter.fa
usr/share/java/bbmap/resources/SIP_spikeins.fa.gz
usr/share/java/bbmap/resources/adapters.fa
usr/share/java/bbmap/resources/adapters_no_transposase.fa.gz
usr/share/java/bbmap/resources/artic3.fasta
usr/share/java/bbmap/resources/bbmerge.bbnet
usr/share/java/bbmap/resources/blacklist_nt_merged.sketch
usr/share/java/bbmap/resources/blacklist_prokprot_merged.sketch
usr/share/java/bbmap/resources/blacklist_refseq_merged.sketch
usr/share/java/bbmap/resources/blacklist_silva_merged.sketch
usr/share/java/bbmap/resources/contents.txt
usr/share/java/bbmap/resources/crelox.fa.gz
usr/share/java/bbmap/resources/crispr.bbnet.gz
usr/share/java/bbmap/resources/crisprs.fa.gz
usr/share/java/bbmap/resources/entropy_k4_w150.tsv
usr/share/java/bbmap/resources/favicon.ico
usr/share/java/bbmap/resources/kapatags.L40.fa
usr/share/java/bbmap/resources/lambda.fa.gz
usr/share/java/bbmap/resources/lfpe.linker.fa.gz
usr/share/java/bbmap/resources/lsu_15mers.fa
usr/share/java/bbmap/resources/m16S_consensus_sequence.fa
usr/share/java/bbmap/resources/m18S_consensus_sequence.fa
usr/share/java/bbmap/resources/minorAlleleCount.txt
usr/share/java/bbmap/resources/model.pgm
usr/share/java/bbmap/resources/mtst.fa
usr/share/java/bbmap/resources/nextera.fa.gz
usr/share/java/bbmap/resources/nextera_LMP_adapter.fa.gz
usr/share/java/bbmap/resources/nextera_LMP_linker.fa.gz
usr/share/java/bbmap/resources/p16S_consensus_sequence.fa
usr/share/java/bbmap/resources/pJET1.2.fa
usr/share/java/bbmap/resources/phix174_ill.ref.fa.gz
usr/share/java/bbmap/resources/phix2.fa.gz
usr/share/java/bbmap/resources/phix_adapters.fa
usr/share/java/bbmap/resources/phix_adapters.fa.gz
usr/share/java/bbmap/resources/polyA.fa.gz
usr/share/java/bbmap/resources/polya.fa
usr/share/java/bbmap/resources/polyc.fa
usr/share/java/bbmap/resources/polyg.fa
usr/share/java/bbmap/resources/polyt.fa
usr/share/java/bbmap/resources/primes.txt.gz
usr/share/java/bbmap/resources/quickbin1D_all.bbnet
usr/share/java/bbmap/resources/quickbinND_all.bbnet
usr/share/java/bbmap/resources/remote_files.txt
usr/share/java/bbmap/resources/remote_files_old.txt
usr/share/java/bbmap/resources/sample1.fq.gz
usr/share/java/bbmap/resources/sample2.fq.gz
usr/share/java/bbmap/resources/sequencing_artifacts.fa.gz
usr/share/java/bbmap/resources/short.fa
usr/share/java/bbmap/resources/shred4merFractions.tsv
usr/share/java/bbmap/resources/ssu_15mers.fa
usr/share/java/bbmap/resources/tRNA_10mers.fa
usr/share/java/bbmap/resources/tRNA_11mers.fa
usr/share/java/bbmap/resources/tRNA_15mers.fa
usr/share/java/bbmap/resources/tRNA_16mers.fa
usr/share/java/bbmap/resources/tRNA_consensus_sequence.fa
usr/share/java/bbmap/resources/tax_server.html
usr/share/java/bbmap/resources/truseq.fa.gz
usr/share/java/bbmap/resources/truseq_rna.fa.gz
