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bin/bbversion.sh
bin/bloomfilter.sh
bin/callvariants.sh
bin/clumpify.sh
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bin/dedupe.sh
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libexec/bbmap/a_sample_mt.sh
libexec/bbmap/addadapters.sh
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libexec/bbmap/adjusthomopolymers.sh
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libexec/bbmap/fix_script_paths.sh
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libexec/bbmap/icecreammaker.sh
libexec/bbmap/idmatrix.sh
libexec/bbmap/idtree.sh
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libexec/bbmap/invertkey.sh
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libexec/bbmap/makecontaminatedgenomes.sh
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libexec/bbmap/makequickbinvector.sh
libexec/bbmap/mantissacompare.sh
libexec/bbmap/mapPacBio.sh
libexec/bbmap/matrixtocolumns.sh
libexec/bbmap/memdetect.sh
libexec/bbmap/mergeOTUs.sh
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libexec/bbmap/quabblealigner.sh
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libexec/bbmap/randomgenome.sh
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libexec/bbmap/regressiontrainer.sh
libexec/bbmap/removebadbarcodes.sh
libexec/bbmap/removecatdogmousehuman.sh
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libexec/bbmap/removemicrobes.sh
libexec/bbmap/removesmartbell.sh
libexec/bbmap/rename.sh
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libexec/bbmap/renamecami.sh
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libexec/bbmap/runhmm.sh
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libexec/bbmap/scalarintervals.sh
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libexec/bbmap/shrinkaccession.sh
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libexec/bbmap/smithwaterman.sh
libexec/bbmap/sortbyname.sh
libexec/bbmap/splitbytaxa.sh
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libexec/bbmap/synthmda.sh
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libexec/bbmap/taxonomy.sh
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libexec/bbmap/testaligners.sh
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libexec/bbmap/testalignerslength.sh
libexec/bbmap/testfilesystem.sh
libexec/bbmap/testformat.sh
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libexec/bbmap/tetramerfreq.sh
libexec/bbmap/textfile.sh
libexec/bbmap/tiledump.sh
libexec/bbmap/train.sh
libexec/bbmap/trainLCHist.sh
libexec/bbmap/translate6frames.sh
libexec/bbmap/trimcontigs.sh
libexec/bbmap/ttllsimulate.sh
libexec/bbmap/unicode2ascii.sh
libexec/bbmap/unzip.sh
libexec/bbmap/vcf2gff.sh
libexec/bbmap/vectorutils.sh
libexec/bbmap/visualizealignment.sh
libexec/bbmap/wavefrontaligner.sh
libexec/bbmap/wavefrontalignerviz.sh
libexec/bbmap/webcheck.sh
libexec/bbmap/wobblealigner.sh
libexec/bbmap/wobbleplusaligner.sh
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libexec/bbmap/zz_rename_package.sh
%%JAVAJARDIR%%/bbmap/align2/AbstractIndex.class
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%%JAVAJARDIR%%/bbmap/aligner/SideChannel3.class
%%JAVAJARDIR%%/bbmap/aligner/SideChannel3.java
%%JAVAJARDIR%%/bbmap/aligner/SideChannel4.class
%%JAVAJARDIR%%/bbmap/aligner/SideChannel4.java
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat.class
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat.java
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat2.class
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat2.java
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat2Amino.class
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat2Amino.java
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat2_1D.class
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat2_1D.java
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat3.class
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat3.java
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlatFloat.class
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlatFloat.java
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerPacBioAdapter.class
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerPacBioAdapter.java
%%JAVAJARDIR%%/bbmap/assemble/AbstractBuildThread.class
%%JAVAJARDIR%%/bbmap/assemble/AbstractBuildThread.java
%%JAVAJARDIR%%/bbmap/assemble/AbstractExploreThread.class
%%JAVAJARDIR%%/bbmap/assemble/AbstractExploreThread.java
%%JAVAJARDIR%%/bbmap/assemble/AbstractProcessContigThread.class
%%JAVAJARDIR%%/bbmap/assemble/AbstractProcessContigThread.java
%%JAVAJARDIR%%/bbmap/assemble/AbstractRemoveThread$RemoveThread1.class
%%JAVAJARDIR%%/bbmap/assemble/AbstractRemoveThread$RemoveThread2.class
%%JAVAJARDIR%%/bbmap/assemble/AbstractRemoveThread.class
%%JAVAJARDIR%%/bbmap/assemble/AbstractRemoveThread.java
%%JAVAJARDIR%%/bbmap/assemble/AbstractShaveThread.class
%%JAVAJARDIR%%/bbmap/assemble/AbstractShaveThread.java
%%JAVAJARDIR%%/bbmap/assemble/BubblePopper.class
%%JAVAJARDIR%%/bbmap/assemble/BubblePopper.java
%%JAVAJARDIR%%/bbmap/assemble/Contig.class
%%JAVAJARDIR%%/bbmap/assemble/Contig.java
%%JAVAJARDIR%%/bbmap/assemble/Edge.class
%%JAVAJARDIR%%/bbmap/assemble/Edge.java
%%JAVAJARDIR%%/bbmap/assemble/ErrorTracker.class
%%JAVAJARDIR%%/bbmap/assemble/ErrorTracker.java
%%JAVAJARDIR%%/bbmap/assemble/KmerCompressor$BuildThread.class
%%JAVAJARDIR%%/bbmap/assemble/KmerCompressor.class
%%JAVAJARDIR%%/bbmap/assemble/KmerCompressor.java
%%JAVAJARDIR%%/bbmap/assemble/Postfilter.class
%%JAVAJARDIR%%/bbmap/assemble/Postfilter.java
%%JAVAJARDIR%%/bbmap/assemble/README.md
%%JAVAJARDIR%%/bbmap/assemble/Reassemble$GenomeRecord.class
%%JAVAJARDIR%%/bbmap/assemble/Reassemble.class
%%JAVAJARDIR%%/bbmap/assemble/Reassemble.java
%%JAVAJARDIR%%/bbmap/assemble/Rollback.class
%%JAVAJARDIR%%/bbmap/assemble/Rollback.java
%%JAVAJARDIR%%/bbmap/assemble/ShaveObject.class
%%JAVAJARDIR%%/bbmap/assemble/ShaveObject.java
%%JAVAJARDIR%%/bbmap/assemble/Shaver.class
%%JAVAJARDIR%%/bbmap/assemble/Shaver.java
%%JAVAJARDIR%%/bbmap/assemble/Shaver1$ExploreThread.class
%%JAVAJARDIR%%/bbmap/assemble/Shaver1$ShaveThread.class
%%JAVAJARDIR%%/bbmap/assemble/Shaver1.class
%%JAVAJARDIR%%/bbmap/assemble/Shaver1.java
%%JAVAJARDIR%%/bbmap/assemble/Shaver2$ExploreThread.class
%%JAVAJARDIR%%/bbmap/assemble/Shaver2$ShaveThread.class
%%JAVAJARDIR%%/bbmap/assemble/Shaver2.class
%%JAVAJARDIR%%/bbmap/assemble/Shaver2.java
%%JAVAJARDIR%%/bbmap/assemble/TadPipe.class
%%JAVAJARDIR%%/bbmap/assemble/TadPipe.java
%%JAVAJARDIR%%/bbmap/assemble/Tadpole$DumpKmersThread.class
%%JAVAJARDIR%%/bbmap/assemble/Tadpole$ExtendThread.class
%%JAVAJARDIR%%/bbmap/assemble/Tadpole$MakeKhistThread.class
%%JAVAJARDIR%%/bbmap/assemble/Tadpole.class
%%JAVAJARDIR%%/bbmap/assemble/Tadpole.java
%%JAVAJARDIR%%/bbmap/assemble/Tadpole1$BuildThread.class
%%JAVAJARDIR%%/bbmap/assemble/Tadpole1$ProcessContigThread.class
%%JAVAJARDIR%%/bbmap/assemble/Tadpole1.class
%%JAVAJARDIR%%/bbmap/assemble/Tadpole1.java
%%JAVAJARDIR%%/bbmap/assemble/Tadpole2$BuildThread.class
%%JAVAJARDIR%%/bbmap/assemble/Tadpole2$ProcessContigThread.class
%%JAVAJARDIR%%/bbmap/assemble/Tadpole2.class
%%JAVAJARDIR%%/bbmap/assemble/Tadpole2.java
%%JAVAJARDIR%%/bbmap/assemble/TadpoleWrapper$1.class
%%JAVAJARDIR%%/bbmap/assemble/TadpoleWrapper$Record.class
%%JAVAJARDIR%%/bbmap/assemble/TadpoleWrapper.class
%%JAVAJARDIR%%/bbmap/assemble/TadpoleWrapper.java
%%JAVAJARDIR%%/bbmap/barcode/AnalyzeBarcodes.class
%%JAVAJARDIR%%/bbmap/barcode/AnalyzeBarcodes.java
%%JAVAJARDIR%%/bbmap/barcode/Barcode.class
%%JAVAJARDIR%%/bbmap/barcode/Barcode.java
%%JAVAJARDIR%%/bbmap/barcode/BarcodeCounter.class
%%JAVAJARDIR%%/bbmap/barcode/BarcodeCounter.java
%%JAVAJARDIR%%/bbmap/barcode/BarcodeMappingStats.class
%%JAVAJARDIR%%/bbmap/barcode/BarcodeMappingStats.java
%%JAVAJARDIR%%/bbmap/barcode/BarcodeStats.class
%%JAVAJARDIR%%/bbmap/barcode/BarcodeStats.java
%%JAVAJARDIR%%/bbmap/barcode/CompareLabels$Label.class
%%JAVAJARDIR%%/bbmap/barcode/CompareLabels.class
%%JAVAJARDIR%%/bbmap/barcode/CompareLabels.java
%%JAVAJARDIR%%/bbmap/barcode/CorrelateBarcodes.class
%%JAVAJARDIR%%/bbmap/barcode/CorrelateBarcodes.java
%%JAVAJARDIR%%/bbmap/barcode/CountBarcodes.class
%%JAVAJARDIR%%/bbmap/barcode/CountBarcodes.java
%%JAVAJARDIR%%/bbmap/barcode/CountBarcodes2.class
%%JAVAJARDIR%%/bbmap/barcode/CountBarcodes2.java
%%JAVAJARDIR%%/bbmap/barcode/DemuxClient.class
%%JAVAJARDIR%%/bbmap/barcode/DemuxClient.java
%%JAVAJARDIR%%/bbmap/barcode/DemuxData.class
%%JAVAJARDIR%%/bbmap/barcode/DemuxData.java
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$BaseHandler.class
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$DemuxHandler.class
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$IconHandler.class
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$KillHandler.class
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$Pair.class
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$StatsHandler.class
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer.class
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer.java
%%JAVAJARDIR%%/bbmap/barcode/LegacyFileWriter$QTag.class
%%JAVAJARDIR%%/bbmap/barcode/LegacyFileWriter.class
%%JAVAJARDIR%%/bbmap/barcode/LegacyFileWriter.java
%%JAVAJARDIR%%/bbmap/barcode/NovaDemux.class
%%JAVAJARDIR%%/bbmap/barcode/NovaDemux.java
%%JAVAJARDIR%%/bbmap/barcode/PCRMatrix$MapLine.class
%%JAVAJARDIR%%/bbmap/barcode/PCRMatrix.class
%%JAVAJARDIR%%/bbmap/barcode/PCRMatrix.java
%%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist$PopThread.class
%%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist.class
%%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist.java
%%JAVAJARDIR%%/bbmap/barcode/README.md
%%JAVAJARDIR%%/bbmap/barcode/TagAndMerge.class
%%JAVAJARDIR%%/bbmap/barcode/TagAndMerge.java
%%JAVAJARDIR%%/bbmap/barcode/Transition.class
%%JAVAJARDIR%%/bbmap/barcode/Transition.java
%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixProb.class
%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixProb.java
%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixProbAbstract.class
%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixProbAbstract.java
%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixTile.class
%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixTile.java
%%JAVAJARDIR%%/bbmap/bbduk/Allocator$AllocThread.class
%%JAVAJARDIR%%/bbmap/bbduk/Allocator.class
%%JAVAJARDIR%%/bbmap/bbduk/Allocator.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk2$LoadThread.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk2$ProcessThread.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk2.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk2.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk3$ProcessThread.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk3.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk3.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk4$ProcessThread.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk4.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk4.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk5$ProcessThread.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk5.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk5.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk6$ProcessThread.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk6.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDuk6.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndex.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndex.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexAbstract.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexAbstract.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexAndLoader$LoadThread.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexAndLoader.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexAndLoader.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexMask.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexMask.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexMask2.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexMask2.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexMod.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexMod.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndex_clean$LoadThread.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndex_clean.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndex_clean.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDukLoader$LoadThread.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukLoader.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukLoader.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDukParser.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukParser.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDukProcessor.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukProcessor.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDukProcessor2.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukProcessor2.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDukProcessorS.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukProcessorS.java
%%JAVAJARDIR%%/bbmap/bbduk/BBDukS$ProcessThread.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukS.class
%%JAVAJARDIR%%/bbmap/bbduk/BBDukS.java
%%JAVAJARDIR%%/bbmap/bbmin/Minimizer.class
%%JAVAJARDIR%%/bbmap/bbmin/Minimizer.java
%%JAVAJARDIR%%/bbmap/bbmin/README.md
%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$EnsembleRefinerParams.class
%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$EvidenceRefinerParams.class
%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$GraphRefinerParams.class
%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$RefinerParams.class
%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner.class
%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner.java
%%JAVAJARDIR%%/bbmap/bin/AdjustEntropy.class
%%JAVAJARDIR%%/bbmap/bin/AdjustEntropy.java
%%JAVAJARDIR%%/bbmap/bin/AllToAllVectorMaker.class
%%JAVAJARDIR%%/bbmap/bin/AllToAllVectorMaker.java
%%JAVAJARDIR%%/bbmap/bin/Bin.class
%%JAVAJARDIR%%/bbmap/bin/Bin.java
%%JAVAJARDIR%%/bbmap/bin/BinComparator.class
%%JAVAJARDIR%%/bbmap/bin/BinComparator.java
%%JAVAJARDIR%%/bbmap/bin/BinObject.class
%%JAVAJARDIR%%/bbmap/bin/BinObject.java
%%JAVAJARDIR%%/bbmap/bin/BinSketcher$ProcessThread.class
%%JAVAJARDIR%%/bbmap/bin/BinSketcher.class
%%JAVAJARDIR%%/bbmap/bin/BinSketcher.java
%%JAVAJARDIR%%/bbmap/bin/BinStats.class
%%JAVAJARDIR%%/bbmap/bin/BinStats.java
%%JAVAJARDIR%%/bbmap/bin/BinStatsComparator.class
%%JAVAJARDIR%%/bbmap/bin/BinStatsComparator.java
%%JAVAJARDIR%%/bbmap/bin/Binner$CompareThread.class
%%JAVAJARDIR%%/bbmap/bin/Binner.class
%%JAVAJARDIR%%/bbmap/bin/Binner.java
%%JAVAJARDIR%%/bbmap/bin/ChartMaker.class
%%JAVAJARDIR%%/bbmap/bin/ChartMaker.java
%%JAVAJARDIR%%/bbmap/bin/Cluster.class
%%JAVAJARDIR%%/bbmap/bin/Cluster.java
%%JAVAJARDIR%%/bbmap/bin/ClusterWriter.class
%%JAVAJARDIR%%/bbmap/bin/ClusterWriter.java
%%JAVAJARDIR%%/bbmap/bin/ClusterWriter2$WriteThread.class
%%JAVAJARDIR%%/bbmap/bin/ClusterWriter2.class
%%JAVAJARDIR%%/bbmap/bin/ClusterWriter2.java
%%JAVAJARDIR%%/bbmap/bin/ConservationModel.class
%%JAVAJARDIR%%/bbmap/bin/ConservationModel.java
%%JAVAJARDIR%%/bbmap/bin/Contig$ContigIterator.class
%%JAVAJARDIR%%/bbmap/bin/Contig.class
%%JAVAJARDIR%%/bbmap/bin/Contig.java
%%JAVAJARDIR%%/bbmap/bin/ContigRenamer$ProcessThread.class
%%JAVAJARDIR%%/bbmap/bin/ContigRenamer$Scaf.class
%%JAVAJARDIR%%/bbmap/bin/ContigRenamer.class
%%JAVAJARDIR%%/bbmap/bin/ContigRenamer.java
%%JAVAJARDIR%%/bbmap/bin/CovMaker.class
%%JAVAJARDIR%%/bbmap/bin/CovMaker.java
%%JAVAJARDIR%%/bbmap/bin/CrystalChamber$Centroid.class
%%JAVAJARDIR%%/bbmap/bin/CrystalChamber.class
%%JAVAJARDIR%%/bbmap/bin/CrystalChamber.java
%%JAVAJARDIR%%/bbmap/bin/CrystalChamber2$Centroid.class
%%JAVAJARDIR%%/bbmap/bin/CrystalChamber2.class
%%JAVAJARDIR%%/bbmap/bin/CrystalChamber2.java
%%JAVAJARDIR%%/bbmap/bin/DataLoader.class
%%JAVAJARDIR%%/bbmap/bin/DataLoader.java
%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner$ConsensusResult.class
%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner$RefinerResult.class
%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner.class
%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner.java
%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner$ContigStatus.class
%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner$DBSCANResult.class
%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner.class
%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner.java
%%JAVAJARDIR%%/bbmap/bin/FileRenamer.class
%%JAVAJARDIR%%/bbmap/bin/FileRenamer.java
%%JAVAJARDIR%%/bbmap/bin/GTDBLine.class
%%JAVAJARDIR%%/bbmap/bin/GTDBLine.java
%%JAVAJARDIR%%/bbmap/bin/GeneTools.class
%%JAVAJARDIR%%/bbmap/bin/GeneTools.java
%%JAVAJARDIR%%/bbmap/bin/GradeBins$CCLine.class
%%JAVAJARDIR%%/bbmap/bin/GradeBins$PTAccumulator.class
%%JAVAJARDIR%%/bbmap/bin/GradeBins$ProcessThread.class
%%JAVAJARDIR%%/bbmap/bin/GradeBins.class
%%JAVAJARDIR%%/bbmap/bin/GradeBins.java
%%JAVAJARDIR%%/bbmap/bin/GraphRefiner$SimilarityGraph$Edge.class
%%JAVAJARDIR%%/bbmap/bin/GraphRefiner$SimilarityGraph.class
%%JAVAJARDIR%%/bbmap/bin/GraphRefiner.class
%%JAVAJARDIR%%/bbmap/bin/GraphRefiner.java
%%JAVAJARDIR%%/bbmap/bin/IDComparator.class
%%JAVAJARDIR%%/bbmap/bin/IDComparator.java
%%JAVAJARDIR%%/bbmap/bin/KeyValue.class
%%JAVAJARDIR%%/bbmap/bin/KeyValue.java
%%JAVAJARDIR%%/bbmap/bin/KmerProb.class
%%JAVAJARDIR%%/bbmap/bin/KmerProb.java
%%JAVAJARDIR%%/bbmap/bin/Oracle.class
%%JAVAJARDIR%%/bbmap/bin/Oracle.java
%%JAVAJARDIR%%/bbmap/bin/QuickBin$ProcessThread.class
%%JAVAJARDIR%%/bbmap/bin/QuickBin.class
%%JAVAJARDIR%%/bbmap/bin/QuickBin.java
%%JAVAJARDIR%%/bbmap/bin/README.md
%%JAVAJARDIR%%/bbmap/bin/RenameCAMI.class
%%JAVAJARDIR%%/bbmap/bin/RenameCAMI.java
%%JAVAJARDIR%%/bbmap/bin/SamLoader3$ParallelWorker.class
%%JAVAJARDIR%%/bbmap/bin/SamLoader3$QueueWorker.class
%%JAVAJARDIR%%/bbmap/bin/SamLoader3$Worker.class
%%JAVAJARDIR%%/bbmap/bin/SamLoader3.class
%%JAVAJARDIR%%/bbmap/bin/SamLoader3.java
%%JAVAJARDIR%%/bbmap/bin/ScoreComparator.class
%%JAVAJARDIR%%/bbmap/bin/ScoreComparator.java
%%JAVAJARDIR%%/bbmap/bin/SimilarityMeasures.class
%%JAVAJARDIR%%/bbmap/bin/SimilarityMeasures.java
%%JAVAJARDIR%%/bbmap/bin/SketchRecord.class
%%JAVAJARDIR%%/bbmap/bin/SketchRecord.java
%%JAVAJARDIR%%/bbmap/bin/Sketchable.class
%%JAVAJARDIR%%/bbmap/bin/Sketchable.java
%%JAVAJARDIR%%/bbmap/bin/SpectraCounter$LoadThread.class
%%JAVAJARDIR%%/bbmap/bin/SpectraCounter.class
%%JAVAJARDIR%%/bbmap/bin/SpectraCounter.java
%%JAVAJARDIR%%/bbmap/bin/Strictness.class
%%JAVAJARDIR%%/bbmap/bin/Strictness.java
%%JAVAJARDIR%%/bbmap/bin/binmap/BinMap.class
%%JAVAJARDIR%%/bbmap/bin/binmap/BinMap.java
%%JAVAJARDIR%%/bbmap/bin/binmap/BinMap2$1.class
%%JAVAJARDIR%%/bbmap/bin/binmap/BinMap2.class
%%JAVAJARDIR%%/bbmap/bin/binmap/BinMap2.java
%%JAVAJARDIR%%/bbmap/bin/binmap/BinMapSlice.class
%%JAVAJARDIR%%/bbmap/bin/binmap/BinMapSlice.java
%%JAVAJARDIR%%/bbmap/bin/binmap/Key.class
%%JAVAJARDIR%%/bbmap/bin/binmap/Key.java
%%JAVAJARDIR%%/bbmap/bin/binmap/Key0.class
%%JAVAJARDIR%%/bbmap/bin/binmap/Key0.java
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyG.class
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyG.java
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGC.class
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGC.java
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGD.class
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGD.java
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGDD.class
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGDD.java
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGH.class
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGH.java
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGHC.class
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGHC.java
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGHCD.class
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGHCD.java
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGHCDD.class
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGHCDD.java
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGHD.class
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGHD.java
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGHDD.class
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGHDD.java
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGHDDD.class
%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGHDDD.java
%%JAVAJARDIR%%/bbmap/bloom/BloomFilter.class
%%JAVAJARDIR%%/bbmap/bloom/BloomFilter.java
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrector.class
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrector.java
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrectorWrapper$ProcessThread.class
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrectorWrapper.class
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrectorWrapper.java
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterWrapper$ProcessThread.class
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterWrapper.class
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterWrapper.java
%%JAVAJARDIR%%/bbmap/bloom/ErrorCorrect$1.class
%%JAVAJARDIR%%/bbmap/bloom/ErrorCorrect.class
%%JAVAJARDIR%%/bbmap/bloom/ErrorCorrect.java
%%JAVAJARDIR%%/bbmap/bloom/IndexCounter$CountThread.class
%%JAVAJARDIR%%/bbmap/bloom/IndexCounter.class
%%JAVAJARDIR%%/bbmap/bloom/IndexCounter.java
%%JAVAJARDIR%%/bbmap/bloom/KCountArray$AllocThread.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray.java
%%JAVAJARDIR%%/bbmap/bloom/KCountArray2.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray2.java
%%JAVAJARDIR%%/bbmap/bloom/KCountArray3.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray3.java
%%JAVAJARDIR%%/bbmap/bloom/KCountArray4.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray4.java
%%JAVAJARDIR%%/bbmap/bloom/KCountArray4MT$WriteThread.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray4MT.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray4MT.java
%%JAVAJARDIR%%/bbmap/bloom/KCountArray5MT$WriteThread.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray5MT.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray5MT.java
%%JAVAJARDIR%%/bbmap/bloom/KCountArray6MT$WriteThread.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray6MT.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray6MT.java
%%JAVAJARDIR%%/bbmap/bloom/KCountArray7MT$WriteThread.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray7MT.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray7MT.java
%%JAVAJARDIR%%/bbmap/bloom/KCountArray7MTA$CountUsedThread.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray7MTA.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray7MTA.java
%%JAVAJARDIR%%/bbmap/bloom/KCountArray8MT$WriteThread.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray8MT.class
%%JAVAJARDIR%%/bbmap/bloom/KCountArray8MT.java
%%JAVAJARDIR%%/bbmap/bloom/KmerCount3.class
%%JAVAJARDIR%%/bbmap/bloom/KmerCount3.java
%%JAVAJARDIR%%/bbmap/bloom/KmerCount4.class
%%JAVAJARDIR%%/bbmap/bloom/KmerCount4.java
%%JAVAJARDIR%%/bbmap/bloom/KmerCount5.class
%%JAVAJARDIR%%/bbmap/bloom/KmerCount5.java
%%JAVAJARDIR%%/bbmap/bloom/KmerCount6.class
%%JAVAJARDIR%%/bbmap/bloom/KmerCount6.java
%%JAVAJARDIR%%/bbmap/bloom/KmerCountAbstract.class
%%JAVAJARDIR%%/bbmap/bloom/KmerCountAbstract.java
%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount.class
%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount.java
%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount2.class
%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount2.java
%%JAVAJARDIR%%/bbmap/bloom/ParseBloomFilter.class
%%JAVAJARDIR%%/bbmap/bloom/ParseBloomFilter.java
%%JAVAJARDIR%%/bbmap/bloom/PolyFilter$ProcessThread.class
%%JAVAJARDIR%%/bbmap/bloom/PolyFilter.class
%%JAVAJARDIR%%/bbmap/bloom/PolyFilter.java
%%JAVAJARDIR%%/bbmap/bloom/README.md
%%JAVAJARDIR%%/bbmap/bloom/ReadCounter$1.class
%%JAVAJARDIR%%/bbmap/bloom/ReadCounter$CountThread.class
%%JAVAJARDIR%%/bbmap/bloom/ReadCounter.class
%%JAVAJARDIR%%/bbmap/bloom/ReadCounter.java
%%JAVAJARDIR%%/bbmap/bloom/TestLargeKmer.class
%%JAVAJARDIR%%/bbmap/bloom/TestLargeKmer.java
%%JAVAJARDIR%%/bbmap/cardinality/AbstractCardStats.class
%%JAVAJARDIR%%/bbmap/cardinality/AbstractCardStats.java
%%JAVAJARDIR%%/bbmap/cardinality/ApacheHLL4Wrapper.class
%%JAVAJARDIR%%/bbmap/cardinality/ApacheHLL4Wrapper.java
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticCompressedDynamicLogLog4.class
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticCompressedDynamicLogLog4.java
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticCompressedDynamicLogLog5.class
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticCompressedDynamicLogLog5.java
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticUltraDynamicLogLog32.class
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticUltraDynamicLogLog32.java
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticUltraDynamicLogLog33.class
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticUltraDynamicLogLog33.java
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticVariableDynamicLogLog32.class
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticVariableDynamicLogLog32.java
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticVariableDynamicLogLog34.class
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticVariableDynamicLogLog34.java
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticVariableDynamicLogLog36.class
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticVariableDynamicLogLog36.java
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticVariableDynamicLogLog64.class
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticVariableDynamicLogLog64.java
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticVariableLogLog.class
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticVariableLogLog.java
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticVariableLogLog2.class
%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticVariableLogLog2.java
%%JAVAJARDIR%%/bbmap/cardinality/AvllMLE.class
%%JAVAJARDIR%%/bbmap/cardinality/AvllMLE.java
%%JAVAJARDIR%%/bbmap/cardinality/BBLog.class
%%JAVAJARDIR%%/bbmap/cardinality/BBLog.java
%%JAVAJARDIR%%/bbmap/cardinality/BBLog_simple.class
%%JAVAJARDIR%%/bbmap/cardinality/BBLog_simple.java
%%JAVAJARDIR%%/bbmap/cardinality/BCLLSimulator.class
%%JAVAJARDIR%%/bbmap/cardinality/BCLLSimulator.java
%%JAVAJARDIR%%/bbmap/cardinality/BCLLTierTrace.class
%%JAVAJARDIR%%/bbmap/cardinality/BCLLTierTrace.java
%%JAVAJARDIR%%/bbmap/cardinality/BCLLTraceTest.class
%%JAVAJARDIR%%/bbmap/cardinality/BCLLTraceTest.java
%%JAVAJARDIR%%/bbmap/cardinality/BankedBiasSimulator.class
%%JAVAJARDIR%%/bbmap/cardinality/BankedBiasSimulator.java
%%JAVAJARDIR%%/bbmap/cardinality/BankedCeilingLogLog.class
%%JAVAJARDIR%%/bbmap/cardinality/BankedCeilingLogLog.java
%%JAVAJARDIR%%/bbmap/cardinality/BankedCompressedDynamicLogLog3.class
%%JAVAJARDIR%%/bbmap/cardinality/BankedCompressedDynamicLogLog3.java
%%JAVAJARDIR%%/bbmap/cardinality/BankedCompressedDynamicLogLog5.class
%%JAVAJARDIR%%/bbmap/cardinality/BankedCompressedDynamicLogLog5.java
%%JAVAJARDIR%%/bbmap/cardinality/BankedDynamicLogLog3.class
%%JAVAJARDIR%%/bbmap/cardinality/BankedDynamicLogLog3.java
%%JAVAJARDIR%%/bbmap/cardinality/BankedDynamicLogLog4.class
%%JAVAJARDIR%%/bbmap/cardinality/BankedDynamicLogLog4.java
%%JAVAJARDIR%%/bbmap/cardinality/BankedDynamicLogLog5.class
%%JAVAJARDIR%%/bbmap/cardinality/BankedDynamicLogLog5.java
%%JAVAJARDIR%%/bbmap/cardinality/BranchRateTest.class
%%JAVAJARDIR%%/bbmap/cardinality/BranchRateTest.java
%%JAVAJARDIR%%/bbmap/cardinality/CardStats.class
%%JAVAJARDIR%%/bbmap/cardinality/CardStats.java
%%JAVAJARDIR%%/bbmap/cardinality/CardinalityParser.class
%%JAVAJARDIR%%/bbmap/cardinality/CardinalityParser.java
%%JAVAJARDIR%%/bbmap/cardinality/CardinalityStats.class
%%JAVAJARDIR%%/bbmap/cardinality/CardinalityStats.java
%%JAVAJARDIR%%/bbmap/cardinality/CardinalityTracker.class
%%JAVAJARDIR%%/bbmap/cardinality/CardinalityTracker.java
%%JAVAJARDIR%%/bbmap/cardinality/ComplexityFarm$BigNet.class
%%JAVAJARDIR%%/bbmap/cardinality/ComplexityFarm$SampleSink.class
%%JAVAJARDIR%%/bbmap/cardinality/ComplexityFarm$Spec.class
%%JAVAJARDIR%%/bbmap/cardinality/ComplexityFarm.class
%%JAVAJARDIR%%/bbmap/cardinality/ComplexityFarm.java
%%JAVAJARDIR%%/bbmap/cardinality/ComplexityFarmW.class
%%JAVAJARDIR%%/bbmap/cardinality/ComplexityFarmW.java
%%JAVAJARDIR%%/bbmap/cardinality/CompressedDynamicLogLog3.class
%%JAVAJARDIR%%/bbmap/cardinality/CompressedDynamicLogLog3.java
%%JAVAJARDIR%%/bbmap/cardinality/CompressedDynamicLogLog4.class
%%JAVAJARDIR%%/bbmap/cardinality/CompressedDynamicLogLog4.java
%%JAVAJARDIR%%/bbmap/cardinality/CompressedDynamicLogLog5.class
%%JAVAJARDIR%%/bbmap/cardinality/CompressedDynamicLogLog5.java
%%JAVAJARDIR%%/bbmap/cardinality/CompressedQuadTailLogLog.class
%%JAVAJARDIR%%/bbmap/cardinality/CompressedQuadTailLogLog.java
%%JAVAJARDIR%%/bbmap/cardinality/CompressedTwinTailLogLog.class
%%JAVAJARDIR%%/bbmap/cardinality/CompressedTwinTailLogLog.java
%%JAVAJARDIR%%/bbmap/cardinality/CorrectionFactor$CFTableData.class
%%JAVAJARDIR%%/bbmap/cardinality/CorrectionFactor.class
%%JAVAJARDIR%%/bbmap/cardinality/CorrectionFactor.java
%%JAVAJARDIR%%/bbmap/cardinality/DDL8.class
%%JAVAJARDIR%%/bbmap/cardinality/DDL8.java
%%JAVAJARDIR%%/bbmap/cardinality/DDL8TierStats.class
%%JAVAJARDIR%%/bbmap/cardinality/DDL8TierStats.java
%%JAVAJARDIR%%/bbmap/cardinality/DDLCalibrationDriver$CalibrationThread.class
%%JAVAJARDIR%%/bbmap/cardinality/DDLCalibrationDriver$ReportRow.class
%%JAVAJARDIR%%/bbmap/cardinality/DDLCalibrationDriver.class
%%JAVAJARDIR%%/bbmap/cardinality/DDLCalibrationDriver.java
%%JAVAJARDIR%%/bbmap/cardinality/DDLCalibrationDriver2$CalThread.class
%%JAVAJARDIR%%/bbmap/cardinality/DDLCalibrationDriver2$MergedResults.class
%%JAVAJARDIR%%/bbmap/cardinality/DDLCalibrationDriver2.class
%%JAVAJARDIR%%/bbmap/cardinality/DDLCalibrationDriver2.java
%%JAVAJARDIR%%/bbmap/cardinality/DLCTierAccuracy$1.class
%%JAVAJARDIR%%/bbmap/cardinality/DLCTierAccuracy.class
%%JAVAJARDIR%%/bbmap/cardinality/DLCTierAccuracy.java
%%JAVAJARDIR%%/bbmap/cardinality/DLCTierVxMap$1.class
%%JAVAJARDIR%%/bbmap/cardinality/DLCTierVxMap.class
%%JAVAJARDIR%%/bbmap/cardinality/DLCTierVxMap.java
%%JAVAJARDIR%%/bbmap/cardinality/DLL4WordSimulator$SimThread.class
%%JAVAJARDIR%%/bbmap/cardinality/DLL4WordSimulator.class
%%JAVAJARDIR%%/bbmap/cardinality/DLL4WordSimulator.java
%%JAVAJARDIR%%/bbmap/cardinality/DebugDLCBest.class
%%JAVAJARDIR%%/bbmap/cardinality/DebugDLCBest.java
%%JAVAJARDIR%%/bbmap/cardinality/DiagnosticRun.class
%%JAVAJARDIR%%/bbmap/cardinality/DiagnosticRun.java
%%JAVAJARDIR%%/bbmap/cardinality/Drivable.class
%%JAVAJARDIR%%/bbmap/cardinality/Drivable.java
%%JAVAJARDIR%%/bbmap/cardinality/DualHashDynamicLogLog4.class
%%JAVAJARDIR%%/bbmap/cardinality/DualHashDynamicLogLog4.java
%%JAVAJARDIR%%/bbmap/cardinality/DynamicDemiLog.class
%%JAVAJARDIR%%/bbmap/cardinality/DynamicDemiLog.java
%%JAVAJARDIR%%/bbmap/cardinality/DynamicDemiLog2.class
%%JAVAJARDIR%%/bbmap/cardinality/DynamicDemiLog2.java
%%JAVAJARDIR%%/bbmap/cardinality/DynamicDemiLog8.class
%%JAVAJARDIR%%/bbmap/cardinality/DynamicDemiLog8.java
%%JAVAJARDIR%%/bbmap/cardinality/DynamicDemiLog8v2.class
%%JAVAJARDIR%%/bbmap/cardinality/DynamicDemiLog8v2.java
%%JAVAJARDIR%%/bbmap/cardinality/DynamicLogLog.class
%%JAVAJARDIR%%/bbmap/cardinality/DynamicLogLog.java
%%JAVAJARDIR%%/bbmap/cardinality/DynamicLogLog2.class
%%JAVAJARDIR%%/bbmap/cardinality/DynamicLogLog2.java
%%JAVAJARDIR%%/bbmap/cardinality/DynamicLogLog3.class
%%JAVAJARDIR%%/bbmap/cardinality/DynamicLogLog3.java
%%JAVAJARDIR%%/bbmap/cardinality/DynamicLogLog3v4.class
%%JAVAJARDIR%%/bbmap/cardinality/DynamicLogLog3v4.java
%%JAVAJARDIR%%/bbmap/cardinality/DynamicLogLog4.class
%%JAVAJARDIR%%/bbmap/cardinality/DynamicLogLog4.java
%%JAVAJARDIR%%/bbmap/cardinality/DynamicLogLog4_Concise.class
%%JAVAJARDIR%%/bbmap/cardinality/DynamicLogLog4_Concise.java
%%JAVAJARDIR%%/bbmap/cardinality/DynamicLogLog4m.class
%%JAVAJARDIR%%/bbmap/cardinality/DynamicLogLog4m.java
%%JAVAJARDIR%%/bbmap/cardinality/ErtlULL.class
%%JAVAJARDIR%%/bbmap/cardinality/ErtlULL.java
%%JAVAJARDIR%%/bbmap/cardinality/ErtlULLTest.class
%%JAVAJARDIR%%/bbmap/cardinality/ErtlULLTest.java
%%JAVAJARDIR%%/bbmap/cardinality/ErtlULLb.class
%%JAVAJARDIR%%/bbmap/cardinality/ErtlULLb.java
%%JAVAJARDIR%%/bbmap/cardinality/ExpandedDynamicLogLog8.class
%%JAVAJARDIR%%/bbmap/cardinality/ExpandedDynamicLogLog8.java
%%JAVAJARDIR%%/bbmap/cardinality/ExpandedDynamicLogLog9.class
%%JAVAJARDIR%%/bbmap/cardinality/ExpandedDynamicLogLog9.java
%%JAVAJARDIR%%/bbmap/cardinality/ExpandedTwinTailLogLog5.class
%%JAVAJARDIR%%/bbmap/cardinality/ExpandedTwinTailLogLog5.java
%%JAVAJARDIR%%/bbmap/cardinality/FLL2Simulator.class
%%JAVAJARDIR%%/bbmap/cardinality/FLL2Simulator.java
%%JAVAJARDIR%%/bbmap/cardinality/FLL2TraceTest.class
%%JAVAJARDIR%%/bbmap/cardinality/FLL2TraceTest.java
%%JAVAJARDIR%%/bbmap/cardinality/FLL2ValidationTest.class
%%JAVAJARDIR%%/bbmap/cardinality/FLL2ValidationTest.java
%%JAVAJARDIR%%/bbmap/cardinality/Fll52$WindowNet.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll52.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll52.java
%%JAVAJARDIR%%/bbmap/cardinality/Fll52Calibrate$Job.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll52Calibrate.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll52Calibrate.java
%%JAVAJARDIR%%/bbmap/cardinality/Fll52MLE.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll52MLE.java
%%JAVAJARDIR%%/bbmap/cardinality/Fll53.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll53.java
%%JAVAJARDIR%%/bbmap/cardinality/Fll53Calibrate$Job.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll53Calibrate.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll53Calibrate.java
%%JAVAJARDIR%%/bbmap/cardinality/Fll53Chron$Sink.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll53Chron$Traj.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll53Chron.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll53Chron.java
%%JAVAJARDIR%%/bbmap/cardinality/Fll53CtrHist.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll53CtrHist.java
%%JAVAJARDIR%%/bbmap/cardinality/Fll53E.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll53E.java
%%JAVAJARDIR%%/bbmap/cardinality/Fll53ESmoke.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll53ESmoke.java
%%JAVAJARDIR%%/bbmap/cardinality/Fll53FactoryTest.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll53FactoryTest.java
%%JAVAJARDIR%%/bbmap/cardinality/Fll53FarmW$Sink.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll53FarmW.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll53FarmW.java
%%JAVAJARDIR%%/bbmap/cardinality/Fll53MLE.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll53MLE.java
%%JAVAJARDIR%%/bbmap/cardinality/Fll53TrajC.class
%%JAVAJARDIR%%/bbmap/cardinality/Fll53TrajC.java
%%JAVAJARDIR%%/bbmap/cardinality/FllComplexity$Spec.class
%%JAVAJARDIR%%/bbmap/cardinality/FllComplexity$TinyNet.class
%%JAVAJARDIR%%/bbmap/cardinality/FllComplexity.class
%%JAVAJARDIR%%/bbmap/cardinality/FllComplexity.java
%%JAVAJARDIR%%/bbmap/cardinality/FllDupCal.class
%%JAVAJARDIR%%/bbmap/cardinality/FllDupCal.java
%%JAVAJARDIR%%/bbmap/cardinality/FllSkewTest$Job.class
%%JAVAJARDIR%%/bbmap/cardinality/FllSkewTest.class
%%JAVAJARDIR%%/bbmap/cardinality/FllSkewTest.java
%%JAVAJARDIR%%/bbmap/cardinality/FutureLogLog2.class
%%JAVAJARDIR%%/bbmap/cardinality/FutureLogLog2.java
%%JAVAJARDIR%%/bbmap/cardinality/HCDLCTierAccuracy$1.class
%%JAVAJARDIR%%/bbmap/cardinality/HCDLCTierAccuracy.class
%%JAVAJARDIR%%/bbmap/cardinality/HCDLCTierAccuracy.java
%%JAVAJARDIR%%/bbmap/cardinality/HLLLWrapper.class
%%JAVAJARDIR%%/bbmap/cardinality/HLLLWrapper.java
%%JAVAJARDIR%%/bbmap/cardinality/HLLTailCut.class
%%JAVAJARDIR%%/bbmap/cardinality/HLLTailCut.java
%%JAVAJARDIR%%/bbmap/cardinality/HLLTailCut4.class
%%JAVAJARDIR%%/bbmap/cardinality/HLLTailCut4.java
%%JAVAJARDIR%%/bbmap/cardinality/Half.class
%%JAVAJARDIR%%/bbmap/cardinality/Half.java
%%JAVAJARDIR%%/bbmap/cardinality/HalfCappedDynamicLogLog4.class
%%JAVAJARDIR%%/bbmap/cardinality/HalfCappedDynamicLogLog4.java
%%JAVAJARDIR%%/bbmap/cardinality/HashStreamEval.class
%%JAVAJARDIR%%/bbmap/cardinality/HashStreamEval.java
%%JAVAJARDIR%%/bbmap/cardinality/HistoryP0Test.class
%%JAVAJARDIR%%/bbmap/cardinality/HistoryP0Test.java
%%JAVAJARDIR%%/bbmap/cardinality/HyperTwoBits.class
%%JAVAJARDIR%%/bbmap/cardinality/HyperTwoBits.java
%%JAVAJARDIR%%/bbmap/cardinality/InvertedLogLog.class
%%JAVAJARDIR%%/bbmap/cardinality/InvertedLogLog.java
%%JAVAJARDIR%%/bbmap/cardinality/LCHistDebug.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistDebug.java
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainer$TrainerThread.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainer.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainer.java
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerACDLL5$TrainerThread.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerACDLL5.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerACDLL5.java
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerAUDLL32$TrainerThread.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerAUDLL32.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerAUDLL32.java
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerAVDLL32$TrainerThread.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerAVDLL32.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerAVDLL32.java
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerAVDLL64$TrainerThread.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerAVDLL64.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerAVDLL64.java
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerBCDLL5$TrainerThread.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerBCDLL5.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerBCDLL5.java
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerBDLL5$TrainerThread.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerBDLL5.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerBDLL5.java
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerCDLL4$TrainerThread.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerCDLL4.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerCDLL4.java
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerEDLL8$TrainerThread.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerEDLL8.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerEDLL8.java
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerTTLL$TrainerThread.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerTTLL.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerTTLL.java
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerTTLL3$TrainerThread.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerTTLL3.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerTTLL3.java
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerVCDLL4$TrainerThread.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerVCDLL4.class
%%JAVAJARDIR%%/bbmap/cardinality/LCHistTrainerVCDLL4.java
%%JAVAJARDIR%%/bbmap/cardinality/LDLCCalibrate.class
%%JAVAJARDIR%%/bbmap/cardinality/LDLCCalibrate.java
%%JAVAJARDIR%%/bbmap/cardinality/LDLCCalibrate2.class
%%JAVAJARDIR%%/bbmap/cardinality/LDLCCalibrate2.java
%%JAVAJARDIR%%/bbmap/cardinality/LDLCCalibrate3.class
%%JAVAJARDIR%%/bbmap/cardinality/LDLCCalibrate3.java
%%JAVAJARDIR%%/bbmap/cardinality/LogLog.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog.java
%%JAVAJARDIR%%/bbmap/cardinality/LogLog16.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog16.java
%%JAVAJARDIR%%/bbmap/cardinality/LogLog2.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog2.java
%%JAVAJARDIR%%/bbmap/cardinality/LogLog30.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog30.java
%%JAVAJARDIR%%/bbmap/cardinality/LogLog6.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog6.java
%%JAVAJARDIR%%/bbmap/cardinality/LogLog8.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog8.java
%%JAVAJARDIR%%/bbmap/cardinality/LogLog8_simple.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog8_simple.java
%%JAVAJARDIR%%/bbmap/cardinality/LogLogWrapper$LogLogThread.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLogWrapper.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLogWrapper.java
%%JAVAJARDIR%%/bbmap/cardinality/LogLog_old$LogLogWrapper$LogLogThread.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog_old$LogLogWrapper.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog_old.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog_old.java
%%JAVAJARDIR%%/bbmap/cardinality/LowComplexityCalibrationDriver$LCWorker.class
%%JAVAJARDIR%%/bbmap/cardinality/LowComplexityCalibrationDriver.class
%%JAVAJARDIR%%/bbmap/cardinality/LowComplexityCalibrationDriver.java
%%JAVAJARDIR%%/bbmap/cardinality/MantissaCompare.class
%%JAVAJARDIR%%/bbmap/cardinality/MantissaCompare.java
%%JAVAJARDIR%%/bbmap/cardinality/MantissaCompare2.class
%%JAVAJARDIR%%/bbmap/cardinality/MantissaCompare2.java
%%JAVAJARDIR%%/bbmap/cardinality/MantissaCompare3$SimThread.class
%%JAVAJARDIR%%/bbmap/cardinality/MantissaCompare3.class
%%JAVAJARDIR%%/bbmap/cardinality/MantissaCompare3.java
%%JAVAJARDIR%%/bbmap/cardinality/MantissaCompareBCDLL5$SimThread.class
%%JAVAJARDIR%%/bbmap/cardinality/MantissaCompareBCDLL5.class
%%JAVAJARDIR%%/bbmap/cardinality/MantissaCompareBCDLL5.java
%%JAVAJARDIR%%/bbmap/cardinality/MergeAccuracyTest.class
%%JAVAJARDIR%%/bbmap/cardinality/MergeAccuracyTest.java
%%JAVAJARDIR%%/bbmap/cardinality/MergeTest.class
%%JAVAJARDIR%%/bbmap/cardinality/MergeTest.java
%%JAVAJARDIR%%/bbmap/cardinality/MultiLogLog.class
%%JAVAJARDIR%%/bbmap/cardinality/MultiLogLog.java
%%JAVAJARDIR%%/bbmap/cardinality/PerTierHistorySimulator.class
%%JAVAJARDIR%%/bbmap/cardinality/PerTierHistorySimulator.java
%%JAVAJARDIR%%/bbmap/cardinality/ProtoLogLog16c.class
%%JAVAJARDIR%%/bbmap/cardinality/ProtoLogLog16c.java
%%JAVAJARDIR%%/bbmap/cardinality/ProtoTierStats.class
%%JAVAJARDIR%%/bbmap/cardinality/ProtoTierStats.java
%%JAVAJARDIR%%/bbmap/cardinality/SetSketch16.class
%%JAVAJARDIR%%/bbmap/cardinality/SetSketch16.java
%%JAVAJARDIR%%/bbmap/cardinality/SpeedTest.class
%%JAVAJARDIR%%/bbmap/cardinality/SpeedTest.java
%%JAVAJARDIR%%/bbmap/cardinality/SpeedTest2.class
%%JAVAJARDIR%%/bbmap/cardinality/SpeedTest2.java
%%JAVAJARDIR%%/bbmap/cardinality/StateTable.class
%%JAVAJARDIR%%/bbmap/cardinality/StateTable.java
%%JAVAJARDIR%%/bbmap/cardinality/StreamSource$Fresh.class
%%JAVAJARDIR%%/bbmap/cardinality/StreamSource$MinRand.class
%%JAVAJARDIR%%/bbmap/cardinality/StreamSource$Onehot.class
%%JAVAJARDIR%%/bbmap/cardinality/StreamSource$UnifPool.class
%%JAVAJARDIR%%/bbmap/cardinality/StreamSource$Zipfish.class
%%JAVAJARDIR%%/bbmap/cardinality/StreamSource.class
%%JAVAJARDIR%%/bbmap/cardinality/StreamSource.java
%%JAVAJARDIR%%/bbmap/cardinality/TTLL3Simulator.class
%%JAVAJARDIR%%/bbmap/cardinality/TTLL3Simulator.java
%%JAVAJARDIR%%/bbmap/cardinality/TTLL4Simulator.class
%%JAVAJARDIR%%/bbmap/cardinality/TTLL4Simulator.java
%%JAVAJARDIR%%/bbmap/cardinality/TTLLDiag.class
%%JAVAJARDIR%%/bbmap/cardinality/TTLLDiag.java
%%JAVAJARDIR%%/bbmap/cardinality/TTLLDualLCDebug.class
%%JAVAJARDIR%%/bbmap/cardinality/TTLLDualLCDebug.java
%%JAVAJARDIR%%/bbmap/cardinality/TTLLSimulator.class
%%JAVAJARDIR%%/bbmap/cardinality/TTLLSimulator.java
%%JAVAJARDIR%%/bbmap/cardinality/TailMLE.class
%%JAVAJARDIR%%/bbmap/cardinality/TailMLE.java
%%JAVAJARDIR%%/bbmap/cardinality/TailWidthSimulator.class
%%JAVAJARDIR%%/bbmap/cardinality/TailWidthSimulator.java
%%JAVAJARDIR%%/bbmap/cardinality/TerminalCfAverager.class
%%JAVAJARDIR%%/bbmap/cardinality/TerminalCfAverager.java
%%JAVAJARDIR%%/bbmap/cardinality/TestACDLL4.class
%%JAVAJARDIR%%/bbmap/cardinality/TestACDLL4.java
%%JAVAJARDIR%%/bbmap/cardinality/TestACDLL5.class
%%JAVAJARDIR%%/bbmap/cardinality/TestACDLL5.java
%%JAVAJARDIR%%/bbmap/cardinality/TestACDLL5Accuracy.class
%%JAVAJARDIR%%/bbmap/cardinality/TestACDLL5Accuracy.java
%%JAVAJARDIR%%/bbmap/cardinality/TestACDLL5Estimates.class
%%JAVAJARDIR%%/bbmap/cardinality/TestACDLL5Estimates.java
%%JAVAJARDIR%%/bbmap/cardinality/TestACDLL5Word.class
%%JAVAJARDIR%%/bbmap/cardinality/TestACDLL5Word.java
%%JAVAJARDIR%%/bbmap/cardinality/TestAVDLL32Hist.class
%%JAVAJARDIR%%/bbmap/cardinality/TestAVDLL32Hist.java
%%JAVAJARDIR%%/bbmap/cardinality/TestBCDLL3.class
%%JAVAJARDIR%%/bbmap/cardinality/TestBCDLL3.java
%%JAVAJARDIR%%/bbmap/cardinality/TestCDLL4HC.class
%%JAVAJARDIR%%/bbmap/cardinality/TestCDLL4HC.java
%%JAVAJARDIR%%/bbmap/cardinality/TestCDLL4Hist.class
%%JAVAJARDIR%%/bbmap/cardinality/TestCDLL4Hist.java
%%JAVAJARDIR%%/bbmap/cardinality/TestCDLL5Hist.class
%%JAVAJARDIR%%/bbmap/cardinality/TestCDLL5Hist.java
%%JAVAJARDIR%%/bbmap/cardinality/TestCard1.class
%%JAVAJARDIR%%/bbmap/cardinality/TestCard1.java
%%JAVAJARDIR%%/bbmap/cardinality/TestDLCBest1.class
%%JAVAJARDIR%%/bbmap/cardinality/TestDLCBest1.java
%%JAVAJARDIR%%/bbmap/cardinality/TestEXP10.class
%%JAVAJARDIR%%/bbmap/cardinality/TestEXP10.java
%%JAVAJARDIR%%/bbmap/cardinality/TestHistModels.class
%%JAVAJARDIR%%/bbmap/cardinality/TestHistModels.java
%%JAVAJARDIR%%/bbmap/cardinality/TestSingleBucket.class
%%JAVAJARDIR%%/bbmap/cardinality/TestSingleBucket.java
%%JAVAJARDIR%%/bbmap/cardinality/TierTransitionDump.class
%%JAVAJARDIR%%/bbmap/cardinality/TierTransitionDump.java
%%JAVAJARDIR%%/bbmap/cardinality/TwinTailLogLog.class
%%JAVAJARDIR%%/bbmap/cardinality/TwinTailLogLog.java
%%JAVAJARDIR%%/bbmap/cardinality/TwinTailLogLog3.class
%%JAVAJARDIR%%/bbmap/cardinality/TwinTailLogLog3.java
%%JAVAJARDIR%%/bbmap/cardinality/TwinTailLogLog4.class
%%JAVAJARDIR%%/bbmap/cardinality/TwinTailLogLog4.java
%%JAVAJARDIR%%/bbmap/cardinality/UDLCCalibrate.class
%%JAVAJARDIR%%/bbmap/cardinality/UDLCCalibrate.java
%%JAVAJARDIR%%/bbmap/cardinality/UDLCDebug.class
%%JAVAJARDIR%%/bbmap/cardinality/UDLCDebug.java
%%JAVAJARDIR%%/bbmap/cardinality/UDLCDense.class
%%JAVAJARDIR%%/bbmap/cardinality/UDLCDense.java
%%JAVAJARDIR%%/bbmap/cardinality/UDLCTest.class
%%JAVAJARDIR%%/bbmap/cardinality/UDLCTest.java
%%JAVAJARDIR%%/bbmap/cardinality/UDLL6Test.class
%%JAVAJARDIR%%/bbmap/cardinality/UDLL6Test.java
%%JAVAJARDIR%%/bbmap/cardinality/ULL8Test.class
%%JAVAJARDIR%%/bbmap/cardinality/ULL8Test.java
%%JAVAJARDIR%%/bbmap/cardinality/ULL8TierStats.class
%%JAVAJARDIR%%/bbmap/cardinality/ULL8TierStats.java
%%JAVAJARDIR%%/bbmap/cardinality/UltraDynamicLogLog36.class
%%JAVAJARDIR%%/bbmap/cardinality/UltraDynamicLogLog36.java
%%JAVAJARDIR%%/bbmap/cardinality/UltraDynamicLogLog6.class
%%JAVAJARDIR%%/bbmap/cardinality/UltraDynamicLogLog6.java
%%JAVAJARDIR%%/bbmap/cardinality/UltraDynamicLogLog6m.class
%%JAVAJARDIR%%/bbmap/cardinality/UltraDynamicLogLog6m.java
%%JAVAJARDIR%%/bbmap/cardinality/UltraLogLog8.class
%%JAVAJARDIR%%/bbmap/cardinality/UltraLogLog8.java
%%JAVAJARDIR%%/bbmap/cardinality/VariableCompressedDynamicLogLog4.class
%%JAVAJARDIR%%/bbmap/cardinality/VariableCompressedDynamicLogLog4.java
%%JAVAJARDIR%%/bbmap/cardinality/WidthWt53C.class
%%JAVAJARDIR%%/bbmap/cardinality/WidthWt53C.java
%%JAVAJARDIR%%/bbmap/clade/Clade.class
%%JAVAJARDIR%%/bbmap/clade/Clade.java
%%JAVAJARDIR%%/bbmap/clade/CladeCalibrator.class
%%JAVAJARDIR%%/bbmap/clade/CladeCalibrator.java
%%JAVAJARDIR%%/bbmap/clade/CladeConfidence.class
%%JAVAJARDIR%%/bbmap/clade/CladeConfidence.java
%%JAVAJARDIR%%/bbmap/clade/CladeContext.class
%%JAVAJARDIR%%/bbmap/clade/CladeContext.java
%%JAVAJARDIR%%/bbmap/clade/CladeIndex.class
%%JAVAJARDIR%%/bbmap/clade/CladeIndex.java
%%JAVAJARDIR%%/bbmap/clade/CladeLoader$1.class
%%JAVAJARDIR%%/bbmap/clade/CladeLoader$ProcessThread.class
%%JAVAJARDIR%%/bbmap/clade/CladeLoader.class
%%JAVAJARDIR%%/bbmap/clade/CladeLoader.java
%%JAVAJARDIR%%/bbmap/clade/CladeLoaderAuto.class
%%JAVAJARDIR%%/bbmap/clade/CladeLoaderAuto.java
%%JAVAJARDIR%%/bbmap/clade/CladeLoaderMF$ProcessThread.class
%%JAVAJARDIR%%/bbmap/clade/CladeLoaderMF.class
%%JAVAJARDIR%%/bbmap/clade/CladeLoaderMF.java
%%JAVAJARDIR%%/bbmap/clade/CladeLoaderMT$1.class
%%JAVAJARDIR%%/bbmap/clade/CladeLoaderMT$2.class
%%JAVAJARDIR%%/bbmap/clade/CladeLoaderMT.class
%%JAVAJARDIR%%/bbmap/clade/CladeLoaderMT.java
%%JAVAJARDIR%%/bbmap/clade/CladeLoaderSF$ProcessThread.class
%%JAVAJARDIR%%/bbmap/clade/CladeLoaderSF.class
%%JAVAJARDIR%%/bbmap/clade/CladeLoaderSF.java
%%JAVAJARDIR%%/bbmap/clade/CladeObject.class
%%JAVAJARDIR%%/bbmap/clade/CladeObject.java
%%JAVAJARDIR%%/bbmap/clade/CladeParseBench$1.class
%%JAVAJARDIR%%/bbmap/clade/CladeParseBench.class
%%JAVAJARDIR%%/bbmap/clade/CladeParseBench.java
%%JAVAJARDIR%%/bbmap/clade/CladeRanking.class
%%JAVAJARDIR%%/bbmap/clade/CladeRanking.java
%%JAVAJARDIR%%/bbmap/clade/CladeRegressionTest.class
%%JAVAJARDIR%%/bbmap/clade/CladeRegressionTest.java
%%JAVAJARDIR%%/bbmap/clade/CladeSearcher$ProcessThread.class
%%JAVAJARDIR%%/bbmap/clade/CladeSearcher.class
%%JAVAJARDIR%%/bbmap/clade/CladeSearcher.java
%%JAVAJARDIR%%/bbmap/clade/CladeServer$BucketSizeHandler.class
%%JAVAJARDIR%%/bbmap/clade/CladeServer$CladeClassificationHandler.class
%%JAVAJARDIR%%/bbmap/clade/CladeServer$CompareSSUHandler.class
%%JAVAJARDIR%%/bbmap/clade/CladeServer$FetchCladeHandler.class
%%JAVAJARDIR%%/bbmap/clade/CladeServer$FetchSSUHandler.class
%%JAVAJARDIR%%/bbmap/clade/CladeServer$IconHandler.class
%%JAVAJARDIR%%/bbmap/clade/CladeServer$KillHandler.class
%%JAVAJARDIR%%/bbmap/clade/CladeServer$StatsHandler.class
%%JAVAJARDIR%%/bbmap/clade/CladeServer$UniversalHandler.class
%%JAVAJARDIR%%/bbmap/clade/CladeServer.class
%%JAVAJARDIR%%/bbmap/clade/CladeServer.java
%%JAVAJARDIR%%/bbmap/clade/Comparison.class
%%JAVAJARDIR%%/bbmap/clade/Comparison.java
%%JAVAJARDIR%%/bbmap/clade/ComparisonFormatTest.class
%%JAVAJARDIR%%/bbmap/clade/ComparisonFormatTest.java
%%JAVAJARDIR%%/bbmap/clade/ComparisonHeap$WorstFirstComparator.class
%%JAVAJARDIR%%/bbmap/clade/ComparisonHeap.class
%%JAVAJARDIR%%/bbmap/clade/ComparisonHeap.java
%%JAVAJARDIR%%/bbmap/clade/ConfidenceEval$Cell.class
%%JAVAJARDIR%%/bbmap/clade/ConfidenceEval.class
%%JAVAJARDIR%%/bbmap/clade/ConfidenceEval.java
%%JAVAJARDIR%%/bbmap/clade/ConfidenceHeadToHead$Cell.class
%%JAVAJARDIR%%/bbmap/clade/ConfidenceHeadToHead.class
%%JAVAJARDIR%%/bbmap/clade/ConfidenceHeadToHead.java
%%JAVAJARDIR%%/bbmap/clade/ConfidenceMultiBundle.class
%%JAVAJARDIR%%/bbmap/clade/ConfidenceMultiBundle.java
%%JAVAJARDIR%%/bbmap/clade/ConfidenceMultiLabel.class
%%JAVAJARDIR%%/bbmap/clade/ConfidenceMultiLabel.java
%%JAVAJARDIR%%/bbmap/clade/ConfidenceMultiVerify.class
%%JAVAJARDIR%%/bbmap/clade/ConfidenceMultiVerify.java
%%JAVAJARDIR%%/bbmap/clade/ConfidenceTest.class
%%JAVAJARDIR%%/bbmap/clade/ConfidenceTest.java
%%JAVAJARDIR%%/bbmap/clade/ConfidenceVectorizer$Hit.class
%%JAVAJARDIR%%/bbmap/clade/ConfidenceVectorizer.class
%%JAVAJARDIR%%/bbmap/clade/ConfidenceVectorizer.java
%%JAVAJARDIR%%/bbmap/clade/LcaAudit.class
%%JAVAJARDIR%%/bbmap/clade/LcaAudit.java
%%JAVAJARDIR%%/bbmap/clade/Organism.class
%%JAVAJARDIR%%/bbmap/clade/Organism.java
%%JAVAJARDIR%%/bbmap/clade/PreClade.class
%%JAVAJARDIR%%/bbmap/clade/PreClade.java
%%JAVAJARDIR%%/bbmap/clade/QueryResult.class
%%JAVAJARDIR%%/bbmap/clade/QueryResult.java
%%JAVAJARDIR%%/bbmap/clade/RankingVectorizer$Hit.class
%%JAVAJARDIR%%/bbmap/clade/RankingVectorizer.class
%%JAVAJARDIR%%/bbmap/clade/RankingVectorizer.java
%%JAVAJARDIR%%/bbmap/clade/SendClade.class
%%JAVAJARDIR%%/bbmap/clade/SendClade.java
%%JAVAJARDIR%%/bbmap/clade/SeqIndex.class
%%JAVAJARDIR%%/bbmap/clade/SeqIndex.java
%%JAVAJARDIR%%/bbmap/clade/SeqIndexResult.class
%%JAVAJARDIR%%/bbmap/clade/SeqIndexResult.java
%%JAVAJARDIR%%/bbmap/clade/Sequence.class
%%JAVAJARDIR%%/bbmap/clade/Sequence.java
%%JAVAJARDIR%%/bbmap/clade/SerialNNLoader$LoadedNets.class
%%JAVAJARDIR%%/bbmap/clade/SerialNNLoader.class
%%JAVAJARDIR%%/bbmap/clade/SerialNNLoader.java
%%JAVAJARDIR%%/bbmap/clump/Clump.class
%%JAVAJARDIR%%/bbmap/clump/Clump.java
%%JAVAJARDIR%%/bbmap/clump/ClumpList$ClumpThread.class
%%JAVAJARDIR%%/bbmap/clump/ClumpList$ProcessThread.class
%%JAVAJARDIR%%/bbmap/clump/ClumpList.class
%%JAVAJARDIR%%/bbmap/clump/ClumpList.java
%%JAVAJARDIR%%/bbmap/clump/ClumpTools.class
%%JAVAJARDIR%%/bbmap/clump/ClumpTools.java
%%JAVAJARDIR%%/bbmap/clump/Clumpify.class
%%JAVAJARDIR%%/bbmap/clump/Clumpify.java
%%JAVAJARDIR%%/bbmap/clump/Hasher.class
%%JAVAJARDIR%%/bbmap/clump/Hasher.java
%%JAVAJARDIR%%/bbmap/clump/KmerComparator$HashThread.class
%%JAVAJARDIR%%/bbmap/clump/KmerComparator.class
%%JAVAJARDIR%%/bbmap/clump/KmerComparator.java
%%JAVAJARDIR%%/bbmap/clump/KmerComparator2.class
%%JAVAJARDIR%%/bbmap/clump/KmerComparator2.java
%%JAVAJARDIR%%/bbmap/clump/KmerComparatorX.class
%%JAVAJARDIR%%/bbmap/clump/KmerComparatorX.java
%%JAVAJARDIR%%/bbmap/clump/KmerComparatorY.class
%%JAVAJARDIR%%/bbmap/clump/KmerComparatorY.java
%%JAVAJARDIR%%/bbmap/clump/KmerReduce$HashThread.class
%%JAVAJARDIR%%/bbmap/clump/KmerReduce.class
%%JAVAJARDIR%%/bbmap/clump/KmerReduce.java
%%JAVAJARDIR%%/bbmap/clump/KmerSort$FetchThread1.class
%%JAVAJARDIR%%/bbmap/clump/KmerSort$HashSplitThread.class
%%JAVAJARDIR%%/bbmap/clump/KmerSort.class
%%JAVAJARDIR%%/bbmap/clump/KmerSort.java
%%JAVAJARDIR%%/bbmap/clump/KmerSort1.class
%%JAVAJARDIR%%/bbmap/clump/KmerSort1.java
%%JAVAJARDIR%%/bbmap/clump/KmerSort2.class
%%JAVAJARDIR%%/bbmap/clump/KmerSort2.java
%%JAVAJARDIR%%/bbmap/clump/KmerSort3$FetchThread3$FetchSubThread.class
%%JAVAJARDIR%%/bbmap/clump/KmerSort3$FetchThread3.class
%%JAVAJARDIR%%/bbmap/clump/KmerSort3.class
%%JAVAJARDIR%%/bbmap/clump/KmerSort3.java
%%JAVAJARDIR%%/bbmap/clump/KmerSplit$HashThread.class
%%JAVAJARDIR%%/bbmap/clump/KmerSplit.class
%%JAVAJARDIR%%/bbmap/clump/KmerSplit.java
%%JAVAJARDIR%%/bbmap/clump/PivotSet$HashThread.class
%%JAVAJARDIR%%/bbmap/clump/PivotSet.class
%%JAVAJARDIR%%/bbmap/clump/PivotSet.java
%%JAVAJARDIR%%/bbmap/clump/README.md
%%JAVAJARDIR%%/bbmap/clump/ReadKey.class
%%JAVAJARDIR%%/bbmap/clump/ReadKey.java
%%JAVAJARDIR%%/bbmap/clump/Splitter.class
%%JAVAJARDIR%%/bbmap/clump/Splitter.java
%%JAVAJARDIR%%/bbmap/clump/StreamToOutput.class
%%JAVAJARDIR%%/bbmap/clump/StreamToOutput.java
%%JAVAJARDIR%%/bbmap/cluster/Cluster.class
%%JAVAJARDIR%%/bbmap/cluster/Cluster.java
%%JAVAJARDIR%%/bbmap/cluster/ClusterTools.class
%%JAVAJARDIR%%/bbmap/cluster/ClusterTools.java
%%JAVAJARDIR%%/bbmap/cluster/MergeReadHeaders.class
%%JAVAJARDIR%%/bbmap/cluster/MergeReadHeaders.java
%%JAVAJARDIR%%/bbmap/cluster/README.md
%%JAVAJARDIR%%/bbmap/cluster/ReadTag.class
%%JAVAJARDIR%%/bbmap/cluster/ReadTag.java
%%JAVAJARDIR%%/bbmap/cluster/ReclusterByKmer$ClusterThread.class
%%JAVAJARDIR%%/bbmap/cluster/ReclusterByKmer.class
%%JAVAJARDIR%%/bbmap/cluster/ReclusterByKmer.java
%%JAVAJARDIR%%/bbmap/consensus/BaseGraph.class
%%JAVAJARDIR%%/bbmap/consensus/BaseGraph.java
%%JAVAJARDIR%%/bbmap/consensus/BaseGraphPart.class
%%JAVAJARDIR%%/bbmap/consensus/BaseGraphPart.java
%%JAVAJARDIR%%/bbmap/consensus/BaseNode.class
%%JAVAJARDIR%%/bbmap/consensus/BaseNode.java
%%JAVAJARDIR%%/bbmap/consensus/ConsensusMaker$ProcessThread.class
%%JAVAJARDIR%%/bbmap/consensus/ConsensusMaker.class
%%JAVAJARDIR%%/bbmap/consensus/ConsensusMaker.java
%%JAVAJARDIR%%/bbmap/consensus/ConsensusObject.class
%%JAVAJARDIR%%/bbmap/consensus/ConsensusObject.java
%%JAVAJARDIR%%/bbmap/consensus/FixScaffoldGaps$ProcessThread.class
%%JAVAJARDIR%%/bbmap/consensus/FixScaffoldGaps$Scaffold.class
%%JAVAJARDIR%%/bbmap/consensus/FixScaffoldGaps.class
%%JAVAJARDIR%%/bbmap/consensus/FixScaffoldGaps.java
%%JAVAJARDIR%%/bbmap/consensus/Lilypad$Contig.class
%%JAVAJARDIR%%/bbmap/consensus/Lilypad$Edge.class
%%JAVAJARDIR%%/bbmap/consensus/Lilypad$ProcessThread.class
%%JAVAJARDIR%%/bbmap/consensus/Lilypad.class
%%JAVAJARDIR%%/bbmap/consensus/Lilypad.java
%%JAVAJARDIR%%/bbmap/consensus/README.md
%%JAVAJARDIR%%/bbmap/covid/README.md
%%JAVAJARDIR%%/bbmap/covid/SummarizeCoverage.class
%%JAVAJARDIR%%/bbmap/covid/SummarizeCoverage.java
%%JAVAJARDIR%%/bbmap/ddl/ANIBenchmark.class
%%JAVAJARDIR%%/bbmap/ddl/ANIBenchmark.java
%%JAVAJARDIR%%/bbmap/ddl/CSRIndex2.class
%%JAVAJARDIR%%/bbmap/ddl/CSRIndex2.java
%%JAVAJARDIR%%/bbmap/ddl/CSRLine.class
%%JAVAJARDIR%%/bbmap/ddl/CSRLine.java
%%JAVAJARDIR%%/bbmap/ddl/CollisionBenchmark.class
%%JAVAJARDIR%%/bbmap/ddl/CollisionBenchmark.java
%%JAVAJARDIR%%/bbmap/ddl/CompareThread.class
%%JAVAJARDIR%%/bbmap/ddl/CompareThread.java
%%JAVAJARDIR%%/bbmap/ddl/DDLBenchmark.class
%%JAVAJARDIR%%/bbmap/ddl/DDLBenchmark.java
%%JAVAJARDIR%%/bbmap/ddl/DDLBitFrequency.class
%%JAVAJARDIR%%/bbmap/ddl/DDLBitFrequency.java
%%JAVAJARDIR%%/bbmap/ddl/DDLBlacklistMaker$BuildThread.class
%%JAVAJARDIR%%/bbmap/ddl/DDLBlacklistMaker$CountThread.class
%%JAVAJARDIR%%/bbmap/ddl/DDLBlacklistMaker$MapThread.class
%%JAVAJARDIR%%/bbmap/ddl/DDLBlacklistMaker.class
%%JAVAJARDIR%%/bbmap/ddl/DDLBlacklistMaker.java
%%JAVAJARDIR%%/bbmap/ddl/DDLCompare$CompareResult.class
%%JAVAJARDIR%%/bbmap/ddl/DDLCompare$CompareThread.class
%%JAVAJARDIR%%/bbmap/ddl/DDLCompare$SSUPGMLoadThread.class
%%JAVAJARDIR%%/bbmap/ddl/DDLCompare.class
%%JAVAJARDIR%%/bbmap/ddl/DDLCompare.java
%%JAVAJARDIR%%/bbmap/ddl/DDLComparison.class
%%JAVAJARDIR%%/bbmap/ddl/DDLComparison.java
%%JAVAJARDIR%%/bbmap/ddl/DDLComparisonHeap.class
%%JAVAJARDIR%%/bbmap/ddl/DDLComparisonHeap.java
%%JAVAJARDIR%%/bbmap/ddl/DDLConverter.class
%%JAVAJARDIR%%/bbmap/ddl/DDLConverter.java
%%JAVAJARDIR%%/bbmap/ddl/DDLFormatter.class
%%JAVAJARDIR%%/bbmap/ddl/DDLFormatter.java
%%JAVAJARDIR%%/bbmap/ddl/DDLIndex.class
%%JAVAJARDIR%%/bbmap/ddl/DDLIndex.java
%%JAVAJARDIR%%/bbmap/ddl/DDLIndexBase.class
%%JAVAJARDIR%%/bbmap/ddl/DDLIndexBase.java
%%JAVAJARDIR%%/bbmap/ddl/DDLIndexCSR.class
%%JAVAJARDIR%%/bbmap/ddl/DDLIndexCSR.java
%%JAVAJARDIR%%/bbmap/ddl/DDLIndexMem.class
%%JAVAJARDIR%%/bbmap/ddl/DDLIndexMem.java
%%JAVAJARDIR%%/bbmap/ddl/DDLIndexStats$1.class
%%JAVAJARDIR%%/bbmap/ddl/DDLIndexStats.class
%%JAVAJARDIR%%/bbmap/ddl/DDLIndexStats.java
%%JAVAJARDIR%%/bbmap/ddl/DDLIndexTest.class
%%JAVAJARDIR%%/bbmap/ddl/DDLIndexTest.java
%%JAVAJARDIR%%/bbmap/ddl/DDLKeyHistogram$1.class
%%JAVAJARDIR%%/bbmap/ddl/DDLKeyHistogram.class
%%JAVAJARDIR%%/bbmap/ddl/DDLKeyHistogram.java
%%JAVAJARDIR%%/bbmap/ddl/DDLLoader.class
%%JAVAJARDIR%%/bbmap/ddl/DDLLoader.java
%%JAVAJARDIR%%/bbmap/ddl/DDLLoaderMT$1.class
%%JAVAJARDIR%%/bbmap/ddl/DDLLoaderMT.class
%%JAVAJARDIR%%/bbmap/ddl/DDLLoaderMT.java
%%JAVAJARDIR%%/bbmap/ddl/DDLMerger$TaggedRecord.class
%%JAVAJARDIR%%/bbmap/ddl/DDLMerger.class
%%JAVAJARDIR%%/bbmap/ddl/DDLMerger.java
%%JAVAJARDIR%%/bbmap/ddl/DDLQueryLoaderSF$ProcessThread.class
%%JAVAJARDIR%%/bbmap/ddl/DDLQueryLoaderSF$SSUFindThread.class
%%JAVAJARDIR%%/bbmap/ddl/DDLQueryLoaderSF.class
%%JAVAJARDIR%%/bbmap/ddl/DDLQueryLoaderSF.java
%%JAVAJARDIR%%/bbmap/ddl/DDLRecord.class
%%JAVAJARDIR%%/bbmap/ddl/DDLRecord.java
%%JAVAJARDIR%%/bbmap/ddl/DDLSSULoader.class
%%JAVAJARDIR%%/bbmap/ddl/DDLSSULoader.java
%%JAVAJARDIR%%/bbmap/ddl/DDLWriter$1.class
%%JAVAJARDIR%%/bbmap/ddl/DDLWriter$TidWorker.class
%%JAVAJARDIR%%/bbmap/ddl/DDLWriter.class
%%JAVAJARDIR%%/bbmap/ddl/DDLWriter.java
%%JAVAJARDIR%%/bbmap/ddl/MapStressTest.class
%%JAVAJARDIR%%/bbmap/ddl/MapStressTest.java
%%JAVAJARDIR%%/bbmap/ddl/MergeDDLBlacklists.class
%%JAVAJARDIR%%/bbmap/ddl/MergeDDLBlacklists.java
%%JAVAJARDIR%%/bbmap/ddl/MultithreadedSketchLoader$SketchThread.class
%%JAVAJARDIR%%/bbmap/ddl/MultithreadedSketchLoader.class
%%JAVAJARDIR%%/bbmap/ddl/MultithreadedSketchLoader.java
%%JAVAJARDIR%%/bbmap/ddl/SSUClassifyTest$1.class
%%JAVAJARDIR%%/bbmap/ddl/SSUClassifyTest.class
%%JAVAJARDIR%%/bbmap/ddl/SSUClassifyTest.java
%%JAVAJARDIR%%/bbmap/ddl/SSUCompare.class
%%JAVAJARDIR%%/bbmap/ddl/SSUCompare.java
%%JAVAJARDIR%%/bbmap/ddl/SSURecord.class
%%JAVAJARDIR%%/bbmap/ddl/SSURecord.java
%%JAVAJARDIR%%/bbmap/ddl/SSUServer$KillHandler.class
%%JAVAJARDIR%%/bbmap/ddl/SSUServer$UniversalHandler.class
%%JAVAJARDIR%%/bbmap/ddl/SSUServer.class
%%JAVAJARDIR%%/bbmap/ddl/SSUServer.java
%%JAVAJARDIR%%/bbmap/ddl/SetRecallTest.class
%%JAVAJARDIR%%/bbmap/ddl/SetRecallTest.java
%%JAVAJARDIR%%/bbmap/ddl/SetSketchCollisionTest.class
%%JAVAJARDIR%%/bbmap/ddl/SetSketchCollisionTest.java
%%JAVAJARDIR%%/bbmap/ddl/SketchCompare.class
%%JAVAJARDIR%%/bbmap/ddl/SketchCompare.java
%%JAVAJARDIR%%/bbmap/dna/AminoAcid.class
%%JAVAJARDIR%%/bbmap/dna/AminoAcid.java
%%JAVAJARDIR%%/bbmap/dna/ChromArrayMaker.class
%%JAVAJARDIR%%/bbmap/dna/ChromArrayMaker.java
%%JAVAJARDIR%%/bbmap/dna/ChromToFasta$1.class
%%JAVAJARDIR%%/bbmap/dna/ChromToFasta.class
%%JAVAJARDIR%%/bbmap/dna/ChromToFasta.java
%%JAVAJARDIR%%/bbmap/dna/ChromosomeArray.class
%%JAVAJARDIR%%/bbmap/dna/ChromosomeArray.java
%%JAVAJARDIR%%/bbmap/dna/Data.class
%%JAVAJARDIR%%/bbmap/dna/Data.java
%%JAVAJARDIR%%/bbmap/dna/Exon.class
%%JAVAJARDIR%%/bbmap/dna/Exon.java
%%JAVAJARDIR%%/bbmap/dna/FastaToChromArrays2$1.class
%%JAVAJARDIR%%/bbmap/dna/FastaToChromArrays2.class
%%JAVAJARDIR%%/bbmap/dna/FastaToChromArrays2.java
%%JAVAJARDIR%%/bbmap/dna/Gene.class
%%JAVAJARDIR%%/bbmap/dna/Gene.java
%%JAVAJARDIR%%/bbmap/dna/GeneSet.class
%%JAVAJARDIR%%/bbmap/dna/GeneSet.java
%%JAVAJARDIR%%/bbmap/dna/Matrix.class
%%JAVAJARDIR%%/bbmap/dna/Matrix.java
%%JAVAJARDIR%%/bbmap/dna/Motif.class
%%JAVAJARDIR%%/bbmap/dna/Motif.java
%%JAVAJARDIR%%/bbmap/dna/MotifMulti.class
%%JAVAJARDIR%%/bbmap/dna/MotifMulti.java
%%JAVAJARDIR%%/bbmap/dna/MotifProbsN.class
%%JAVAJARDIR%%/bbmap/dna/MotifProbsN.java
%%JAVAJARDIR%%/bbmap/dna/MotifSimple.class
%%JAVAJARDIR%%/bbmap/dna/MotifSimple.java
%%JAVAJARDIR%%/bbmap/dna/README.md
%%JAVAJARDIR%%/bbmap/dna/ScafLoc.class
%%JAVAJARDIR%%/bbmap/dna/ScafLoc.java
%%JAVAJARDIR%%/bbmap/dna/Scaffold.class
%%JAVAJARDIR%%/bbmap/dna/Scaffold.java
%%JAVAJARDIR%%/bbmap/driver/BBVersion.class
%%JAVAJARDIR%%/bbmap/driver/BBVersion.java
%%JAVAJARDIR%%/bbmap/driver/ClearRam.class
%%JAVAJARDIR%%/bbmap/driver/ClearRam.java
%%JAVAJARDIR%%/bbmap/driver/CollateSpikeIn.class
%%JAVAJARDIR%%/bbmap/driver/CollateSpikeIn.java
%%JAVAJARDIR%%/bbmap/driver/CompareReferenceGenomes.class
%%JAVAJARDIR%%/bbmap/driver/CompareReferenceGenomes.java
%%JAVAJARDIR%%/bbmap/driver/CompareSequences.class
%%JAVAJARDIR%%/bbmap/driver/CompareSequences.java
%%JAVAJARDIR%%/bbmap/driver/ConcatenateFiles.class
%%JAVAJARDIR%%/bbmap/driver/ConcatenateFiles.java
%%JAVAJARDIR%%/bbmap/driver/ConcatenateTextFiles$1.class
%%JAVAJARDIR%%/bbmap/driver/ConcatenateTextFiles$WriteThread.class
%%JAVAJARDIR%%/bbmap/driver/ConcatenateTextFiles.class
%%JAVAJARDIR%%/bbmap/driver/ConcatenateTextFiles.java
%%JAVAJARDIR%%/bbmap/driver/Concatenator.class
%%JAVAJARDIR%%/bbmap/driver/Concatenator.java
%%JAVAJARDIR%%/bbmap/driver/ConvertSamToAln.class
%%JAVAJARDIR%%/bbmap/driver/ConvertSamToAln.java
%%JAVAJARDIR%%/bbmap/driver/CorrelateIdentity.class
%%JAVAJARDIR%%/bbmap/driver/CorrelateIdentity.java
%%JAVAJARDIR%%/bbmap/driver/CountRNAs.class
%%JAVAJARDIR%%/bbmap/driver/CountRNAs.java
%%JAVAJARDIR%%/bbmap/driver/CountSharedLines.class
%%JAVAJARDIR%%/bbmap/driver/CountSharedLines.java
%%JAVAJARDIR%%/bbmap/driver/EstherFilter.class
%%JAVAJARDIR%%/bbmap/driver/EstherFilter.java
%%JAVAJARDIR%%/bbmap/driver/FilterAssemblySummary.class
%%JAVAJARDIR%%/bbmap/driver/FilterAssemblySummary.java
%%JAVAJARDIR%%/bbmap/driver/FilterLines.class
%%JAVAJARDIR%%/bbmap/driver/FilterLines.java
%%JAVAJARDIR%%/bbmap/driver/FilterReadsByName.class
%%JAVAJARDIR%%/bbmap/driver/FilterReadsByName.java
%%JAVAJARDIR%%/bbmap/driver/FilterReadsByNameOld.class
%%JAVAJARDIR%%/bbmap/driver/FilterReadsByNameOld.java
%%JAVAJARDIR%%/bbmap/driver/FindMotifs.class
%%JAVAJARDIR%%/bbmap/driver/FindMotifs.java
%%JAVAJARDIR%%/bbmap/driver/FixChr.class
%%JAVAJARDIR%%/bbmap/driver/FixChr.java
%%JAVAJARDIR%%/bbmap/driver/FixDumbFile.class
%%JAVAJARDIR%%/bbmap/driver/FixDumbFile.java
%%JAVAJARDIR%%/bbmap/driver/GenerateNoCallsFromCoverage.class
%%JAVAJARDIR%%/bbmap/driver/GenerateNoCallsFromCoverage.java
%%JAVAJARDIR%%/bbmap/driver/GetSequence.class
%%JAVAJARDIR%%/bbmap/driver/GetSequence.java
%%JAVAJARDIR%%/bbmap/driver/GetUniquePrefixes.class
%%JAVAJARDIR%%/bbmap/driver/GetUniquePrefixes.java
%%JAVAJARDIR%%/bbmap/driver/Grep.class
%%JAVAJARDIR%%/bbmap/driver/Grep.java
%%JAVAJARDIR%%/bbmap/driver/Life.class
%%JAVAJARDIR%%/bbmap/driver/Life.java
%%JAVAJARDIR%%/bbmap/driver/LineCount.class
%%JAVAJARDIR%%/bbmap/driver/LineCount.java
%%JAVAJARDIR%%/bbmap/driver/LoadReads.class
%%JAVAJARDIR%%/bbmap/driver/LoadReads.java
%%JAVAJARDIR%%/bbmap/driver/LookAtID.class
%%JAVAJARDIR%%/bbmap/driver/LookAtID.java
%%JAVAJARDIR%%/bbmap/driver/MakeTestScript.class
%%JAVAJARDIR%%/bbmap/driver/MakeTestScript.java
%%JAVAJARDIR%%/bbmap/driver/MakeTestScriptScoreOnly.class
%%JAVAJARDIR%%/bbmap/driver/MakeTestScriptScoreOnly.java
%%JAVAJARDIR%%/bbmap/driver/MeasureGene.class
%%JAVAJARDIR%%/bbmap/driver/MeasureGene.java
%%JAVAJARDIR%%/bbmap/driver/MergeBigelow.class
%%JAVAJARDIR%%/bbmap/driver/MergeBigelow.java
%%JAVAJARDIR%%/bbmap/driver/MergeCoverageOTU.class
%%JAVAJARDIR%%/bbmap/driver/MergeCoverageOTU.java
%%JAVAJARDIR%%/bbmap/driver/MergeTextFiles.class
%%JAVAJARDIR%%/bbmap/driver/MergeTextFiles.java
%%JAVAJARDIR%%/bbmap/driver/MergeTextFiles2.class
%%JAVAJARDIR%%/bbmap/driver/MergeTextFiles2.java
%%JAVAJARDIR%%/bbmap/driver/MoveFiles.class
%%JAVAJARDIR%%/bbmap/driver/MoveFiles.java
%%JAVAJARDIR%%/bbmap/driver/ParseCrossblockResults$ResultsLine.class
%%JAVAJARDIR%%/bbmap/driver/ParseCrossblockResults.class
%%JAVAJARDIR%%/bbmap/driver/ParseCrossblockResults.java
%%JAVAJARDIR%%/bbmap/driver/PlotGC.class
%%JAVAJARDIR%%/bbmap/driver/PlotGC.java
%%JAVAJARDIR%%/bbmap/driver/PrintEnv.class
%%JAVAJARDIR%%/bbmap/driver/PrintEnv.java
%%JAVAJARDIR%%/bbmap/driver/ProcessFragMerging.class
%%JAVAJARDIR%%/bbmap/driver/ProcessFragMerging.java
%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed.class
%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed.java
%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed2.class
%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed2.java
%%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.class
%%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.java
%%JAVAJARDIR%%/bbmap/driver/README.md
%%JAVAJARDIR%%/bbmap/driver/ReduceSilva.class
%%JAVAJARDIR%%/bbmap/driver/ReduceSilva.java
%%JAVAJARDIR%%/bbmap/driver/RenameAndMux$MuxThread.class
%%JAVAJARDIR%%/bbmap/driver/RenameAndMux.class
%%JAVAJARDIR%%/bbmap/driver/RenameAndMux.java
%%JAVAJARDIR%%/bbmap/driver/RenameByHeader.class
%%JAVAJARDIR%%/bbmap/driver/RenameByHeader.java
%%JAVAJARDIR%%/bbmap/driver/RenameNcbiToTid.class
%%JAVAJARDIR%%/bbmap/driver/RenameNcbiToTid.java
%%JAVAJARDIR%%/bbmap/driver/RenameRefseqFiles.class
%%JAVAJARDIR%%/bbmap/driver/RenameRefseqFiles.java
%%JAVAJARDIR%%/bbmap/driver/Sample.class
%%JAVAJARDIR%%/bbmap/driver/Sample.java
%%JAVAJARDIR%%/bbmap/driver/Search.class
%%JAVAJARDIR%%/bbmap/driver/Search.java
%%JAVAJARDIR%%/bbmap/driver/SelectReads.class
%%JAVAJARDIR%%/bbmap/driver/SelectReads.java
%%JAVAJARDIR%%/bbmap/driver/SniffSplices.class
%%JAVAJARDIR%%/bbmap/driver/SniffSplices.java
%%JAVAJARDIR%%/bbmap/driver/SummarizeContamReport$ComparatorA.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeContamReport$ComparatorB.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeContamReport$StringLongLong.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeContamReport.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeContamReport.java
%%JAVAJARDIR%%/bbmap/driver/SummarizeCoverage.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeCoverage.java
%%JAVAJARDIR%%/bbmap/driver/SummarizeCrossblock.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeCrossblock.java
%%JAVAJARDIR%%/bbmap/driver/SummarizeMSDIN.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeMSDIN.java
%%JAVAJARDIR%%/bbmap/driver/SummarizeQuast$Entry.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeQuast$QuastSummary.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeQuast.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeQuast.java
%%JAVAJARDIR%%/bbmap/driver/SummarizeSealCrosstalk$Result.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeSealCrosstalk.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeSealCrosstalk.java
%%JAVAJARDIR%%/bbmap/driver/SummarizeSealStats$SealSummary.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeSealStats.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeSealStats.java
%%JAVAJARDIR%%/bbmap/driver/TestCompressionSpeed.class
%%JAVAJARDIR%%/bbmap/driver/TestCompressionSpeed.java
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$1.class
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$AtomBox.class
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$CountBox.class
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$CountThread.class
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$LockBox.class
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$VolatileBox.class
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed.class
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed.java
%%JAVAJARDIR%%/bbmap/driver/Translator.class
%%JAVAJARDIR%%/bbmap/driver/Translator.java
%%JAVAJARDIR%%/bbmap/driver/Translator2.class
%%JAVAJARDIR%%/bbmap/driver/Translator2.java
%%JAVAJARDIR%%/bbmap/driver/TransposeTextFile.class
%%JAVAJARDIR%%/bbmap/driver/TransposeTextFile.java
%%JAVAJARDIR%%/bbmap/driver/TrimSamFile.class
%%JAVAJARDIR%%/bbmap/driver/TrimSamFile.java
%%JAVAJARDIR%%/bbmap/fileIO/ArrayFile.class
%%JAVAJARDIR%%/bbmap/fileIO/ArrayFile.java
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile.java
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1.java
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1F.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1F.java
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1Fc.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1Fc.java
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1old.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1old.java
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile2$BF1Thread.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile2.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile2.java
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile3$BufferJob.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile3$ProcessThread.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile3.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile3.java
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile4$BufferJob.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile4$ProcessThread.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile4.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile4.java
%%JAVAJARDIR%%/bbmap/fileIO/ByteStreamWriter.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteStreamWriter.java
%%JAVAJARDIR%%/bbmap/fileIO/ChainBlock.class
%%JAVAJARDIR%%/bbmap/fileIO/ChainBlock.java
%%JAVAJARDIR%%/bbmap/fileIO/ChainLine.class
%%JAVAJARDIR%%/bbmap/fileIO/ChainLine.java
%%JAVAJARDIR%%/bbmap/fileIO/CompressFiles.class
%%JAVAJARDIR%%/bbmap/fileIO/CompressFiles.java
%%JAVAJARDIR%%/bbmap/fileIO/Concatenate.class
%%JAVAJARDIR%%/bbmap/fileIO/Concatenate.java
%%JAVAJARDIR%%/bbmap/fileIO/Concatenate2.class
%%JAVAJARDIR%%/bbmap/fileIO/Concatenate2.java
%%JAVAJARDIR%%/bbmap/fileIO/CopyFile$1.class
%%JAVAJARDIR%%/bbmap/fileIO/CopyFile.class
%%JAVAJARDIR%%/bbmap/fileIO/CopyFile.java
%%JAVAJARDIR%%/bbmap/fileIO/CopyFiles.class
%%JAVAJARDIR%%/bbmap/fileIO/CopyFiles.java
%%JAVAJARDIR%%/bbmap/fileIO/CopyFiles2.class
%%JAVAJARDIR%%/bbmap/fileIO/CopyFiles2.java
%%JAVAJARDIR%%/bbmap/fileIO/FileFormat.class
%%JAVAJARDIR%%/bbmap/fileIO/FileFormat.java
%%JAVAJARDIR%%/bbmap/fileIO/FindFiles.class
%%JAVAJARDIR%%/bbmap/fileIO/FindFiles.java
%%JAVAJARDIR%%/bbmap/fileIO/GenericTextFile.class
%%JAVAJARDIR%%/bbmap/fileIO/GenericTextFile.java
%%JAVAJARDIR%%/bbmap/fileIO/LoadThread.class
%%JAVAJARDIR%%/bbmap/fileIO/LoadThread.java
%%JAVAJARDIR%%/bbmap/fileIO/MatrixFile.class
%%JAVAJARDIR%%/bbmap/fileIO/MatrixFile.java
%%JAVAJARDIR%%/bbmap/fileIO/OpenFile.class
%%JAVAJARDIR%%/bbmap/fileIO/OpenFile.java
%%JAVAJARDIR%%/bbmap/fileIO/PipeThread.class
%%JAVAJARDIR%%/bbmap/fileIO/PipeThread.java
%%JAVAJARDIR%%/bbmap/fileIO/QuickFile.class
%%JAVAJARDIR%%/bbmap/fileIO/QuickFile.java
%%JAVAJARDIR%%/bbmap/fileIO/README.md
%%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$1.class
%%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$WriteObjectThread.class
%%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$WriteStringThread.class
%%JAVAJARDIR%%/bbmap/fileIO/ReadWrite.class
%%JAVAJARDIR%%/bbmap/fileIO/ReadWrite.java
%%JAVAJARDIR%%/bbmap/fileIO/SummaryFile$1.class
%%JAVAJARDIR%%/bbmap/fileIO/SummaryFile.class
%%JAVAJARDIR%%/bbmap/fileIO/SummaryFile.java
%%JAVAJARDIR%%/bbmap/fileIO/TextFile.class
%%JAVAJARDIR%%/bbmap/fileIO/TextFile.java
%%JAVAJARDIR%%/bbmap/fileIO/TextStreamWriter.class
%%JAVAJARDIR%%/bbmap/fileIO/TextStreamWriter.java
%%JAVAJARDIR%%/bbmap/fun/BenchIntAppend2.class
%%JAVAJARDIR%%/bbmap/fun/BenchIntAppend2.java
%%JAVAJARDIR%%/bbmap/fun/BenchLongAppend.class
%%JAVAJARDIR%%/bbmap/fun/BenchLongAppend.java
%%JAVAJARDIR%%/bbmap/fun/BenchStringAppend.class
%%JAVAJARDIR%%/bbmap/fun/BenchStringAppend.java
%%JAVAJARDIR%%/bbmap/fun/BenchStringAppend2.class
%%JAVAJARDIR%%/bbmap/fun/BenchStringAppend2.java
%%JAVAJARDIR%%/bbmap/fun/BenchmarkA48.class
%%JAVAJARDIR%%/bbmap/fun/BenchmarkA48.java
%%JAVAJARDIR%%/bbmap/fun/BenchmarkIntAppend.class
%%JAVAJARDIR%%/bbmap/fun/BenchmarkIntAppend.java
%%JAVAJARDIR%%/bbmap/fun/BenchmarkReverse.class
%%JAVAJARDIR%%/bbmap/fun/BenchmarkReverse.java
%%JAVAJARDIR%%/bbmap/fun/ByteVectorBench.class
%%JAVAJARDIR%%/bbmap/fun/ByteVectorBench.java
%%JAVAJARDIR%%/bbmap/fun/Calc.class
%%JAVAJARDIR%%/bbmap/fun/Calc.java
%%JAVAJARDIR%%/bbmap/fun/Chance.class
%%JAVAJARDIR%%/bbmap/fun/Chance.java
%%JAVAJARDIR%%/bbmap/fun/Crunch.class
%%JAVAJARDIR%%/bbmap/fun/Crunch.java
%%JAVAJARDIR%%/bbmap/fun/DiskBench$ReadThread.class
%%JAVAJARDIR%%/bbmap/fun/DiskBench$WriteThread.class
%%JAVAJARDIR%%/bbmap/fun/DiskBench.class
%%JAVAJARDIR%%/bbmap/fun/DiskBench.java
%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer$1.class
%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer$2.class
%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer$DirSize.class
%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer.class
%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer.java
%%JAVAJARDIR%%/bbmap/fun/Dongle.class
%%JAVAJARDIR%%/bbmap/fun/Dongle.java
%%JAVAJARDIR%%/bbmap/fun/FindPath$Edge.class
%%JAVAJARDIR%%/bbmap/fun/FindPath$Node.class
%%JAVAJARDIR%%/bbmap/fun/FindPath$Path.class
%%JAVAJARDIR%%/bbmap/fun/FindPath.class
%%JAVAJARDIR%%/bbmap/fun/FindPath.java
%%JAVAJARDIR%%/bbmap/fun/FindPrimes.class
%%JAVAJARDIR%%/bbmap/fun/FindPrimes.java
%%JAVAJARDIR%%/bbmap/fun/Foo.class
%%JAVAJARDIR%%/bbmap/fun/Foo.java
%%JAVAJARDIR%%/bbmap/fun/Foo2.class
%%JAVAJARDIR%%/bbmap/fun/Foo2.java
%%JAVAJARDIR%%/bbmap/fun/Foo3$LongList.class
%%JAVAJARDIR%%/bbmap/fun/Foo3$Pair.class
%%JAVAJARDIR%%/bbmap/fun/Foo3.class
%%JAVAJARDIR%%/bbmap/fun/Foo3.java
%%JAVAJARDIR%%/bbmap/fun/Foo4$Pair.class
%%JAVAJARDIR%%/bbmap/fun/Foo4.class
%%JAVAJARDIR%%/bbmap/fun/Foo4.java
%%JAVAJARDIR%%/bbmap/fun/Foo5$LongList.class
%%JAVAJARDIR%%/bbmap/fun/Foo5.class
%%JAVAJARDIR%%/bbmap/fun/Foo5.java
%%JAVAJARDIR%%/bbmap/fun/Foo6.class
%%JAVAJARDIR%%/bbmap/fun/Foo6.java
%%JAVAJARDIR%%/bbmap/fun/Foo7.class
%%JAVAJARDIR%%/bbmap/fun/Foo7.java
%%JAVAJARDIR%%/bbmap/fun/Genetic$Bug.class
%%JAVAJARDIR%%/bbmap/fun/Genetic.class
%%JAVAJARDIR%%/bbmap/fun/Genetic.java
%%JAVAJARDIR%%/bbmap/fun/Life.class
%%JAVAJARDIR%%/bbmap/fun/Life.java
%%JAVAJARDIR%%/bbmap/fun/MakeAdjacencyList$1.class
%%JAVAJARDIR%%/bbmap/fun/MakeAdjacencyList.class
%%JAVAJARDIR%%/bbmap/fun/MakeAdjacencyList.java
%%JAVAJARDIR%%/bbmap/fun/Merced$Person.class
%%JAVAJARDIR%%/bbmap/fun/Merced.class
%%JAVAJARDIR%%/bbmap/fun/Merced.java
%%JAVAJARDIR%%/bbmap/fun/PalSim.class
%%JAVAJARDIR%%/bbmap/fun/PalSim.java
%%JAVAJARDIR%%/bbmap/fun/Palindrome.class
%%JAVAJARDIR%%/bbmap/fun/Palindrome.java
%%JAVAJARDIR%%/bbmap/fun/Palindrome2$Drome.class
%%JAVAJARDIR%%/bbmap/fun/Palindrome2.class
%%JAVAJARDIR%%/bbmap/fun/Palindrome2.java
%%JAVAJARDIR%%/bbmap/fun/ParseDouble.class
%%JAVAJARDIR%%/bbmap/fun/ParseDouble.java
%%JAVAJARDIR%%/bbmap/fun/ProbShared.class
%%JAVAJARDIR%%/bbmap/fun/ProbShared.java
%%JAVAJARDIR%%/bbmap/fun/ProbShared2.class
%%JAVAJARDIR%%/bbmap/fun/ProbShared2.java
%%JAVAJARDIR%%/bbmap/fun/ProbShared3.class
%%JAVAJARDIR%%/bbmap/fun/ProbShared3.java
%%JAVAJARDIR%%/bbmap/fun/README.md
%%JAVAJARDIR%%/bbmap/gff/CompareGff.class
%%JAVAJARDIR%%/bbmap/gff/CompareGff.java
%%JAVAJARDIR%%/bbmap/gff/CutGff$ProcessThread.class
%%JAVAJARDIR%%/bbmap/gff/CutGff.class
%%JAVAJARDIR%%/bbmap/gff/CutGff.java
%%JAVAJARDIR%%/bbmap/gff/CutGff_ST.class
%%JAVAJARDIR%%/bbmap/gff/CutGff_ST.java
%%JAVAJARDIR%%/bbmap/gff/GbffFeature.class
%%JAVAJARDIR%%/bbmap/gff/GbffFeature.java
%%JAVAJARDIR%%/bbmap/gff/GbffFile.class
%%JAVAJARDIR%%/bbmap/gff/GbffFile.java
%%JAVAJARDIR%%/bbmap/gff/GbffLocus.class
%%JAVAJARDIR%%/bbmap/gff/GbffLocus.java
%%JAVAJARDIR%%/bbmap/gff/GffLine.class
%%JAVAJARDIR%%/bbmap/gff/GffLine.java
%%JAVAJARDIR%%/bbmap/gff/GtfLine.class
%%JAVAJARDIR%%/bbmap/gff/GtfLine.java
%%JAVAJARDIR%%/bbmap/gff/ParseCrispr.class
%%JAVAJARDIR%%/bbmap/gff/ParseCrispr.java
%%JAVAJARDIR%%/bbmap/gff/README.md
%%JAVAJARDIR%%/bbmap/gff/VcfToGff$1.class
%%JAVAJARDIR%%/bbmap/gff/VcfToGff.class
%%JAVAJARDIR%%/bbmap/gff/VcfToGff.java
%%JAVAJARDIR%%/bbmap/hiseq/AnalyzeFlowCell$ProcessThread.class
%%JAVAJARDIR%%/bbmap/hiseq/AnalyzeFlowCell.class
%%JAVAJARDIR%%/bbmap/hiseq/AnalyzeFlowCell.java
%%JAVAJARDIR%%/bbmap/hiseq/BGI2Illumina.class
%%JAVAJARDIR%%/bbmap/hiseq/BGI2Illumina.java
%%JAVAJARDIR%%/bbmap/hiseq/BGIHeaderParser.class
%%JAVAJARDIR%%/bbmap/hiseq/BGIHeaderParser.java
%%JAVAJARDIR%%/bbmap/hiseq/BGIHeaderParser2.class
%%JAVAJARDIR%%/bbmap/hiseq/BGIHeaderParser2.java
%%JAVAJARDIR%%/bbmap/hiseq/CycleTracker.class
%%JAVAJARDIR%%/bbmap/hiseq/CycleTracker.java
%%JAVAJARDIR%%/bbmap/hiseq/FlowCell.class
%%JAVAJARDIR%%/bbmap/hiseq/FlowCell.java
%%JAVAJARDIR%%/bbmap/hiseq/FlowcellCoordinate.class
%%JAVAJARDIR%%/bbmap/hiseq/FlowcellCoordinate.java
%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser1.class
%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser1.java
%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser2.class
%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser2.java
%%JAVAJARDIR%%/bbmap/hiseq/Lane$TileIterator.class
%%JAVAJARDIR%%/bbmap/hiseq/Lane.class
%%JAVAJARDIR%%/bbmap/hiseq/Lane.java
%%JAVAJARDIR%%/bbmap/hiseq/MicroTile.class
%%JAVAJARDIR%%/bbmap/hiseq/MicroTile.java
%%JAVAJARDIR%%/bbmap/hiseq/PlotFlowCell$WorkerThread.class
%%JAVAJARDIR%%/bbmap/hiseq/PlotFlowCell.class
%%JAVAJARDIR%%/bbmap/hiseq/PlotFlowCell.java
%%JAVAJARDIR%%/bbmap/hiseq/PlotHist.class
%%JAVAJARDIR%%/bbmap/hiseq/PlotHist.java
%%JAVAJARDIR%%/bbmap/hiseq/PlotReadPosition.class
%%JAVAJARDIR%%/bbmap/hiseq/PlotReadPosition.java
%%JAVAJARDIR%%/bbmap/hiseq/README.md
%%JAVAJARDIR%%/bbmap/hiseq/ReadHeaderParser.class
%%JAVAJARDIR%%/bbmap/hiseq/ReadHeaderParser.java
%%JAVAJARDIR%%/bbmap/hiseq/Tile.class
%%JAVAJARDIR%%/bbmap/hiseq/Tile.java
%%JAVAJARDIR%%/bbmap/hiseq/TileDump.class
%%JAVAJARDIR%%/bbmap/hiseq/TileDump.java
%%JAVAJARDIR%%/bbmap/hmm/HMMSearchLine.class
%%JAVAJARDIR%%/bbmap/hmm/HMMSearchLine.java
%%JAVAJARDIR%%/bbmap/hmm/HMMSearchReport.class
%%JAVAJARDIR%%/bbmap/hmm/HMMSearchReport.java
%%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.class
%%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.java
%%JAVAJARDIR%%/bbmap/hmm/README.md
%%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.class
%%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.java
%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJNI.class
%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJNI.java
%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJava.class
%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJava.java
%%JAVAJARDIR%%/bbmap/icecream/IceCreamFinder$ProcessThread.class
%%JAVAJARDIR%%/bbmap/icecream/IceCreamFinder.class
%%JAVAJARDIR%%/bbmap/icecream/IceCreamFinder.java
%%JAVAJARDIR%%/bbmap/icecream/IceCreamGrader.class
%%JAVAJARDIR%%/bbmap/icecream/IceCreamGrader.java
%%JAVAJARDIR%%/bbmap/icecream/IceCreamMaker$ProcessThread.class
%%JAVAJARDIR%%/bbmap/icecream/IceCreamMaker.class
%%JAVAJARDIR%%/bbmap/icecream/IceCreamMaker.java
%%JAVAJARDIR%%/bbmap/icecream/PBHeader.class
%%JAVAJARDIR%%/bbmap/icecream/PBHeader.java
%%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.class
%%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.java
%%JAVAJARDIR%%/bbmap/icecream/README.md
%%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.class
%%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.java
%%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio$ProcessThread.class
%%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio.class
%%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio.java
%%JAVAJARDIR%%/bbmap/icecream/ZMW.class
%%JAVAJARDIR%%/bbmap/icecream/ZMW.java
%%JAVAJARDIR%%/bbmap/icecream/ZMWStreamer.class
%%JAVAJARDIR%%/bbmap/icecream/ZMWStreamer.java
%%JAVAJARDIR%%/bbmap/idaligner/AlignerBenchmark$SynHeader.class
%%JAVAJARDIR%%/bbmap/idaligner/AlignerBenchmark.class
%%JAVAJARDIR%%/bbmap/idaligner/AlignerBenchmark.java
%%JAVAJARDIR%%/bbmap/idaligner/AlignmentStats.class
%%JAVAJARDIR%%/bbmap/idaligner/AlignmentStats.java
%%JAVAJARDIR%%/bbmap/idaligner/BandedAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/BandedAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/BandedAlignerConcise.class
%%JAVAJARDIR%%/bbmap/idaligner/BandedAlignerConcise.java
%%JAVAJARDIR%%/bbmap/idaligner/BandedAlignerInt.class
%%JAVAJARDIR%%/bbmap/idaligner/BandedAlignerInt.java
%%JAVAJARDIR%%/bbmap/idaligner/BandedAlignerM.class
%%JAVAJARDIR%%/bbmap/idaligner/BandedAlignerM.java
%%JAVAJARDIR%%/bbmap/idaligner/BandedByteAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/BandedByteAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAligner2.class
%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAligner2.java
%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAligner3.class
%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAligner3.java
%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAlignerInt.class
%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAlignerInt.java
%%JAVAJARDIR%%/bbmap/idaligner/CrossCutAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/CrossCutAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/DiagonalAligner$ExtzResult.class
%%JAVAJARDIR%%/bbmap/idaligner/DiagonalAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/DiagonalAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/DriftingAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/DriftingAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/DriftingAlignerConcise.class
%%JAVAJARDIR%%/bbmap/idaligner/DriftingAlignerConcise.java
%%JAVAJARDIR%%/bbmap/idaligner/DriftingAlignerM.class
%%JAVAJARDIR%%/bbmap/idaligner/DriftingAlignerM.java
%%JAVAJARDIR%%/bbmap/idaligner/DriftingPlusAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/DriftingPlusAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/DriftingPlusAligner2.class
%%JAVAJARDIR%%/bbmap/idaligner/DriftingPlusAligner2.java
%%JAVAJARDIR%%/bbmap/idaligner/DriftingPlusAligner3.class
%%JAVAJARDIR%%/bbmap/idaligner/DriftingPlusAligner3.java
%%JAVAJARDIR%%/bbmap/idaligner/Factory.class
%%JAVAJARDIR%%/bbmap/idaligner/Factory.java
%%JAVAJARDIR%%/bbmap/idaligner/GlocalAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/GlocalAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/GlocalAlignerConcise.class
%%JAVAJARDIR%%/bbmap/idaligner/GlocalAlignerConcise.java
%%JAVAJARDIR%%/bbmap/idaligner/GlocalAlignerInt.class
%%JAVAJARDIR%%/bbmap/idaligner/GlocalAlignerInt.java
%%JAVAJARDIR%%/bbmap/idaligner/GlocalAlignerOld.class
%%JAVAJARDIR%%/bbmap/idaligner/GlocalAlignerOld.java
%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner2.class
%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner2.java
%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner3.class
%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner3.java
%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner4.class
%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner4.java
%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner5.class
%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner5.java
%%JAVAJARDIR%%/bbmap/idaligner/IDAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/IDAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/IDAlignerStatics.class
%%JAVAJARDIR%%/bbmap/idaligner/IDAlignerStatics.java
%%JAVAJARDIR%%/bbmap/idaligner/IntListAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/IntListAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/Parallelogram.class
%%JAVAJARDIR%%/bbmap/idaligner/Parallelogram.java
%%JAVAJARDIR%%/bbmap/idaligner/QuabbleAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/QuabbleAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/QuantumAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/QuantumAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerConcise.class
%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerConcise.java
%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerConcise2.class
%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerConcise2.java
%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerM.class
%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerM.java
%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerQC.class
%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerQC.java
%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner2.class
%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner2.java
%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner3.class
%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner3.java
%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner4.class
%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner4.java
%%JAVAJARDIR%%/bbmap/idaligner/RelativeAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/RelativeAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/ScrabbleAffine.class
%%JAVAJARDIR%%/bbmap/idaligner/ScrabbleAffine.java
%%JAVAJARDIR%%/bbmap/idaligner/ScrabbleAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/ScrabbleAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/ScrabbleAligner2.class
%%JAVAJARDIR%%/bbmap/idaligner/ScrabbleAligner2.java
%%JAVAJARDIR%%/bbmap/idaligner/SmithWaterman.class
%%JAVAJARDIR%%/bbmap/idaligner/SmithWaterman.java
%%JAVAJARDIR%%/bbmap/idaligner/Test$Runner.class
%%JAVAJARDIR%%/bbmap/idaligner/Test.class
%%JAVAJARDIR%%/bbmap/idaligner/Test.java
%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerBatch.class
%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerBatch.java
%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerLength.class
%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerLength.java
%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerSuite$Job.class
%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerSuite$Worker.class
%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerSuite.class
%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerSuite.java
%%JAVAJARDIR%%/bbmap/idaligner/Tracer.class
%%JAVAJARDIR%%/bbmap/idaligner/Tracer.java
%%JAVAJARDIR%%/bbmap/idaligner/TracerAffine.class
%%JAVAJARDIR%%/bbmap/idaligner/TracerAffine.java
%%JAVAJARDIR%%/bbmap/idaligner/VisualizationConverter.class
%%JAVAJARDIR%%/bbmap/idaligner/VisualizationConverter.java
%%JAVAJARDIR%%/bbmap/idaligner/Visualizer.class
%%JAVAJARDIR%%/bbmap/idaligner/Visualizer.java
%%JAVAJARDIR%%/bbmap/idaligner/WaveFrontAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/WaveFrontAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/WaveFrontAligner2.class
%%JAVAJARDIR%%/bbmap/idaligner/WaveFrontAligner2.java
%%JAVAJARDIR%%/bbmap/idaligner/WaveFrontAlignerViz.class
%%JAVAJARDIR%%/bbmap/idaligner/WaveFrontAlignerViz.java
%%JAVAJARDIR%%/bbmap/idaligner/WobbleAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/WobbleAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/WobbleAlignerConcise.class
%%JAVAJARDIR%%/bbmap/idaligner/WobbleAlignerConcise.java
%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner.java
%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner2.class
%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner2.java
%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner3.class
%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner3.java
%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner4.class
%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner4.java
%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner5.class
%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner5.java
%%JAVAJARDIR%%/bbmap/idaligner/XDropHAligner.class
%%JAVAJARDIR%%/bbmap/idaligner/XDropHAligner.java
%%JAVAJARDIR%%/bbmap/ifa/ClippingTest.class
%%JAVAJARDIR%%/bbmap/ifa/ClippingTest.java
%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner$ProcessThread.class
%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner.class
%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner.java
%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner2$ProcessThread.class
%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner2.class
%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner2.java
%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner3$ProcessThread.class
%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner3.class
%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner3.java
%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner4$ProcessThread.class
%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner4.class
%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner4.java
%%JAVAJARDIR%%/bbmap/ifa/IntIndex.class
%%JAVAJARDIR%%/bbmap/ifa/IntIndex.java
%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculator.class
%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculator.java
%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculator2.class
%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculator2.java
%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculator3.class
%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculator3.java
%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculatorOld.class
%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculatorOld.java
%%JAVAJARDIR%%/bbmap/ifa/PackedIndex.class
%%JAVAJARDIR%%/bbmap/ifa/PackedIndex.java
%%JAVAJARDIR%%/bbmap/ifa/PackedIndex4.class
%%JAVAJARDIR%%/bbmap/ifa/PackedIndex4.java
%%JAVAJARDIR%%/bbmap/ifa/Query.class
%%JAVAJARDIR%%/bbmap/ifa/Query.java
%%JAVAJARDIR%%/bbmap/illumina/Cbcl2Text.class
%%JAVAJARDIR%%/bbmap/illumina/Cbcl2Text.java
%%JAVAJARDIR%%/bbmap/illumina/CbclDecoder.class
%%JAVAJARDIR%%/bbmap/illumina/CbclDecoder.java
%%JAVAJARDIR%%/bbmap/illumina/CbclHeader.class
%%JAVAJARDIR%%/bbmap/illumina/CbclHeader.java
%%JAVAJARDIR%%/bbmap/illumina/CbclInspector.class
%%JAVAJARDIR%%/bbmap/illumina/CbclInspector.java
%%JAVAJARDIR%%/bbmap/illumina/ClusterData.class
%%JAVAJARDIR%%/bbmap/illumina/ClusterData.java
%%JAVAJARDIR%%/bbmap/illumina/FilterReader.class
%%JAVAJARDIR%%/bbmap/illumina/FilterReader.java
%%JAVAJARDIR%%/bbmap/illumina/LocsReader.class
%%JAVAJARDIR%%/bbmap/illumina/LocsReader.java
%%JAVAJARDIR%%/bbmap/illumina/RunInfoParser.class
%%JAVAJARDIR%%/bbmap/illumina/RunInfoParser.java
%%JAVAJARDIR%%/bbmap/jasper/KmerPosition.class
%%JAVAJARDIR%%/bbmap/jasper/KmerPosition.java
%%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.class
%%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.java
%%JAVAJARDIR%%/bbmap/jasper/README.md
%%JAVAJARDIR%%/bbmap/jgi/AddAdapters.class
%%JAVAJARDIR%%/bbmap/jgi/AddAdapters.java
%%JAVAJARDIR%%/bbmap/jgi/AdjustHomopolymers.class
%%JAVAJARDIR%%/bbmap/jgi/AdjustHomopolymers.java
%%JAVAJARDIR%%/bbmap/jgi/Assembly.class
%%JAVAJARDIR%%/bbmap/jgi/Assembly.java
%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2$Triple.class
%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2.class
%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2.java
%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats3.class
%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats3.java
%%JAVAJARDIR%%/bbmap/jgi/AssemblyStatsWrapper.class
%%JAVAJARDIR%%/bbmap/jgi/AssemblyStatsWrapper.java
%%JAVAJARDIR%%/bbmap/jgi/BBDuk$LoadThread.class
%%JAVAJARDIR%%/bbmap/jgi/BBDuk$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/BBDuk.class
%%JAVAJARDIR%%/bbmap/jgi/BBDuk.java
%%JAVAJARDIR%%/bbmap/jgi/BBMask$MaskLowEntropyThread.class
%%JAVAJARDIR%%/bbmap/jgi/BBMask$MaskRepeatThread.class
%%JAVAJARDIR%%/bbmap/jgi/BBMask$MaskSamThread.class
%%JAVAJARDIR%%/bbmap/jgi/BBMask.class
%%JAVAJARDIR%%/bbmap/jgi/BBMask.java
%%JAVAJARDIR%%/bbmap/jgi/BBMerge$MateThread.class
%%JAVAJARDIR%%/bbmap/jgi/BBMerge.class
%%JAVAJARDIR%%/bbmap/jgi/BBMerge.java
%%JAVAJARDIR%%/bbmap/jgi/BBMergeOverlapper.class
%%JAVAJARDIR%%/bbmap/jgi/BBMergeOverlapper.java
%%JAVAJARDIR%%/bbmap/jgi/BBQC.class
%%JAVAJARDIR%%/bbmap/jgi/BBQC.java
%%JAVAJARDIR%%/bbmap/jgi/CalcTrueQuality$CountMatrixSet.class
%%JAVAJARDIR%%/bbmap/jgi/CalcTrueQuality$GBMatrixSet.class
%%JAVAJARDIR%%/bbmap/jgi/CalcTrueQuality$Worker.class
%%JAVAJARDIR%%/bbmap/jgi/CalcTrueQuality.class
%%JAVAJARDIR%%/bbmap/jgi/CalcTrueQuality.java
%%JAVAJARDIR%%/bbmap/jgi/CalcUniqueness$Counter.class
%%JAVAJARDIR%%/bbmap/jgi/CalcUniqueness.class
%%JAVAJARDIR%%/bbmap/jgi/CalcUniqueness.java
%%JAVAJARDIR%%/bbmap/jgi/CallPeaks$Peak.class
%%JAVAJARDIR%%/bbmap/jgi/CallPeaks.class
%%JAVAJARDIR%%/bbmap/jgi/CallPeaks.java
%%JAVAJARDIR%%/bbmap/jgi/CheckStrand.class
%%JAVAJARDIR%%/bbmap/jgi/CheckStrand.java
%%JAVAJARDIR%%/bbmap/jgi/CheckStrand2$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/CheckStrand2$Seq.class
%%JAVAJARDIR%%/bbmap/jgi/CheckStrand2.class
%%JAVAJARDIR%%/bbmap/jgi/CheckStrand2.java
%%JAVAJARDIR%%/bbmap/jgi/Consect.class
%%JAVAJARDIR%%/bbmap/jgi/Consect.java
%%JAVAJARDIR%%/bbmap/jgi/CountDuplicates$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/CountDuplicates.class
%%JAVAJARDIR%%/bbmap/jgi/CountDuplicates.java
%%JAVAJARDIR%%/bbmap/jgi/CountDuplicatesBuffered$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/CountDuplicatesBuffered.class
%%JAVAJARDIR%%/bbmap/jgi/CountDuplicatesBuffered.java
%%JAVAJARDIR%%/bbmap/jgi/CountGC$1.class
%%JAVAJARDIR%%/bbmap/jgi/CountGC.class
%%JAVAJARDIR%%/bbmap/jgi/CountGC.java
%%JAVAJARDIR%%/bbmap/jgi/CountUniqueness.class
%%JAVAJARDIR%%/bbmap/jgi/CountUniqueness.java
%%JAVAJARDIR%%/bbmap/jgi/CovStatsLine.class
%%JAVAJARDIR%%/bbmap/jgi/CovStatsLine.java
%%JAVAJARDIR%%/bbmap/jgi/CoveragePileup.class
%%JAVAJARDIR%%/bbmap/jgi/CoveragePileup.java
%%JAVAJARDIR%%/bbmap/jgi/CoveragePileupMT$LoadThread.class
%%JAVAJARDIR%%/bbmap/jgi/CoveragePileupMT.class
%%JAVAJARDIR%%/bbmap/jgi/CoveragePileupMT.java
%%JAVAJARDIR%%/bbmap/jgi/CrisprFinder$1.class
%%JAVAJARDIR%%/bbmap/jgi/CrisprFinder$Alignment.class
%%JAVAJARDIR%%/bbmap/jgi/CrisprFinder$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/CrisprFinder.class
%%JAVAJARDIR%%/bbmap/jgi/CrisprFinder.java
%%JAVAJARDIR%%/bbmap/jgi/CutPrimers.class
%%JAVAJARDIR%%/bbmap/jgi/CutPrimers.java
%%JAVAJARDIR%%/bbmap/jgi/DecontaminateByNormalization.class
%%JAVAJARDIR%%/bbmap/jgi/DecontaminateByNormalization.java
%%JAVAJARDIR%%/bbmap/jgi/Dedupe$ClusterLengthComparator.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe$ClusterThread.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe$HashThread.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe$MstThread.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe$Overlap.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe$Unit.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe$UnitOffsetComparator.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe.java
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2$ClusterLengthComparator.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2$ClusterThread.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2$HashThread.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2$MstThread.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2$Overlap.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2$Unit.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2$UnitOffsetComparator.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2.class
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2.java
%%JAVAJARDIR%%/bbmap/jgi/DedupeByMapping$Quad.class
%%JAVAJARDIR%%/bbmap/jgi/DedupeByMapping.class
%%JAVAJARDIR%%/bbmap/jgi/DedupeByMapping.java
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein$ClusterLengthComparator.class
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein$ClusterThread.class
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein$HashThread.class
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein$MstThread.class
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein$Overlap.class
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein$Unit.class
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein$UnitOffsetComparator.class
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein.class
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein.java
%%JAVAJARDIR%%/bbmap/jgi/DemuxByName.class
%%JAVAJARDIR%%/bbmap/jgi/DemuxByName.java
%%JAVAJARDIR%%/bbmap/jgi/DemuxByName2.class
%%JAVAJARDIR%%/bbmap/jgi/DemuxByName2.java
%%JAVAJARDIR%%/bbmap/jgi/Difference.class
%%JAVAJARDIR%%/bbmap/jgi/Difference.java
%%JAVAJARDIR%%/bbmap/jgi/FilterByCoverage.class
%%JAVAJARDIR%%/bbmap/jgi/FilterByCoverage.java
%%JAVAJARDIR%%/bbmap/jgi/FilterBySequence$Code.class
%%JAVAJARDIR%%/bbmap/jgi/FilterBySequence$LoadThread.class
%%JAVAJARDIR%%/bbmap/jgi/FilterBySequence$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/FilterBySequence.class
%%JAVAJARDIR%%/bbmap/jgi/FilterBySequence.java
%%JAVAJARDIR%%/bbmap/jgi/FilterReadsWithSubs.class
%%JAVAJARDIR%%/bbmap/jgi/FilterReadsWithSubs.java
%%JAVAJARDIR%%/bbmap/jgi/FindHiCJunctions.class
%%JAVAJARDIR%%/bbmap/jgi/FindHiCJunctions.java
%%JAVAJARDIR%%/bbmap/jgi/FindPrimers$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/FindPrimers.class
%%JAVAJARDIR%%/bbmap/jgi/FindPrimers.java
%%JAVAJARDIR%%/bbmap/jgi/FindString.class
%%JAVAJARDIR%%/bbmap/jgi/FindString.java
%%JAVAJARDIR%%/bbmap/jgi/FungalRelease.class
%%JAVAJARDIR%%/bbmap/jgi/FungalRelease.java
%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$KapaEntry.class
%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$Plate.class
%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$TagData.class
%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$Well.class
%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats.class
%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats.java
%%JAVAJARDIR%%/bbmap/jgi/GetReads.class
%%JAVAJARDIR%%/bbmap/jgi/GetReads.java
%%JAVAJARDIR%%/bbmap/jgi/GradeMergedReads.class
%%JAVAJARDIR%%/bbmap/jgi/GradeMergedReads.java
%%JAVAJARDIR%%/bbmap/jgi/GreedyBarCodeFinder.class
%%JAVAJARDIR%%/bbmap/jgi/GreedyBarCodeFinder.java
%%JAVAJARDIR%%/bbmap/jgi/IdentityMatrix$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/IdentityMatrix.class
%%JAVAJARDIR%%/bbmap/jgi/IdentityMatrix.java
%%JAVAJARDIR%%/bbmap/jgi/Info.class
%%JAVAJARDIR%%/bbmap/jgi/Info.java
%%JAVAJARDIR%%/bbmap/jgi/KExpand.class
%%JAVAJARDIR%%/bbmap/jgi/KExpand.java
%%JAVAJARDIR%%/bbmap/jgi/KeepBestCopy.class
%%JAVAJARDIR%%/bbmap/jgi/KeepBestCopy.java
%%JAVAJARDIR%%/bbmap/jgi/KmerCountExact$DumpKmersThread.class
%%JAVAJARDIR%%/bbmap/jgi/KmerCountExact$MakeKhistThread.class
%%JAVAJARDIR%%/bbmap/jgi/KmerCountExact.class
%%JAVAJARDIR%%/bbmap/jgi/KmerCountExact.java
%%JAVAJARDIR%%/bbmap/jgi/KmerCountMulti$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/KmerCountMulti.class
%%JAVAJARDIR%%/bbmap/jgi/KmerCountMulti.java
%%JAVAJARDIR%%/bbmap/jgi/KmerCountShort$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/KmerCountShort.class
%%JAVAJARDIR%%/bbmap/jgi/KmerCountShort.java
%%JAVAJARDIR%%/bbmap/jgi/KmerCoverage$1.class
%%JAVAJARDIR%%/bbmap/jgi/KmerCoverage$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/KmerCoverage.class
%%JAVAJARDIR%%/bbmap/jgi/KmerCoverage.java
%%JAVAJARDIR%%/bbmap/jgi/KmerFilterSetMaker.class
%%JAVAJARDIR%%/bbmap/jgi/KmerFilterSetMaker.java
%%JAVAJARDIR%%/bbmap/jgi/KmerHashDump.class
%%JAVAJARDIR%%/bbmap/jgi/KmerHashDump.java
%%JAVAJARDIR%%/bbmap/jgi/KmerNormalize$1.class
%%JAVAJARDIR%%/bbmap/jgi/KmerNormalize$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/KmerNormalize.class
%%JAVAJARDIR%%/bbmap/jgi/KmerNormalize.java
%%JAVAJARDIR%%/bbmap/jgi/KmerSample.class
%%JAVAJARDIR%%/bbmap/jgi/KmerSample.java
%%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram$1.class
%%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.class
%%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.java
%%JAVAJARDIR%%/bbmap/jgi/MakePolymers.class
%%JAVAJARDIR%%/bbmap/jgi/MakePolymers.java
%%JAVAJARDIR%%/bbmap/jgi/MergeBarcodes.class
%%JAVAJARDIR%%/bbmap/jgi/MergeBarcodes.java
%%JAVAJARDIR%%/bbmap/jgi/MergeSam.class
%%JAVAJARDIR%%/bbmap/jgi/MergeSam.java
%%JAVAJARDIR%%/bbmap/jgi/MergeSam2.class
%%JAVAJARDIR%%/bbmap/jgi/MergeSam2.java
%%JAVAJARDIR%%/bbmap/jgi/Orf.class
%%JAVAJARDIR%%/bbmap/jgi/Orf.java
%%JAVAJARDIR%%/bbmap/jgi/PhylipToFasta.class
%%JAVAJARDIR%%/bbmap/jgi/PhylipToFasta.java
%%JAVAJARDIR%%/bbmap/jgi/PickSubset$Edge.class
%%JAVAJARDIR%%/bbmap/jgi/PickSubset$Node.class
%%JAVAJARDIR%%/bbmap/jgi/PickSubset.class
%%JAVAJARDIR%%/bbmap/jgi/PickSubset.java
%%JAVAJARDIR%%/bbmap/jgi/README.md
%%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.class
%%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.java
%%JAVAJARDIR%%/bbmap/jgi/RQCFilter3.class
%%JAVAJARDIR%%/bbmap/jgi/RQCFilter3.java
%%JAVAJARDIR%%/bbmap/jgi/RQCFilterStats.class
%%JAVAJARDIR%%/bbmap/jgi/RQCFilterStats.java
%%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution$1.class
%%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution.class
%%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution.java
%%JAVAJARDIR%%/bbmap/jgi/RedirectTest.class
%%JAVAJARDIR%%/bbmap/jgi/RedirectTest.java
%%JAVAJARDIR%%/bbmap/jgi/RefRenamer.class
%%JAVAJARDIR%%/bbmap/jgi/RefRenamer.java
%%JAVAJARDIR%%/bbmap/jgi/Reformat2$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/Reformat2.class
%%JAVAJARDIR%%/bbmap/jgi/Reformat2.java
%%JAVAJARDIR%%/bbmap/jgi/ReformatReads.class
%%JAVAJARDIR%%/bbmap/jgi/ReformatReads.java
%%JAVAJARDIR%%/bbmap/jgi/ReformatReadsOld.class
%%JAVAJARDIR%%/bbmap/jgi/ReformatReadsOld.java
%%JAVAJARDIR%%/bbmap/jgi/ReformatStreamer$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/ReformatStreamer.class
%%JAVAJARDIR%%/bbmap/jgi/ReformatStreamer.java
%%JAVAJARDIR%%/bbmap/jgi/RemapQuality.class
%%JAVAJARDIR%%/bbmap/jgi/RemapQuality.java
%%JAVAJARDIR%%/bbmap/jgi/RemoveBadBarcodes.class
%%JAVAJARDIR%%/bbmap/jgi/RemoveBadBarcodes.java
%%JAVAJARDIR%%/bbmap/jgi/RenameReads.class
%%JAVAJARDIR%%/bbmap/jgi/RenameReads.java
%%JAVAJARDIR%%/bbmap/jgi/ReplaceHeaders.class
%%JAVAJARDIR%%/bbmap/jgi/ReplaceHeaders.java
%%JAVAJARDIR%%/bbmap/jgi/RepresentativeSet$Edge.class
%%JAVAJARDIR%%/bbmap/jgi/RepresentativeSet$Node.class
%%JAVAJARDIR%%/bbmap/jgi/RepresentativeSet.class
%%JAVAJARDIR%%/bbmap/jgi/RepresentativeSet.java
%%JAVAJARDIR%%/bbmap/jgi/SamToEst$1.class
%%JAVAJARDIR%%/bbmap/jgi/SamToEst$EST.class
%%JAVAJARDIR%%/bbmap/jgi/SamToEst.class
%%JAVAJARDIR%%/bbmap/jgi/SamToEst.java
%%JAVAJARDIR%%/bbmap/jgi/Seal$LoadThread.class
%%JAVAJARDIR%%/bbmap/jgi/Seal$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/Seal.class
%%JAVAJARDIR%%/bbmap/jgi/Seal.java
%%JAVAJARDIR%%/bbmap/jgi/SealRefInfo.class
%%JAVAJARDIR%%/bbmap/jgi/SealRefInfo.java
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$CountComparator.class
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$Kmer.class
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$NumComparator.class
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency.class
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency.java
%%JAVAJARDIR%%/bbmap/jgi/SplitNexteraLMP.class
%%JAVAJARDIR%%/bbmap/jgi/SplitNexteraLMP.java
%%JAVAJARDIR%%/bbmap/jgi/SplitPairsAndSingles.class
%%JAVAJARDIR%%/bbmap/jgi/SplitPairsAndSingles.java
%%JAVAJARDIR%%/bbmap/jgi/SplitSam4Way.class
%%JAVAJARDIR%%/bbmap/jgi/SplitSam4Way.java
%%JAVAJARDIR%%/bbmap/jgi/SplitSam6Way.class
%%JAVAJARDIR%%/bbmap/jgi/SplitSam6Way.java
%%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.class
%%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.java
%%JAVAJARDIR%%/bbmap/jgi/TestFilesystem$WriteThread.class
%%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.class
%%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.java
%%JAVAJARDIR%%/bbmap/jgi/TestFormat$TestThread.class
%%JAVAJARDIR%%/bbmap/jgi/TestFormat.class
%%JAVAJARDIR%%/bbmap/jgi/TestFormat.java
%%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies$Line.class
%%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies$PrintThread.class
%%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies.class
%%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies.java
%%JAVAJARDIR%%/bbmap/jgi/TranslateSixFrames.class
%%JAVAJARDIR%%/bbmap/jgi/TranslateSixFrames.java
%%JAVAJARDIR%%/bbmap/jgi/TrimContigs$Range.class
%%JAVAJARDIR%%/bbmap/jgi/TrimContigs.class
%%JAVAJARDIR%%/bbmap/jgi/TrimContigs.java
%%JAVAJARDIR%%/bbmap/jgi/UnicodeToAscii.class
%%JAVAJARDIR%%/bbmap/jgi/UnicodeToAscii.java
%%JAVAJARDIR%%/bbmap/jgi/Unzip.class
%%JAVAJARDIR%%/bbmap/jgi/Unzip.java
%%JAVAJARDIR%%/bbmap/json/JsonLiteral.class
%%JAVAJARDIR%%/bbmap/json/JsonLiteral.java
%%JAVAJARDIR%%/bbmap/json/JsonObject.class
%%JAVAJARDIR%%/bbmap/json/JsonObject.java
%%JAVAJARDIR%%/bbmap/json/JsonParser.class
%%JAVAJARDIR%%/bbmap/json/JsonParser.java
%%JAVAJARDIR%%/bbmap/json/README.md
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable$AllocThread.class
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.class
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.java
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet$CountGCThread.class
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.class
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.java
%%JAVAJARDIR%%/bbmap/kmer/DumpThread.class
%%JAVAJARDIR%%/bbmap/kmer/DumpThread.java
%%JAVAJARDIR%%/bbmap/kmer/HashArray.class
%%JAVAJARDIR%%/bbmap/kmer/HashArray.java
%%JAVAJARDIR%%/bbmap/kmer/HashArray1D$Walker1D.class
%%JAVAJARDIR%%/bbmap/kmer/HashArray1D.class
%%JAVAJARDIR%%/bbmap/kmer/HashArray1D.java
%%JAVAJARDIR%%/bbmap/kmer/HashArray2D.class
%%JAVAJARDIR%%/bbmap/kmer/HashArray2D.java
%%JAVAJARDIR%%/bbmap/kmer/HashArrayHybrid.class
%%JAVAJARDIR%%/bbmap/kmer/HashArrayHybrid.java
%%JAVAJARDIR%%/bbmap/kmer/HashArrayHybridFast.class
%%JAVAJARDIR%%/bbmap/kmer/HashArrayHybridFast.java
%%JAVAJARDIR%%/bbmap/kmer/HashBuffer.class
%%JAVAJARDIR%%/bbmap/kmer/HashBuffer.java
%%JAVAJARDIR%%/bbmap/kmer/HashForest.class
%%JAVAJARDIR%%/bbmap/kmer/HashForest.java
%%JAVAJARDIR%%/bbmap/kmer/HistogramMaker$FillThread.class
%%JAVAJARDIR%%/bbmap/kmer/HistogramMaker.class
%%JAVAJARDIR%%/bbmap/kmer/HistogramMaker.java
%%JAVAJARDIR%%/bbmap/kmer/KmerBuffer.class
%%JAVAJARDIR%%/bbmap/kmer/KmerBuffer.java
%%JAVAJARDIR%%/bbmap/kmer/KmerLink.class
%%JAVAJARDIR%%/bbmap/kmer/KmerLink.java
%%JAVAJARDIR%%/bbmap/kmer/KmerNode.class
%%JAVAJARDIR%%/bbmap/kmer/KmerNode.java
%%JAVAJARDIR%%/bbmap/kmer/KmerNode1D.class
%%JAVAJARDIR%%/bbmap/kmer/KmerNode1D.java
%%JAVAJARDIR%%/bbmap/kmer/KmerNode2D.class
%%JAVAJARDIR%%/bbmap/kmer/KmerNode2D.java
%%JAVAJARDIR%%/bbmap/kmer/KmerTable.class
%%JAVAJARDIR%%/bbmap/kmer/KmerTable.java
%%JAVAJARDIR%%/bbmap/kmer/KmerTableInterface.class
%%JAVAJARDIR%%/bbmap/kmer/KmerTableInterface.java
%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet$LoadThread.class
%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet$WalkerKST.class
%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet.class
%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet.java
%%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.class
%%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.java
%%JAVAJARDIR%%/bbmap/kmer/README.md
%%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.class
%%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.java
%%JAVAJARDIR%%/bbmap/kmer/SimpleKmerTable.class
%%JAVAJARDIR%%/bbmap/kmer/SimpleKmerTable.java
%%JAVAJARDIR%%/bbmap/kmer/TableLoaderLockFree$LoadThread.class
%%JAVAJARDIR%%/bbmap/kmer/TableLoaderLockFree.class
%%JAVAJARDIR%%/bbmap/kmer/TableLoaderLockFree.java
%%JAVAJARDIR%%/bbmap/kmer/TableReader.class
%%JAVAJARDIR%%/bbmap/kmer/TableReader.java
%%JAVAJARDIR%%/bbmap/kmer/Walker.class
%%JAVAJARDIR%%/bbmap/kmer/Walker.java
%%JAVAJARDIR%%/bbmap/map/AbstractBitSet.class
%%JAVAJARDIR%%/bbmap/map/AbstractBitSet.java
%%JAVAJARDIR%%/bbmap/map/AbstractIntHashMap.class
%%JAVAJARDIR%%/bbmap/map/AbstractIntHashMap.java
%%JAVAJARDIR%%/bbmap/map/AtomicBitSet.class
%%JAVAJARDIR%%/bbmap/map/AtomicBitSet.java
%%JAVAJARDIR%%/bbmap/map/IntHashMap.class
%%JAVAJARDIR%%/bbmap/map/IntHashMap.java
%%JAVAJARDIR%%/bbmap/map/IntHashMap2.class
%%JAVAJARDIR%%/bbmap/map/IntHashMap2.java
%%JAVAJARDIR%%/bbmap/map/IntHashMap3.class
%%JAVAJARDIR%%/bbmap/map/IntHashMap3.java
%%JAVAJARDIR%%/bbmap/map/IntHashMapBinary.class
%%JAVAJARDIR%%/bbmap/map/IntHashMapBinary.java
%%JAVAJARDIR%%/bbmap/map/IntHashMapInterface.class
%%JAVAJARDIR%%/bbmap/map/IntHashMapInterface.java
%%JAVAJARDIR%%/bbmap/map/IntHashSet.class
%%JAVAJARDIR%%/bbmap/map/IntHashSet.java
%%JAVAJARDIR%%/bbmap/map/IntHashSetList.class
%%JAVAJARDIR%%/bbmap/map/IntHashSetList.java
%%JAVAJARDIR%%/bbmap/map/IntListHashMap.class
%%JAVAJARDIR%%/bbmap/map/IntListHashMap.java
%%JAVAJARDIR%%/bbmap/map/IntListHashMap3.class
%%JAVAJARDIR%%/bbmap/map/IntListHashMap3.java
%%JAVAJARDIR%%/bbmap/map/IntLongHashMap.class
%%JAVAJARDIR%%/bbmap/map/IntLongHashMap.java
%%JAVAJARDIR%%/bbmap/map/IntLongHashMap2.class
%%JAVAJARDIR%%/bbmap/map/IntLongHashMap2.java
%%JAVAJARDIR%%/bbmap/map/IntLongHashMap3.class
%%JAVAJARDIR%%/bbmap/map/IntLongHashMap3.java
%%JAVAJARDIR%%/bbmap/map/IntObjectMap.class
%%JAVAJARDIR%%/bbmap/map/IntObjectMap.java
%%JAVAJARDIR%%/bbmap/map/LongArrayListHashMap.class
%%JAVAJARDIR%%/bbmap/map/LongArrayListHashMap.java
%%JAVAJARDIR%%/bbmap/map/LongHashMap.class
%%JAVAJARDIR%%/bbmap/map/LongHashMap.java
%%JAVAJARDIR%%/bbmap/map/LongHashSet.class
%%JAVAJARDIR%%/bbmap/map/LongHashSet.java
%%JAVAJARDIR%%/bbmap/map/LongIntMap.class
%%JAVAJARDIR%%/bbmap/map/LongIntMap.java
%%JAVAJARDIR%%/bbmap/map/LongIntMapX.class
%%JAVAJARDIR%%/bbmap/map/LongIntMapX.java
%%JAVAJARDIR%%/bbmap/map/LongListSet$LongListSetIterator.class
%%JAVAJARDIR%%/bbmap/map/LongListSet.class
%%JAVAJARDIR%%/bbmap/map/LongListSet.java
%%JAVAJARDIR%%/bbmap/map/LongLongHashMap.class
%%JAVAJARDIR%%/bbmap/map/LongLongHashMap.java
%%JAVAJARDIR%%/bbmap/map/LongLongHashMap2.class
%%JAVAJARDIR%%/bbmap/map/LongLongHashMap2.java
%%JAVAJARDIR%%/bbmap/map/LongLongHashMapHybrid.class
%%JAVAJARDIR%%/bbmap/map/LongLongHashMapHybrid.java
%%JAVAJARDIR%%/bbmap/map/LongLongListHashMap.class
%%JAVAJARDIR%%/bbmap/map/LongLongListHashMap.java
%%JAVAJARDIR%%/bbmap/map/LongObjectMap.class
%%JAVAJARDIR%%/bbmap/map/LongObjectMap.java
%%JAVAJARDIR%%/bbmap/map/MultiBitSet.class
%%JAVAJARDIR%%/bbmap/map/MultiBitSet.java
%%JAVAJARDIR%%/bbmap/map/ObjectDoubleMap.class
%%JAVAJARDIR%%/bbmap/map/ObjectDoubleMap.java
%%JAVAJARDIR%%/bbmap/map/ObjectIntMap.class
%%JAVAJARDIR%%/bbmap/map/ObjectIntMap.java
%%JAVAJARDIR%%/bbmap/map/ObjectMap.class
%%JAVAJARDIR%%/bbmap/map/ObjectMap.java
%%JAVAJARDIR%%/bbmap/map/ObjectSet.class
%%JAVAJARDIR%%/bbmap/map/ObjectSet.java
%%JAVAJARDIR%%/bbmap/map/RawBitSet.class
%%JAVAJARDIR%%/bbmap/map/RawBitSet.java
%%JAVAJARDIR%%/bbmap/map/SeqMap$1.class
%%JAVAJARDIR%%/bbmap/map/SeqMap$2.class
%%JAVAJARDIR%%/bbmap/map/SeqMap$3.class
%%JAVAJARDIR%%/bbmap/map/SeqMap.class
%%JAVAJARDIR%%/bbmap/map/SeqMap.java
%%JAVAJARDIR%%/bbmap/map/SeqPos.class
%%JAVAJARDIR%%/bbmap/map/SeqPos.java
%%JAVAJARDIR%%/bbmap/map/SeqPosM.class
%%JAVAJARDIR%%/bbmap/map/SeqPosM.java
%%JAVAJARDIR%%/bbmap/ml/BBNetExporter.class
%%JAVAJARDIR%%/bbmap/ml/BBNetExporter.java
%%JAVAJARDIR%%/bbmap/ml/Bell.class
%%JAVAJARDIR%%/bbmap/ml/Bell.java
%%JAVAJARDIR%%/bbmap/ml/Calibrate$Accum.class
%%JAVAJARDIR%%/bbmap/ml/Calibrate$Hist.class
%%JAVAJARDIR%%/bbmap/ml/Calibrate$Lut.class
%%JAVAJARDIR%%/bbmap/ml/Calibrate.class
%%JAVAJARDIR%%/bbmap/ml/Calibrate.java
%%JAVAJARDIR%%/bbmap/ml/Cell.class
%%JAVAJARDIR%%/bbmap/ml/Cell.java
%%JAVAJARDIR%%/bbmap/ml/CellNet.class
%%JAVAJARDIR%%/bbmap/ml/CellNet.java
%%JAVAJARDIR%%/bbmap/ml/CellNetParser.class
%%JAVAJARDIR%%/bbmap/ml/CellNetParser.java
%%JAVAJARDIR%%/bbmap/ml/CellNetReverseComparator.class
%%JAVAJARDIR%%/bbmap/ml/CellNetReverseComparator.java
%%JAVAJARDIR%%/bbmap/ml/DataLoader$Triple.class
%%JAVAJARDIR%%/bbmap/ml/DataLoader.class
%%JAVAJARDIR%%/bbmap/ml/DataLoader.java
%%JAVAJARDIR%%/bbmap/ml/EnrichFailures.class
%%JAVAJARDIR%%/bbmap/ml/EnrichFailures.java
%%JAVAJARDIR%%/bbmap/ml/ErrorTaper.class
%%JAVAJARDIR%%/bbmap/ml/ErrorTaper.java
%%JAVAJARDIR%%/bbmap/ml/ExtendedMSig.class
%%JAVAJARDIR%%/bbmap/ml/ExtendedMSig.java
%%JAVAJARDIR%%/bbmap/ml/ExtendedSigmoid.class
%%JAVAJARDIR%%/bbmap/ml/ExtendedSigmoid.java
%%JAVAJARDIR%%/bbmap/ml/Function.class
%%JAVAJARDIR%%/bbmap/ml/Function.java
%%JAVAJARDIR%%/bbmap/ml/Functions.class
%%JAVAJARDIR%%/bbmap/ml/Functions.java
%%JAVAJARDIR%%/bbmap/ml/JobData.class
%%JAVAJARDIR%%/bbmap/ml/JobData.java
%%JAVAJARDIR%%/bbmap/ml/JobResults.class
%%JAVAJARDIR%%/bbmap/ml/JobResults.java
%%JAVAJARDIR%%/bbmap/ml/Linear.class
%%JAVAJARDIR%%/bbmap/ml/Linear.java
%%JAVAJARDIR%%/bbmap/ml/MSig.class
%%JAVAJARDIR%%/bbmap/ml/MSig.java
%%JAVAJARDIR%%/bbmap/ml/Matrix.class
%%JAVAJARDIR%%/bbmap/ml/Matrix.java
%%JAVAJARDIR%%/bbmap/ml/NetConvert.class
%%JAVAJARDIR%%/bbmap/ml/NetConvert.java
%%JAVAJARDIR%%/bbmap/ml/NetFilter$ProcessThread.class
%%JAVAJARDIR%%/bbmap/ml/NetFilter.class
%%JAVAJARDIR%%/bbmap/ml/NetFilter.java
%%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders$Header.class
%%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders.class
%%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders.java
%%JAVAJARDIR%%/bbmap/ml/Profiler.class
%%JAVAJARDIR%%/bbmap/ml/Profiler.java
%%JAVAJARDIR%%/bbmap/ml/README.md
%%JAVAJARDIR%%/bbmap/ml/RSLog.class
%%JAVAJARDIR%%/bbmap/ml/RSLog.java
%%JAVAJARDIR%%/bbmap/ml/RankingEval.class
%%JAVAJARDIR%%/bbmap/ml/RankingEval.java
%%JAVAJARDIR%%/bbmap/ml/ReduceColumns.class
%%JAVAJARDIR%%/bbmap/ml/ReduceColumns.java
%%JAVAJARDIR%%/bbmap/ml/RegCalEval$Result.class
%%JAVAJARDIR%%/bbmap/ml/RegCalEval.class
%%JAVAJARDIR%%/bbmap/ml/RegCalEval.java
%%JAVAJARDIR%%/bbmap/ml/RegressionTrainer.class
%%JAVAJARDIR%%/bbmap/ml/RegressionTrainer.java
%%JAVAJARDIR%%/bbmap/ml/Sample.class
%%JAVAJARDIR%%/bbmap/ml/Sample.java
%%JAVAJARDIR%%/bbmap/ml/SampleErrorComparator.class
%%JAVAJARDIR%%/bbmap/ml/SampleErrorComparator.java
%%JAVAJARDIR%%/bbmap/ml/SampleSet.class
%%JAVAJARDIR%%/bbmap/ml/SampleSet.java
%%JAVAJARDIR%%/bbmap/ml/SampleValueComparator.class
%%JAVAJARDIR%%/bbmap/ml/SampleValueComparator.java
%%JAVAJARDIR%%/bbmap/ml/ScannerThread$LaunchThread.class
%%JAVAJARDIR%%/bbmap/ml/ScannerThread.class
%%JAVAJARDIR%%/bbmap/ml/ScannerThread.java
%%JAVAJARDIR%%/bbmap/ml/ScoreSequence.class
%%JAVAJARDIR%%/bbmap/ml/ScoreSequence.java
%%JAVAJARDIR%%/bbmap/ml/Seed.class
%%JAVAJARDIR%%/bbmap/ml/Seed.java
%%JAVAJARDIR%%/bbmap/ml/SequenceToVector$1.class
%%JAVAJARDIR%%/bbmap/ml/SequenceToVector.class
%%JAVAJARDIR%%/bbmap/ml/SequenceToVector.java
%%JAVAJARDIR%%/bbmap/ml/Sigmoid.class
%%JAVAJARDIR%%/bbmap/ml/Sigmoid.java
%%JAVAJARDIR%%/bbmap/ml/Source.class
%%JAVAJARDIR%%/bbmap/ml/Source.java
%%JAVAJARDIR%%/bbmap/ml/Status.class
%%JAVAJARDIR%%/bbmap/ml/Status.java
%%JAVAJARDIR%%/bbmap/ml/Subset.class
%%JAVAJARDIR%%/bbmap/ml/Subset.java
%%JAVAJARDIR%%/bbmap/ml/Swish.class
%%JAVAJARDIR%%/bbmap/ml/Swish.java
%%JAVAJARDIR%%/bbmap/ml/Tanh.class
%%JAVAJARDIR%%/bbmap/ml/Tanh.java
%%JAVAJARDIR%%/bbmap/ml/Trainer.class
%%JAVAJARDIR%%/bbmap/ml/Trainer.java
%%JAVAJARDIR%%/bbmap/ml/TrainerThread$LaunchThread.class
%%JAVAJARDIR%%/bbmap/ml/TrainerThread.class
%%JAVAJARDIR%%/bbmap/ml/TrainerThread.java
%%JAVAJARDIR%%/bbmap/ml/VectorUtils$1.class
%%JAVAJARDIR%%/bbmap/ml/VectorUtils.class
%%JAVAJARDIR%%/bbmap/ml/VectorUtils.java
%%JAVAJARDIR%%/bbmap/ml/WorkerThread.class
%%JAVAJARDIR%%/bbmap/ml/WorkerThread.java
%%JAVAJARDIR%%/bbmap/pacbio/CalcCoverageFromSites$1.class
%%JAVAJARDIR%%/bbmap/pacbio/CalcCoverageFromSites.class
%%JAVAJARDIR%%/bbmap/pacbio/CalcCoverageFromSites.java
%%JAVAJARDIR%%/bbmap/pacbio/GenerateMultiChrom.class
%%JAVAJARDIR%%/bbmap/pacbio/GenerateMultiChrom.java
%%JAVAJARDIR%%/bbmap/pacbio/MakePacBioScript.class
%%JAVAJARDIR%%/bbmap/pacbio/MakePacBioScript.java
%%JAVAJARDIR%%/bbmap/pacbio/MergeFastaContigs$1.class
%%JAVAJARDIR%%/bbmap/pacbio/MergeFastaContigs.class
%%JAVAJARDIR%%/bbmap/pacbio/MergeFastaContigs.java
%%JAVAJARDIR%%/bbmap/pacbio/MergeReadsAndGenome$1.class
%%JAVAJARDIR%%/bbmap/pacbio/MergeReadsAndGenome.class
%%JAVAJARDIR%%/bbmap/pacbio/MergeReadsAndGenome.java
%%JAVAJARDIR%%/bbmap/pacbio/PartitionFastaFile.class
%%JAVAJARDIR%%/bbmap/pacbio/PartitionFastaFile.java
%%JAVAJARDIR%%/bbmap/pacbio/PartitionReads$1.class
%%JAVAJARDIR%%/bbmap/pacbio/PartitionReads.class
%%JAVAJARDIR%%/bbmap/pacbio/PartitionReads.java
%%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized$1.class
%%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized$Buffer.class
%%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized$Ssra.class
%%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized.class
%%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized.java
%%JAVAJARDIR%%/bbmap/pacbio/README.md
%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2$1.class
%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2$ProcessThread.class
%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2.class
%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2.java
%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters3$ProcessThread.class
%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters3.class
%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters3.java
%%JAVAJARDIR%%/bbmap/pacbio/SiteR.class
%%JAVAJARDIR%%/bbmap/pacbio/SiteR.java
%%JAVAJARDIR%%/bbmap/pacbio/SortSites$1.class
%%JAVAJARDIR%%/bbmap/pacbio/SortSites.class
%%JAVAJARDIR%%/bbmap/pacbio/SortSites.java
%%JAVAJARDIR%%/bbmap/pacbio/SplitOffPerfectContigs$1.class
%%JAVAJARDIR%%/bbmap/pacbio/SplitOffPerfectContigs.class
%%JAVAJARDIR%%/bbmap/pacbio/SplitOffPerfectContigs.java
%%JAVAJARDIR%%/bbmap/pacbio/StackSites$1.class
%%JAVAJARDIR%%/bbmap/pacbio/StackSites$Glob.class
%%JAVAJARDIR%%/bbmap/pacbio/StackSites.class
%%JAVAJARDIR%%/bbmap/pacbio/StackSites.java
%%JAVAJARDIR%%/bbmap/pacbio/StackSites2$1.class
%%JAVAJARDIR%%/bbmap/pacbio/StackSites2$Glob.class
%%JAVAJARDIR%%/bbmap/pacbio/StackSites2.class
%%JAVAJARDIR%%/bbmap/pacbio/StackSites2.java
%%JAVAJARDIR%%/bbmap/parse/LineParser.class
%%JAVAJARDIR%%/bbmap/parse/LineParser.java
%%JAVAJARDIR%%/bbmap/parse/LineParser1.class
%%JAVAJARDIR%%/bbmap/parse/LineParser1.java
%%JAVAJARDIR%%/bbmap/parse/LineParser2.class
%%JAVAJARDIR%%/bbmap/parse/LineParser2.java
%%JAVAJARDIR%%/bbmap/parse/LineParser4.class
%%JAVAJARDIR%%/bbmap/parse/LineParser4.java
%%JAVAJARDIR%%/bbmap/parse/LineParserS.class
%%JAVAJARDIR%%/bbmap/parse/LineParserS.java
%%JAVAJARDIR%%/bbmap/parse/LineParserS1.class
%%JAVAJARDIR%%/bbmap/parse/LineParserS1.java
%%JAVAJARDIR%%/bbmap/parse/LineParserS2.class
%%JAVAJARDIR%%/bbmap/parse/LineParserS2.java
%%JAVAJARDIR%%/bbmap/parse/LineParserS3.class
%%JAVAJARDIR%%/bbmap/parse/LineParserS3.java
%%JAVAJARDIR%%/bbmap/parse/LineParserS4.class
%%JAVAJARDIR%%/bbmap/parse/LineParserS4.java
%%JAVAJARDIR%%/bbmap/parse/LineParserS4Reverse.class
%%JAVAJARDIR%%/bbmap/parse/LineParserS4Reverse.java
%%JAVAJARDIR%%/bbmap/parse/LineParserSimple.class
%%JAVAJARDIR%%/bbmap/parse/LineParserSimple.java
%%JAVAJARDIR%%/bbmap/parse/Parse.class
%%JAVAJARDIR%%/bbmap/parse/Parse.java
%%JAVAJARDIR%%/bbmap/parse/Parser.class
%%JAVAJARDIR%%/bbmap/parse/Parser.java
%%JAVAJARDIR%%/bbmap/parse/PreParser.class
%%JAVAJARDIR%%/bbmap/parse/PreParser.java
%%JAVAJARDIR%%/bbmap/processor/Processor.class
%%JAVAJARDIR%%/bbmap/processor/Processor.java
%%JAVAJARDIR%%/bbmap/processor/ReformatProcessor.class
%%JAVAJARDIR%%/bbmap/processor/ReformatProcessor.java
%%JAVAJARDIR%%/bbmap/prok/AnalyzeGenes$FileThread.class
%%JAVAJARDIR%%/bbmap/prok/AnalyzeGenes.class
%%JAVAJARDIR%%/bbmap/prok/AnalyzeGenes.java
%%JAVAJARDIR%%/bbmap/prok/CallGenes$ProcessThread.class
%%JAVAJARDIR%%/bbmap/prok/CallGenes.class
%%JAVAJARDIR%%/bbmap/prok/CallGenes.java
%%JAVAJARDIR%%/bbmap/prok/FetchProks$ProcessThread.class
%%JAVAJARDIR%%/bbmap/prok/FetchProks$Stats.class
%%JAVAJARDIR%%/bbmap/prok/FetchProks.class
%%JAVAJARDIR%%/bbmap/prok/FetchProks.java
%%JAVAJARDIR%%/bbmap/prok/FilterSilva.class
%%JAVAJARDIR%%/bbmap/prok/FilterSilva.java
%%JAVAJARDIR%%/bbmap/prok/FrameStats.class
%%JAVAJARDIR%%/bbmap/prok/FrameStats.java
%%JAVAJARDIR%%/bbmap/prok/GeneCaller.class
%%JAVAJARDIR%%/bbmap/prok/GeneCaller.java
%%JAVAJARDIR%%/bbmap/prok/GeneModel.class
%%JAVAJARDIR%%/bbmap/prok/GeneModel.java
%%JAVAJARDIR%%/bbmap/prok/GeneModelParser.class
%%JAVAJARDIR%%/bbmap/prok/GeneModelParser.java
%%JAVAJARDIR%%/bbmap/prok/MergeRibo$ListComparator.class
%%JAVAJARDIR%%/bbmap/prok/MergeRibo$ProcessThread.class
%%JAVAJARDIR%%/bbmap/prok/MergeRibo$Ribo.class
%%JAVAJARDIR%%/bbmap/prok/MergeRibo.class
%%JAVAJARDIR%%/bbmap/prok/MergeRibo.java
%%JAVAJARDIR%%/bbmap/prok/MergeRibo_Fast$ProcessThread.class
%%JAVAJARDIR%%/bbmap/prok/MergeRibo_Fast$Ribo.class
%%JAVAJARDIR%%/bbmap/prok/MergeRibo_Fast.class
%%JAVAJARDIR%%/bbmap/prok/MergeRibo_Fast.java
%%JAVAJARDIR%%/bbmap/prok/Orf.class
%%JAVAJARDIR%%/bbmap/prok/Orf.java
%%JAVAJARDIR%%/bbmap/prok/PFeature$FeatureComparatorScore.class
%%JAVAJARDIR%%/bbmap/prok/PFeature.class
%%JAVAJARDIR%%/bbmap/prok/PFeature.java
%%JAVAJARDIR%%/bbmap/prok/PGMTools$1.class
%%JAVAJARDIR%%/bbmap/prok/PGMTools.class
%%JAVAJARDIR%%/bbmap/prok/PGMTools.java
%%JAVAJARDIR%%/bbmap/prok/ProkObject.class
%%JAVAJARDIR%%/bbmap/prok/ProkObject.java
%%JAVAJARDIR%%/bbmap/prok/README.md
%%JAVAJARDIR%%/bbmap/prok/RiboMaker$ProcessThread.class
%%JAVAJARDIR%%/bbmap/prok/RiboMaker.class
%%JAVAJARDIR%%/bbmap/prok/RiboMaker.java
%%JAVAJARDIR%%/bbmap/prok/ScafData.class
%%JAVAJARDIR%%/bbmap/prok/ScafData.java
%%JAVAJARDIR%%/bbmap/prok/ScoreTracker.class
%%JAVAJARDIR%%/bbmap/prok/ScoreTracker.java
%%JAVAJARDIR%%/bbmap/prok/SplitRibo$ProcessThread.class
%%JAVAJARDIR%%/bbmap/prok/SplitRibo.class
%%JAVAJARDIR%%/bbmap/prok/SplitRibo.java
%%JAVAJARDIR%%/bbmap/prok/StatsContainer.class
%%JAVAJARDIR%%/bbmap/prok/StatsContainer.java
%%JAVAJARDIR%%/bbmap/rand/FastRandom.class
%%JAVAJARDIR%%/bbmap/rand/FastRandom.java
%%JAVAJARDIR%%/bbmap/rand/FastRandomAES.class
%%JAVAJARDIR%%/bbmap/rand/FastRandomAES.java
%%JAVAJARDIR%%/bbmap/rand/FastRandomSIMD.class
%%JAVAJARDIR%%/bbmap/rand/FastRandomSIMD.java
%%JAVAJARDIR%%/bbmap/rand/FastRandomXoshiro.class
%%JAVAJARDIR%%/bbmap/rand/FastRandomXoshiro.java
%%JAVAJARDIR%%/bbmap/rand/JavaRandom.class
%%JAVAJARDIR%%/bbmap/rand/JavaRandom.java
%%JAVAJARDIR%%/bbmap/repeat/Palindrome.class
%%JAVAJARDIR%%/bbmap/repeat/Palindrome.java
%%JAVAJARDIR%%/bbmap/repeat/PalindromeFinder.class
%%JAVAJARDIR%%/bbmap/repeat/PalindromeFinder.java
%%JAVAJARDIR%%/bbmap/repeat/Repeat$PosComparator.class
%%JAVAJARDIR%%/bbmap/repeat/Repeat$PosComparator2.class
%%JAVAJARDIR%%/bbmap/repeat/Repeat.class
%%JAVAJARDIR%%/bbmap/repeat/Repeat.java
%%JAVAJARDIR%%/bbmap/repeat/RepeatFinder$ProcessThread.class
%%JAVAJARDIR%%/bbmap/repeat/RepeatFinder.class
%%JAVAJARDIR%%/bbmap/repeat/RepeatFinder.java
%%JAVAJARDIR%%/bbmap/repeat/RepeatSet.class
%%JAVAJARDIR%%/bbmap/repeat/RepeatSet.java
%%JAVAJARDIR%%/bbmap/scalar/CloudPlot.class
%%JAVAJARDIR%%/bbmap/scalar/CloudPlot.java
%%JAVAJARDIR%%/bbmap/scalar/PartitionReads$Partition.class
%%JAVAJARDIR%%/bbmap/scalar/PartitionReads.class
%%JAVAJARDIR%%/bbmap/scalar/PartitionReads.java
%%JAVAJARDIR%%/bbmap/scalar/PartitionReads2$Partition.class
%%JAVAJARDIR%%/bbmap/scalar/PartitionReads2$Peak.class
%%JAVAJARDIR%%/bbmap/scalar/PartitionReads2.class
%%JAVAJARDIR%%/bbmap/scalar/PartitionReads2.java
%%JAVAJARDIR%%/bbmap/scalar/PartitionReads3$Partition.class
%%JAVAJARDIR%%/bbmap/scalar/PartitionReads3$Peak.class
%%JAVAJARDIR%%/bbmap/scalar/PartitionReads3$PeakComparator.class
%%JAVAJARDIR%%/bbmap/scalar/PartitionReads3.class
%%JAVAJARDIR%%/bbmap/scalar/PartitionReads3.java
%%JAVAJARDIR%%/bbmap/scalar/ScalarData.class
%%JAVAJARDIR%%/bbmap/scalar/ScalarData.java
%%JAVAJARDIR%%/bbmap/scalar/ScalarInterval.class
%%JAVAJARDIR%%/bbmap/scalar/ScalarInterval.java
%%JAVAJARDIR%%/bbmap/scalar/ScalarIntervals$ProcessThread.class
%%JAVAJARDIR%%/bbmap/scalar/ScalarIntervals$SDAccumulator.class
%%JAVAJARDIR%%/bbmap/scalar/ScalarIntervals.class
%%JAVAJARDIR%%/bbmap/scalar/ScalarIntervals.java
%%JAVAJARDIR%%/bbmap/scalar/Scalars.class
%%JAVAJARDIR%%/bbmap/scalar/Scalars.java
%%JAVAJARDIR%%/bbmap/server/PercentEncoding.class
%%JAVAJARDIR%%/bbmap/server/PercentEncoding.java
%%JAVAJARDIR%%/bbmap/server/README.md
%%JAVAJARDIR%%/bbmap/server/ServerTools$1.class
%%JAVAJARDIR%%/bbmap/server/ServerTools.class
%%JAVAJARDIR%%/bbmap/server/ServerTools.java
%%JAVAJARDIR%%/bbmap/server/SimpleHttpServer$GetHandler.class
%%JAVAJARDIR%%/bbmap/server/SimpleHttpServer.class
%%JAVAJARDIR%%/bbmap/server/SimpleHttpServer.java
%%JAVAJARDIR%%/bbmap/server/StressTest.class
%%JAVAJARDIR%%/bbmap/server/StressTest.java
%%JAVAJARDIR%%/bbmap/server/StressTest2$1.class
%%JAVAJARDIR%%/bbmap/server/StressTest2.class
%%JAVAJARDIR%%/bbmap/server/StressTest2.java
%%JAVAJARDIR%%/bbmap/server/StressTest3.class
%%JAVAJARDIR%%/bbmap/server/StressTest3.java
%%JAVAJARDIR%%/bbmap/shared/Colors.class
%%JAVAJARDIR%%/bbmap/shared/Colors.java
%%JAVAJARDIR%%/bbmap/shared/FieldCopier.class
%%JAVAJARDIR%%/bbmap/shared/FieldCopier.java
%%JAVAJARDIR%%/bbmap/shared/KillSwitch.class
%%JAVAJARDIR%%/bbmap/shared/KillSwitch.java
%%JAVAJARDIR%%/bbmap/shared/MetadataWriter.class
%%JAVAJARDIR%%/bbmap/shared/MetadataWriter.java
%%JAVAJARDIR%%/bbmap/shared/NameMapper.class
%%JAVAJARDIR%%/bbmap/shared/NameMapper.java
%%JAVAJARDIR%%/bbmap/shared/NameMapperTest.class
%%JAVAJARDIR%%/bbmap/shared/NameMapperTest.java
%%JAVAJARDIR%%/bbmap/shared/Primes.class
%%JAVAJARDIR%%/bbmap/shared/Primes.java
%%JAVAJARDIR%%/bbmap/shared/README.md
%%JAVAJARDIR%%/bbmap/shared/Random.class
%%JAVAJARDIR%%/bbmap/shared/Random.java
%%JAVAJARDIR%%/bbmap/shared/Resources.class
%%JAVAJARDIR%%/bbmap/shared/Resources.java
%%JAVAJARDIR%%/bbmap/shared/Shared.class
%%JAVAJARDIR%%/bbmap/shared/Shared.java
%%JAVAJARDIR%%/bbmap/shared/SyncHeart.class
%%JAVAJARDIR%%/bbmap/shared/SyncHeart.java
%%JAVAJARDIR%%/bbmap/shared/Timer.class
%%JAVAJARDIR%%/bbmap/shared/Timer.java
%%JAVAJARDIR%%/bbmap/shared/Tools$1.class
%%JAVAJARDIR%%/bbmap/shared/Tools.class
%%JAVAJARDIR%%/bbmap/shared/Tools.java
%%JAVAJARDIR%%/bbmap/shared/TrimRead.class
%%JAVAJARDIR%%/bbmap/shared/TrimRead.java
%%JAVAJARDIR%%/bbmap/simd/SIMD.class
%%JAVAJARDIR%%/bbmap/simd/SIMD.java
%%JAVAJARDIR%%/bbmap/simd/SIMDAlign.class
%%JAVAJARDIR%%/bbmap/simd/SIMDAlign.java
%%JAVAJARDIR%%/bbmap/simd/SIMDAlignByte.class
%%JAVAJARDIR%%/bbmap/simd/SIMDAlignByte.java
%%JAVAJARDIR%%/bbmap/simd/SIMDByte256.class
%%JAVAJARDIR%%/bbmap/simd/SIMDByte256.java
%%JAVAJARDIR%%/bbmap/simd/SIMDByte256_only.class
%%JAVAJARDIR%%/bbmap/simd/SIMDByte256_only.java
%%JAVAJARDIR%%/bbmap/simd/SIMDLogLog.class
%%JAVAJARDIR%%/bbmap/simd/SIMDLogLog.java
%%JAVAJARDIR%%/bbmap/simd/SIMDLogLogTest.class
%%JAVAJARDIR%%/bbmap/simd/SIMDLogLogTest.java
%%JAVAJARDIR%%/bbmap/simd/VarHandler.class
%%JAVAJARDIR%%/bbmap/simd/VarHandler.java
%%JAVAJARDIR%%/bbmap/simd/Vector.class
%%JAVAJARDIR%%/bbmap/simd/Vector.java
%%JAVAJARDIR%%/bbmap/sketch/AddSSU$SketchHeader.class
%%JAVAJARDIR%%/bbmap/sketch/AddSSU.class
%%JAVAJARDIR%%/bbmap/sketch/AddSSU.java
%%JAVAJARDIR%%/bbmap/sketch/AlignmentJob.class
%%JAVAJARDIR%%/bbmap/sketch/AlignmentJob.java
%%JAVAJARDIR%%/bbmap/sketch/AlignmentThreadPool$AlignmentThread.class
%%JAVAJARDIR%%/bbmap/sketch/AlignmentThreadPool.class
%%JAVAJARDIR%%/bbmap/sketch/AlignmentThreadPool.java
%%JAVAJARDIR%%/bbmap/sketch/AnalyzeSketchResults$SSUThread.class
%%JAVAJARDIR%%/bbmap/sketch/AnalyzeSketchResults.class
%%JAVAJARDIR%%/bbmap/sketch/AnalyzeSketchResults.java
%%JAVAJARDIR%%/bbmap/sketch/Blacklist.class
%%JAVAJARDIR%%/bbmap/sketch/Blacklist.java
%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker$ProcessThread.class
%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker.class
%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker.java
%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker2$KeyPair.class
%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker2$ProcessThread.class
%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker2.class
%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker2.java
%%JAVAJARDIR%%/bbmap/sketch/CompareBuffer.class
%%JAVAJARDIR%%/bbmap/sketch/CompareBuffer.java
%%JAVAJARDIR%%/bbmap/sketch/CompareSSU$ProcessThread.class
%%JAVAJARDIR%%/bbmap/sketch/CompareSSU.class
%%JAVAJARDIR%%/bbmap/sketch/CompareSSU.java
%%JAVAJARDIR%%/bbmap/sketch/CompareSketch$CompareThread.class
%%JAVAJARDIR%%/bbmap/sketch/CompareSketch.class
%%JAVAJARDIR%%/bbmap/sketch/CompareSketch.java
%%JAVAJARDIR%%/bbmap/sketch/Comparison$Depth2Comparator.class
%%JAVAJARDIR%%/bbmap/sketch/Comparison$DepthComparator.class
%%JAVAJARDIR%%/bbmap/sketch/Comparison$HitsComparator.class
%%JAVAJARDIR%%/bbmap/sketch/Comparison$KIDComparator.class
%%JAVAJARDIR%%/bbmap/sketch/Comparison$SSUComparator.class
%%JAVAJARDIR%%/bbmap/sketch/Comparison$ScoreComparator.class
%%JAVAJARDIR%%/bbmap/sketch/Comparison$VolumeComparator.class
%%JAVAJARDIR%%/bbmap/sketch/Comparison$WKIDComparator.class
%%JAVAJARDIR%%/bbmap/sketch/Comparison.class
%%JAVAJARDIR%%/bbmap/sketch/Comparison.java
%%JAVAJARDIR%%/bbmap/sketch/DisplayParams.class
%%JAVAJARDIR%%/bbmap/sketch/DisplayParams.java
%%JAVAJARDIR%%/bbmap/sketch/InvertKey.class
%%JAVAJARDIR%%/bbmap/sketch/InvertKey.java
%%JAVAJARDIR%%/bbmap/sketch/KmerLimit$ProcessThread.class
%%JAVAJARDIR%%/bbmap/sketch/KmerLimit.class
%%JAVAJARDIR%%/bbmap/sketch/KmerLimit.java
%%JAVAJARDIR%%/bbmap/sketch/KmerLimit2$ProcessThread.class
%%JAVAJARDIR%%/bbmap/sketch/KmerLimit2.class
%%JAVAJARDIR%%/bbmap/sketch/KmerLimit2.java
%%JAVAJARDIR%%/bbmap/sketch/MergeSketch.class
%%JAVAJARDIR%%/bbmap/sketch/MergeSketch.java
%%JAVAJARDIR%%/bbmap/sketch/README.md
%%JAVAJARDIR%%/bbmap/sketch/Record.class
%%JAVAJARDIR%%/bbmap/sketch/Record.java
%%JAVAJARDIR%%/bbmap/sketch/RecordSet.class
%%JAVAJARDIR%%/bbmap/sketch/RecordSet.java
%%JAVAJARDIR%%/bbmap/sketch/ResultLineParser.class
%%JAVAJARDIR%%/bbmap/sketch/ResultLineParser.java
%%JAVAJARDIR%%/bbmap/sketch/SSUMap.class
%%JAVAJARDIR%%/bbmap/sketch/SSUMap.java
%%JAVAJARDIR%%/bbmap/sketch/SendSketch.class
%%JAVAJARDIR%%/bbmap/sketch/SendSketch.java
%%JAVAJARDIR%%/bbmap/sketch/Sketch.class
%%JAVAJARDIR%%/bbmap/sketch/Sketch.java
%%JAVAJARDIR%%/bbmap/sketch/SketchHeap.class
%%JAVAJARDIR%%/bbmap/sketch/SketchHeap.java
%%JAVAJARDIR%%/bbmap/sketch/SketchIdComparator.class
%%JAVAJARDIR%%/bbmap/sketch/SketchIdComparator.java
%%JAVAJARDIR%%/bbmap/sketch/SketchIndex$IndexThread.class
%%JAVAJARDIR%%/bbmap/sketch/SketchIndex.class
%%JAVAJARDIR%%/bbmap/sketch/SketchIndex.java
%%JAVAJARDIR%%/bbmap/sketch/SketchMaker$ProcessThread.class
%%JAVAJARDIR%%/bbmap/sketch/SketchMaker$WriteThread.class
%%JAVAJARDIR%%/bbmap/sketch/SketchMaker.class
%%JAVAJARDIR%%/bbmap/sketch/SketchMaker.java
%%JAVAJARDIR%%/bbmap/sketch/SketchMakerMini.class
%%JAVAJARDIR%%/bbmap/sketch/SketchMakerMini.java
%%JAVAJARDIR%%/bbmap/sketch/SketchObject.class
%%JAVAJARDIR%%/bbmap/sketch/SketchObject.java
%%JAVAJARDIR%%/bbmap/sketch/SketchResults.class
%%JAVAJARDIR%%/bbmap/sketch/SketchResults.java
%%JAVAJARDIR%%/bbmap/sketch/SketchSearcher$CompareThread.class
%%JAVAJARDIR%%/bbmap/sketch/SketchSearcher.class
%%JAVAJARDIR%%/bbmap/sketch/SketchSearcher.java
%%JAVAJARDIR%%/bbmap/sketch/SketchTool$LoadThread.class
%%JAVAJARDIR%%/bbmap/sketch/SketchTool$LoadThread2.class
%%JAVAJARDIR%%/bbmap/sketch/SketchTool$SketchThread.class
%%JAVAJARDIR%%/bbmap/sketch/SketchTool.class
%%JAVAJARDIR%%/bbmap/sketch/SketchTool.java
%%JAVAJARDIR%%/bbmap/sketch/SubSketch.class
%%JAVAJARDIR%%/bbmap/sketch/SubSketch.java
%%JAVAJARDIR%%/bbmap/sketch/SummarizeSketchStats$SketchResultsLine.class
%%JAVAJARDIR%%/bbmap/sketch/SummarizeSketchStats$SketchResultsSummary.class
%%JAVAJARDIR%%/bbmap/sketch/SummarizeSketchStats.class
%%JAVAJARDIR%%/bbmap/sketch/SummarizeSketchStats.java
%%JAVAJARDIR%%/bbmap/sketch/Whitelist.class
%%JAVAJARDIR%%/bbmap/sketch/Whitelist.java
%%JAVAJARDIR%%/bbmap/sort/ContigLengthComparator.class
%%JAVAJARDIR%%/bbmap/sort/ContigLengthComparator.java
%%JAVAJARDIR%%/bbmap/sort/MergeSorted.class
%%JAVAJARDIR%%/bbmap/sort/MergeSorted.java
%%JAVAJARDIR%%/bbmap/sort/README.md
%%JAVAJARDIR%%/bbmap/sort/ReadComparator.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparator.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorClump.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorClump.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorCrispr.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorCrispr.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorFlowcell.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorFlowcell.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorID.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorID.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorList.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorList.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorMapping.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorMapping.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorName.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorName.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorPosition.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorPosition.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorRandom.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorRandom.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTaxa.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTaxa.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological5Bit.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological5Bit.java
%%JAVAJARDIR%%/bbmap/sort/ReadErrorComparator.class
%%JAVAJARDIR%%/bbmap/sort/ReadErrorComparator.java
%%JAVAJARDIR%%/bbmap/sort/ReadLengthComparator.class
%%JAVAJARDIR%%/bbmap/sort/ReadLengthComparator.java
%%JAVAJARDIR%%/bbmap/sort/ReadQualityComparator.class
%%JAVAJARDIR%%/bbmap/sort/ReadQualityComparator.java
%%JAVAJARDIR%%/bbmap/sort/Shuffle$ShuffleThread.class
%%JAVAJARDIR%%/bbmap/sort/Shuffle.class
%%JAVAJARDIR%%/bbmap/sort/Shuffle.java
%%JAVAJARDIR%%/bbmap/sort/Shuffle2$WriteThread.class
%%JAVAJARDIR%%/bbmap/sort/Shuffle2.class
%%JAVAJARDIR%%/bbmap/sort/Shuffle2.java
%%JAVAJARDIR%%/bbmap/sort/SortByName$WriteThread.class
%%JAVAJARDIR%%/bbmap/sort/SortByName.class
%%JAVAJARDIR%%/bbmap/sort/SortByName.java
%%JAVAJARDIR%%/bbmap/stream/ArrayListSet$Pack.class
%%JAVAJARDIR%%/bbmap/stream/ArrayListSet.class
%%JAVAJARDIR%%/bbmap/stream/ArrayListSet.java
%%JAVAJARDIR%%/bbmap/stream/BamStreamer$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/BamStreamer.class
%%JAVAJARDIR%%/bbmap/stream/BamStreamer.java
%%JAVAJARDIR%%/bbmap/stream/BamWriter$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/BamWriter$SamWriterInputJob.class
%%JAVAJARDIR%%/bbmap/stream/BamWriter$SamWriterOutputJob.class
%%JAVAJARDIR%%/bbmap/stream/BamWriter.class
%%JAVAJARDIR%%/bbmap/stream/BamWriter.java
%%JAVAJARDIR%%/bbmap/stream/BedReadFilter.class
%%JAVAJARDIR%%/bbmap/stream/BedReadFilter.java
%%JAVAJARDIR%%/bbmap/stream/BufferedMultiCros.class
%%JAVAJARDIR%%/bbmap/stream/BufferedMultiCros.java
%%JAVAJARDIR%%/bbmap/stream/CigarNormalizer.class
%%JAVAJARDIR%%/bbmap/stream/CigarNormalizer.java
%%JAVAJARDIR%%/bbmap/stream/ConcurrentCollectionReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentCollectionReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/ConcurrentDepot.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentDepot.java
%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadInputStream$1.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadInputStream$ReadThread.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadOutputStream.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadOutputStream.java
%%JAVAJARDIR%%/bbmap/stream/ConcurrentLegacyReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentLegacyReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadInputStreamD.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadInputStreamD.java
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadListDepot.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadListDepot.java
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStream.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStream.java
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStreamD$ListenThread.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStreamD.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStreamD.java
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadStreamInterface.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadStreamInterface.java
%%JAVAJARDIR%%/bbmap/stream/CrisContainer.class
%%JAVAJARDIR%%/bbmap/stream/CrisContainer.java
%%JAVAJARDIR%%/bbmap/stream/CrisWrapper.class
%%JAVAJARDIR%%/bbmap/stream/CrisWrapper.java
%%JAVAJARDIR%%/bbmap/stream/CustomHeader.class
%%JAVAJARDIR%%/bbmap/stream/CustomHeader.java
%%JAVAJARDIR%%/bbmap/stream/DualCris.class
%%JAVAJARDIR%%/bbmap/stream/DualCris.java
%%JAVAJARDIR%%/bbmap/stream/EmblReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/EmblReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/FASTQ.class
%%JAVAJARDIR%%/bbmap/stream/FASTQ.java
%%JAVAJARDIR%%/bbmap/stream/FastaQualReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/FastaQualReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/FastaQualStreamer$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/FastaQualStreamer.class
%%JAVAJARDIR%%/bbmap/stream/FastaQualStreamer.java
%%JAVAJARDIR%%/bbmap/stream/FastaQualStreamerZT.class
%%JAVAJARDIR%%/bbmap/stream/FastaQualStreamerZT.java
%%JAVAJARDIR%%/bbmap/stream/FastaQualWriterST$WriterRunnable.class
%%JAVAJARDIR%%/bbmap/stream/FastaQualWriterST.class
%%JAVAJARDIR%%/bbmap/stream/FastaQualWriterST.java
%%JAVAJARDIR%%/bbmap/stream/FastaQualWriterZT.class
%%JAVAJARDIR%%/bbmap/stream/FastaQualWriterZT.java
%%JAVAJARDIR%%/bbmap/stream/FastaReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/FastaReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/FastaShredInputStream.class
%%JAVAJARDIR%%/bbmap/stream/FastaShredInputStream.java
%%JAVAJARDIR%%/bbmap/stream/FastaStreamer$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/FastaStreamer.class
%%JAVAJARDIR%%/bbmap/stream/FastaStreamer.java
%%JAVAJARDIR%%/bbmap/stream/FastaStreamer2ST$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/FastaStreamer2ST.class
%%JAVAJARDIR%%/bbmap/stream/FastaStreamer2ST.java
%%JAVAJARDIR%%/bbmap/stream/FastaStreamer2ZT.class
%%JAVAJARDIR%%/bbmap/stream/FastaStreamer2ZT.java
%%JAVAJARDIR%%/bbmap/stream/FastaStreamerST$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/FastaStreamerST.class
%%JAVAJARDIR%%/bbmap/stream/FastaStreamerST.java
%%JAVAJARDIR%%/bbmap/stream/FastaStreamerZT.class
%%JAVAJARDIR%%/bbmap/stream/FastaStreamerZT.java
%%JAVAJARDIR%%/bbmap/stream/FastqReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/FastqReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/FastqScan.class
%%JAVAJARDIR%%/bbmap/stream/FastqScan.java
%%JAVAJARDIR%%/bbmap/stream/FastqScanFC.class
%%JAVAJARDIR%%/bbmap/stream/FastqScanFC.java
%%JAVAJARDIR%%/bbmap/stream/FastqScanMT$ScanThread.class
%%JAVAJARDIR%%/bbmap/stream/FastqScanMT.class
%%JAVAJARDIR%%/bbmap/stream/FastqScanMT.java
%%JAVAJARDIR%%/bbmap/stream/FastqScanStreamer$ReaderRunnable.class
%%JAVAJARDIR%%/bbmap/stream/FastqScanStreamer.class
%%JAVAJARDIR%%/bbmap/stream/FastqScanStreamer.java
%%JAVAJARDIR%%/bbmap/stream/FastqStreamer$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/FastqStreamer.class
%%JAVAJARDIR%%/bbmap/stream/FastqStreamer.java
%%JAVAJARDIR%%/bbmap/stream/FastqStreamerST$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/FastqStreamerST.class
%%JAVAJARDIR%%/bbmap/stream/FastqStreamerST.java
%%JAVAJARDIR%%/bbmap/stream/FastqWriter$FastqWriterInputJob.class
%%JAVAJARDIR%%/bbmap/stream/FastqWriter$FastqWriterOutputJob.class
%%JAVAJARDIR%%/bbmap/stream/FastqWriter$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/FastqWriter.class
%%JAVAJARDIR%%/bbmap/stream/FastqWriter.java
%%JAVAJARDIR%%/bbmap/stream/FastqWriterST.class
%%JAVAJARDIR%%/bbmap/stream/FastqWriterST.java
%%JAVAJARDIR%%/bbmap/stream/FastqWriterST2$WriterRunnable.class
%%JAVAJARDIR%%/bbmap/stream/FastqWriterST2.class
%%JAVAJARDIR%%/bbmap/stream/FastqWriterST2.java
%%JAVAJARDIR%%/bbmap/stream/FileScanMT$ScanThread.class
%%JAVAJARDIR%%/bbmap/stream/FileScanMT.class
%%JAVAJARDIR%%/bbmap/stream/FileScanMT.java
%%JAVAJARDIR%%/bbmap/stream/GbkReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/GbkReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/GfaReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/GfaReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/GfaStreamerST$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/GfaStreamerST.class
%%JAVAJARDIR%%/bbmap/stream/GfaStreamerST.java
%%JAVAJARDIR%%/bbmap/stream/HasID.class
%%JAVAJARDIR%%/bbmap/stream/HasID.java
%%JAVAJARDIR%%/bbmap/stream/HeaderInputStream.class
%%JAVAJARDIR%%/bbmap/stream/HeaderInputStream.java
%%JAVAJARDIR%%/bbmap/stream/JobQueue$HasIDComparator.class
%%JAVAJARDIR%%/bbmap/stream/JobQueue.class
%%JAVAJARDIR%%/bbmap/stream/JobQueue.java
%%JAVAJARDIR%%/bbmap/stream/MDWalker.class
%%JAVAJARDIR%%/bbmap/stream/MDWalker.java
%%JAVAJARDIR%%/bbmap/stream/MDWalker2.class
%%JAVAJARDIR%%/bbmap/stream/MDWalker2.java
%%JAVAJARDIR%%/bbmap/stream/MultiCros.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros.java
%%JAVAJARDIR%%/bbmap/stream/MultiCros2$Buffer.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros2.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros2.java
%%JAVAJARDIR%%/bbmap/stream/MultiCros3$Buffer.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros3.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros3.java
%%JAVAJARDIR%%/bbmap/stream/MultiCros4$Buffer.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros4$RetireThread.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros4$Token.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros4.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros4.java
%%JAVAJARDIR%%/bbmap/stream/MultiCros5$Buffer.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros5.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros5.java
%%JAVAJARDIR%%/bbmap/stream/MultiCros6$Buffer.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros6$TimestampComparator.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros6.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros6.java
%%JAVAJARDIR%%/bbmap/stream/NullOutputStream.class
%%JAVAJARDIR%%/bbmap/stream/NullOutputStream.java
%%JAVAJARDIR%%/bbmap/stream/OnelineReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/OnelineReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/OrderedQueueSystem.class
%%JAVAJARDIR%%/bbmap/stream/OrderedQueueSystem.java
%%JAVAJARDIR%%/bbmap/stream/OrderedQueueSystem2.class
%%JAVAJARDIR%%/bbmap/stream/OrderedQueueSystem2.java
%%JAVAJARDIR%%/bbmap/stream/PairStreamer.class
%%JAVAJARDIR%%/bbmap/stream/PairStreamer.java
%%JAVAJARDIR%%/bbmap/stream/PairedWriter.class
%%JAVAJARDIR%%/bbmap/stream/PairedWriter.java
%%JAVAJARDIR%%/bbmap/stream/RTextInputStream.class
%%JAVAJARDIR%%/bbmap/stream/RTextInputStream.java
%%JAVAJARDIR%%/bbmap/stream/RandomReadInputStream3.class
%%JAVAJARDIR%%/bbmap/stream/RandomReadInputStream3.java
%%JAVAJARDIR%%/bbmap/stream/Read.class
%%JAVAJARDIR%%/bbmap/stream/Read.java
%%JAVAJARDIR%%/bbmap/stream/ReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/ReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/ReadStreamByteWriter.class
%%JAVAJARDIR%%/bbmap/stream/ReadStreamByteWriter.java
%%JAVAJARDIR%%/bbmap/stream/ReadStreamSamWriter.class
%%JAVAJARDIR%%/bbmap/stream/ReadStreamSamWriter.java
%%JAVAJARDIR%%/bbmap/stream/ReadStreamWriter$Job.class
%%JAVAJARDIR%%/bbmap/stream/ReadStreamWriter.class
%%JAVAJARDIR%%/bbmap/stream/ReadStreamWriter.java
%%JAVAJARDIR%%/bbmap/stream/SamHeader.class
%%JAVAJARDIR%%/bbmap/stream/SamHeader.java
%%JAVAJARDIR%%/bbmap/stream/SamHeaderWriter$WriterThread.class
%%JAVAJARDIR%%/bbmap/stream/SamHeaderWriter.class
%%JAVAJARDIR%%/bbmap/stream/SamHeaderWriter.java
%%JAVAJARDIR%%/bbmap/stream/SamLine.class
%%JAVAJARDIR%%/bbmap/stream/SamLine.java
%%JAVAJARDIR%%/bbmap/stream/SamReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/SamReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/SamStreamer$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/SamStreamer.class
%%JAVAJARDIR%%/bbmap/stream/SamStreamer.java
%%JAVAJARDIR%%/bbmap/stream/SamStreamerMF.class
%%JAVAJARDIR%%/bbmap/stream/SamStreamerMF.java
%%JAVAJARDIR%%/bbmap/stream/SamStreamerST$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/SamStreamerST.class
%%JAVAJARDIR%%/bbmap/stream/SamStreamerST.java
%%JAVAJARDIR%%/bbmap/stream/SamStreamerWrapper.class
%%JAVAJARDIR%%/bbmap/stream/SamStreamerWrapper.java
%%JAVAJARDIR%%/bbmap/stream/SamWriter$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/SamWriter$SamWriterInputJob.class
%%JAVAJARDIR%%/bbmap/stream/SamWriter$SamWriterOutputJob.class
%%JAVAJARDIR%%/bbmap/stream/SamWriter.class
%%JAVAJARDIR%%/bbmap/stream/SamWriter.java
%%JAVAJARDIR%%/bbmap/stream/SamWriterST.class
%%JAVAJARDIR%%/bbmap/stream/SamWriterST.java
%%JAVAJARDIR%%/bbmap/stream/SamWriterST2$WriterRunnable.class
%%JAVAJARDIR%%/bbmap/stream/SamWriterST2.class
%%JAVAJARDIR%%/bbmap/stream/SamWriterST2.java
%%JAVAJARDIR%%/bbmap/stream/ScaffoldCoordinates.class
%%JAVAJARDIR%%/bbmap/stream/ScaffoldCoordinates.java
%%JAVAJARDIR%%/bbmap/stream/ScaffoldRenamer.class
%%JAVAJARDIR%%/bbmap/stream/ScaffoldRenamer.java
%%JAVAJARDIR%%/bbmap/stream/ScarfReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/ScarfReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/ScarfStreamer$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/ScarfStreamer.class
%%JAVAJARDIR%%/bbmap/stream/ScarfStreamer.java
%%JAVAJARDIR%%/bbmap/stream/SequentialReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/SequentialReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/SiteScore$PositionComparator.class
%%JAVAJARDIR%%/bbmap/stream/SiteScore.class
%%JAVAJARDIR%%/bbmap/stream/SiteScore.java
%%JAVAJARDIR%%/bbmap/stream/SiteScoreR$IDComparator.class
%%JAVAJARDIR%%/bbmap/stream/SiteScoreR$NormalizedComparator.class
%%JAVAJARDIR%%/bbmap/stream/SiteScoreR$PositionComparator.class
%%JAVAJARDIR%%/bbmap/stream/SiteScoreR.class
%%JAVAJARDIR%%/bbmap/stream/SiteScoreR.java
%%JAVAJARDIR%%/bbmap/stream/Streamer.class
%%JAVAJARDIR%%/bbmap/stream/Streamer.java
%%JAVAJARDIR%%/bbmap/stream/StreamerFactory.class
%%JAVAJARDIR%%/bbmap/stream/StreamerFactory.java
%%JAVAJARDIR%%/bbmap/stream/StreamerWrapper.class
%%JAVAJARDIR%%/bbmap/stream/StreamerWrapper.java
%%JAVAJARDIR%%/bbmap/stream/TestMDWalker.class
%%JAVAJARDIR%%/bbmap/stream/TestMDWalker.java
%%JAVAJARDIR%%/bbmap/stream/Writer.class
%%JAVAJARDIR%%/bbmap/stream/Writer.java
%%JAVAJARDIR%%/bbmap/stream/WriterFactory.class
%%JAVAJARDIR%%/bbmap/stream/WriterFactory.java
%%JAVAJARDIR%%/bbmap/stream/bam/BamIndexWriter$BinData.class
%%JAVAJARDIR%%/bbmap/stream/bam/BamIndexWriter$ReferenceIndex.class
%%JAVAJARDIR%%/bbmap/stream/bam/BamIndexWriter.class
%%JAVAJARDIR%%/bbmap/stream/bam/BamIndexWriter.java
%%JAVAJARDIR%%/bbmap/stream/bam/BamInputStream.class
%%JAVAJARDIR%%/bbmap/stream/bam/BamInputStream.java
%%JAVAJARDIR%%/bbmap/stream/bam/BamOutputStream.class
%%JAVAJARDIR%%/bbmap/stream/bam/BamOutputStream.java
%%JAVAJARDIR%%/bbmap/stream/bam/BamReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/bam/BamReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/bam/BamReadInputStreamST.class
%%JAVAJARDIR%%/bbmap/stream/bam/BamReadInputStreamST.java
%%JAVAJARDIR%%/bbmap/stream/bam/BamReader.class
%%JAVAJARDIR%%/bbmap/stream/bam/BamReader.java
%%JAVAJARDIR%%/bbmap/stream/bam/BamToSamConverter.class
%%JAVAJARDIR%%/bbmap/stream/bam/BamToSamConverter.java
%%JAVAJARDIR%%/bbmap/stream/bam/BamWriterHelper.class
%%JAVAJARDIR%%/bbmap/stream/bam/BamWriterHelper.java
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputJob.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputJob.java
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStream$PrefixedInputStream.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStream.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStream.java
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT$1.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT$2.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT$PrefixedInputStream.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT.java
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT2$1.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT2$2.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT2$PrefixedInputStream.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT2.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT2.java
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT3$1.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT3$2.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT3$PrefixedInputStream.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT3.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT3.java
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfJob.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfJob.java
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStream.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStream.java
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStreamMT$1.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStreamMT$2.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStreamMT.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStreamMT.java
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStreamMT2$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStreamMT2.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStreamMT2.java
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfSettings.class
%%JAVAJARDIR%%/bbmap/stream/bam/BgzfSettings.java
%%JAVAJARDIR%%/bbmap/stream/bam/DebugBgzfRead.class
%%JAVAJARDIR%%/bbmap/stream/bam/DebugBgzfRead.java
%%JAVAJARDIR%%/bbmap/stream/bam/DebugBgzfWrite.class
%%JAVAJARDIR%%/bbmap/stream/bam/DebugBgzfWrite.java
%%JAVAJARDIR%%/bbmap/stream/bam/SamToBamConverter.class
%%JAVAJARDIR%%/bbmap/stream/bam/SamToBamConverter.java
%%JAVAJARDIR%%/bbmap/stream/bam/TestBamIndexWriter.class
%%JAVAJARDIR%%/bbmap/stream/bam/TestBamIndexWriter.java
%%JAVAJARDIR%%/bbmap/stream/bam/TestBamReader.class
%%JAVAJARDIR%%/bbmap/stream/bam/TestBamReader.java
%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfA80k.class
%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfA80k.java
%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfMultithreaded.class
%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfMultithreaded.java
%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfSimple.class
%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfSimple.java
%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfSystematic.class
%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfSystematic.java
%%JAVAJARDIR%%/bbmap/stream/bam/TestEarlyClose.class
%%JAVAJARDIR%%/bbmap/stream/bam/TestEarlyClose.java
%%JAVAJARDIR%%/bbmap/stream/bam/TestSeqReverse.class
%%JAVAJARDIR%%/bbmap/stream/bam/TestSeqReverse.java
%%JAVAJARDIR%%/bbmap/stream/bam/TestSimpleBgzfRead.class
%%JAVAJARDIR%%/bbmap/stream/bam/TestSimpleBgzfRead.java
%%JAVAJARDIR%%/bbmap/structures/AbstractIntHashMap.class
%%JAVAJARDIR%%/bbmap/structures/AbstractIntHashMap.java
%%JAVAJARDIR%%/bbmap/structures/AtomicStringNum.class
%%JAVAJARDIR%%/bbmap/structures/AtomicStringNum.java
%%JAVAJARDIR%%/bbmap/structures/BinaryByteWrapperLE.class
%%JAVAJARDIR%%/bbmap/structures/BinaryByteWrapperLE.java
%%JAVAJARDIR%%/bbmap/structures/ByteBuilder.class
%%JAVAJARDIR%%/bbmap/structures/ByteBuilder.java
%%JAVAJARDIR%%/bbmap/structures/BytePrefixDispatcher.class
%%JAVAJARDIR%%/bbmap/structures/BytePrefixDispatcher.java
%%JAVAJARDIR%%/bbmap/structures/CRange.class
%%JAVAJARDIR%%/bbmap/structures/CRange.java
%%JAVAJARDIR%%/bbmap/structures/CoverageArray.class
%%JAVAJARDIR%%/bbmap/structures/CoverageArray.java
%%JAVAJARDIR%%/bbmap/structures/CoverageArray2.class
%%JAVAJARDIR%%/bbmap/structures/CoverageArray2.java
%%JAVAJARDIR%%/bbmap/structures/CoverageArray2A.class
%%JAVAJARDIR%%/bbmap/structures/CoverageArray2A.java
%%JAVAJARDIR%%/bbmap/structures/CoverageArray3.class
%%JAVAJARDIR%%/bbmap/structures/CoverageArray3.java
%%JAVAJARDIR%%/bbmap/structures/CoverageArray3A.class
%%JAVAJARDIR%%/bbmap/structures/CoverageArray3A.java
%%JAVAJARDIR%%/bbmap/structures/Crispr.class
%%JAVAJARDIR%%/bbmap/structures/Crispr.java
%%JAVAJARDIR%%/bbmap/structures/DoubleList.class
%%JAVAJARDIR%%/bbmap/structures/DoubleList.java
%%JAVAJARDIR%%/bbmap/structures/Feature.class
%%JAVAJARDIR%%/bbmap/structures/Feature.java
%%JAVAJARDIR%%/bbmap/structures/FloatList.class
%%JAVAJARDIR%%/bbmap/structures/FloatList.java
%%JAVAJARDIR%%/bbmap/structures/Heap$HeapIterator.class
%%JAVAJARDIR%%/bbmap/structures/Heap.class
%%JAVAJARDIR%%/bbmap/structures/Heap.java
%%JAVAJARDIR%%/bbmap/structures/HeapLoc$HeapIterator.class
%%JAVAJARDIR%%/bbmap/structures/HeapLoc.class
%%JAVAJARDIR%%/bbmap/structures/HeapLoc.java
%%JAVAJARDIR%%/bbmap/structures/IntHashMap.class
%%JAVAJARDIR%%/bbmap/structures/IntHashMap.java
%%JAVAJARDIR%%/bbmap/structures/IntHashMapBinary.class
%%JAVAJARDIR%%/bbmap/structures/IntHashMapBinary.java
%%JAVAJARDIR%%/bbmap/structures/IntList.class
%%JAVAJARDIR%%/bbmap/structures/IntList.java
%%JAVAJARDIR%%/bbmap/structures/IntList2.class
%%JAVAJARDIR%%/bbmap/structures/IntList2.java
%%JAVAJARDIR%%/bbmap/structures/IntList3.class
%%JAVAJARDIR%%/bbmap/structures/IntList3.java
%%JAVAJARDIR%%/bbmap/structures/IntListCompressor.class
%%JAVAJARDIR%%/bbmap/structures/IntListCompressor.java
%%JAVAJARDIR%%/bbmap/structures/IntLongHashMap.class
%%JAVAJARDIR%%/bbmap/structures/IntLongHashMap.java
%%JAVAJARDIR%%/bbmap/structures/IntMap.class
%%JAVAJARDIR%%/bbmap/structures/IntMap.java
%%JAVAJARDIR%%/bbmap/structures/IntRingBuffer.class
%%JAVAJARDIR%%/bbmap/structures/IntRingBuffer.java
%%JAVAJARDIR%%/bbmap/structures/IntRingBufferCond.class
%%JAVAJARDIR%%/bbmap/structures/IntRingBufferCond.java
%%JAVAJARDIR%%/bbmap/structures/ListNum.class
%%JAVAJARDIR%%/bbmap/structures/ListNum.java
%%JAVAJARDIR%%/bbmap/structures/LongHeap.class
%%JAVAJARDIR%%/bbmap/structures/LongHeap.java
%%JAVAJARDIR%%/bbmap/structures/LongHeapMap.class
%%JAVAJARDIR%%/bbmap/structures/LongHeapMap.java
%%JAVAJARDIR%%/bbmap/structures/LongHeapSet.class
%%JAVAJARDIR%%/bbmap/structures/LongHeapSet.java
%%JAVAJARDIR%%/bbmap/structures/LongHeapSetInterface.class
%%JAVAJARDIR%%/bbmap/structures/LongHeapSetInterface.java
%%JAVAJARDIR%%/bbmap/structures/LongList.class
%%JAVAJARDIR%%/bbmap/structures/LongList.java
%%JAVAJARDIR%%/bbmap/structures/LongList2.class
%%JAVAJARDIR%%/bbmap/structures/LongList2.java
%%JAVAJARDIR%%/bbmap/structures/LongList3.class
%%JAVAJARDIR%%/bbmap/structures/LongList3.java
%%JAVAJARDIR%%/bbmap/structures/LongM.class
%%JAVAJARDIR%%/bbmap/structures/LongM.java
%%JAVAJARDIR%%/bbmap/structures/LongPair.class
%%JAVAJARDIR%%/bbmap/structures/LongPair.java
%%JAVAJARDIR%%/bbmap/structures/Point.class
%%JAVAJARDIR%%/bbmap/structures/Point.java
%%JAVAJARDIR%%/bbmap/structures/Quantizer.class
%%JAVAJARDIR%%/bbmap/structures/Quantizer.java
%%JAVAJARDIR%%/bbmap/structures/README.md
%%JAVAJARDIR%%/bbmap/structures/Range.class
%%JAVAJARDIR%%/bbmap/structures/Range.java
%%JAVAJARDIR%%/bbmap/structures/RingBuffer.class
%%JAVAJARDIR%%/bbmap/structures/RingBuffer.java
%%JAVAJARDIR%%/bbmap/structures/RingBufferMask.class
%%JAVAJARDIR%%/bbmap/structures/RingBufferMask.java
%%JAVAJARDIR%%/bbmap/structures/RingBufferMod.class
%%JAVAJARDIR%%/bbmap/structures/RingBufferMod.java
%%JAVAJARDIR%%/bbmap/structures/SeqCount.class
%%JAVAJARDIR%%/bbmap/structures/SeqCount.java
%%JAVAJARDIR%%/bbmap/structures/SeqCountM.class
%%JAVAJARDIR%%/bbmap/structures/SeqCountM.java
%%JAVAJARDIR%%/bbmap/structures/SetLoc.class
%%JAVAJARDIR%%/bbmap/structures/SetLoc.java
%%JAVAJARDIR%%/bbmap/structures/StandardDeviator$ProcessThread.class
%%JAVAJARDIR%%/bbmap/structures/StandardDeviator.class
%%JAVAJARDIR%%/bbmap/structures/StandardDeviator.java
%%JAVAJARDIR%%/bbmap/structures/StringCount.class
%%JAVAJARDIR%%/bbmap/structures/StringCount.java
%%JAVAJARDIR%%/bbmap/structures/StringNum.class
%%JAVAJARDIR%%/bbmap/structures/StringNum.java
%%JAVAJARDIR%%/bbmap/structures/StringPair.class
%%JAVAJARDIR%%/bbmap/structures/StringPair.java
%%JAVAJARDIR%%/bbmap/structures/SuperLongList.class
%%JAVAJARDIR%%/bbmap/structures/SuperLongList.java
%%JAVAJARDIR%%/bbmap/structures/XNum.class
%%JAVAJARDIR%%/bbmap/structures/XNum.java
%%JAVAJARDIR%%/bbmap/synth/CoverageModel.class
%%JAVAJARDIR%%/bbmap/synth/CoverageModel.java
%%JAVAJARDIR%%/bbmap/synth/CrossContaminate$Vessel.class
%%JAVAJARDIR%%/bbmap/synth/CrossContaminate.class
%%JAVAJARDIR%%/bbmap/synth/CrossContaminate.java
%%JAVAJARDIR%%/bbmap/synth/FakeReads.class
%%JAVAJARDIR%%/bbmap/synth/FakeReads.java
%%JAVAJARDIR%%/bbmap/synth/FuseByTaxa.class
%%JAVAJARDIR%%/bbmap/synth/FuseByTaxa.java
%%JAVAJARDIR%%/bbmap/synth/FuseSequence.class
%%JAVAJARDIR%%/bbmap/synth/FuseSequence.java
%%JAVAJARDIR%%/bbmap/synth/GCBias.class
%%JAVAJARDIR%%/bbmap/synth/GCBias.java
%%JAVAJARDIR%%/bbmap/synth/MakeChimeras.class
%%JAVAJARDIR%%/bbmap/synth/MakeChimeras.java
%%JAVAJARDIR%%/bbmap/synth/MakeContaminatedGenomes.class
%%JAVAJARDIR%%/bbmap/synth/MakeContaminatedGenomes.java
%%JAVAJARDIR%%/bbmap/synth/MutateGenome$SmallVar.class
%%JAVAJARDIR%%/bbmap/synth/MutateGenome.class
%%JAVAJARDIR%%/bbmap/synth/MutateGenome.java
%%JAVAJARDIR%%/bbmap/synth/MutateGenome2$SmallVar.class
%%JAVAJARDIR%%/bbmap/synth/MutateGenome2.class
%%JAVAJARDIR%%/bbmap/synth/MutateGenome2.java
%%JAVAJARDIR%%/bbmap/synth/RandomGenome.class
%%JAVAJARDIR%%/bbmap/synth/RandomGenome.java
%%JAVAJARDIR%%/bbmap/synth/RandomHexamer.class
%%JAVAJARDIR%%/bbmap/synth/RandomHexamer.java
%%JAVAJARDIR%%/bbmap/synth/RandomReads3$1.class
%%JAVAJARDIR%%/bbmap/synth/RandomReads3.class
%%JAVAJARDIR%%/bbmap/synth/RandomReads3.java
%%JAVAJARDIR%%/bbmap/synth/RandomReadsMG$ProcessThread.class
%%JAVAJARDIR%%/bbmap/synth/RandomReadsMG.class
%%JAVAJARDIR%%/bbmap/synth/RandomReadsMG.java
%%JAVAJARDIR%%/bbmap/synth/Shred.class
%%JAVAJARDIR%%/bbmap/synth/Shred.java
%%JAVAJARDIR%%/bbmap/synth/SynthMDA.class
%%JAVAJARDIR%%/bbmap/synth/SynthMDA.java
%%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid$HashThread.class
%%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid.class
%%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid.java
%%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession$ProcessThread.class
%%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession.class
%%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession.java
%%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession_ST.class
%%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession_ST.java
%%JAVAJARDIR%%/bbmap/tax/CanonicalLineage.class
%%JAVAJARDIR%%/bbmap/tax/CanonicalLineage.java
%%JAVAJARDIR%%/bbmap/tax/ExplodeTree.class
%%JAVAJARDIR%%/bbmap/tax/ExplodeTree.java
%%JAVAJARDIR%%/bbmap/tax/FilterByTaxa.class
%%JAVAJARDIR%%/bbmap/tax/FilterByTaxa.java
%%JAVAJARDIR%%/bbmap/tax/FindAncestor.class
%%JAVAJARDIR%%/bbmap/tax/FindAncestor.java
%%JAVAJARDIR%%/bbmap/tax/GiToTaxid.class
%%JAVAJARDIR%%/bbmap/tax/GiToTaxid.java
%%JAVAJARDIR%%/bbmap/tax/GiToTaxidInt.class
%%JAVAJARDIR%%/bbmap/tax/GiToTaxidInt.java
%%JAVAJARDIR%%/bbmap/tax/IDNode.class
%%JAVAJARDIR%%/bbmap/tax/IDNode.java
%%JAVAJARDIR%%/bbmap/tax/IDTree.class
%%JAVAJARDIR%%/bbmap/tax/IDTree.java
%%JAVAJARDIR%%/bbmap/tax/ImgRecord.class
%%JAVAJARDIR%%/bbmap/tax/ImgRecord.java
%%JAVAJARDIR%%/bbmap/tax/ImgRecord2.class
%%JAVAJARDIR%%/bbmap/tax/ImgRecord2.java
%%JAVAJARDIR%%/bbmap/tax/Lineage.class
%%JAVAJARDIR%%/bbmap/tax/Lineage.java
%%JAVAJARDIR%%/bbmap/tax/PrintTaxonomy.class
%%JAVAJARDIR%%/bbmap/tax/PrintTaxonomy.java
%%JAVAJARDIR%%/bbmap/tax/Query.class
%%JAVAJARDIR%%/bbmap/tax/Query.java
%%JAVAJARDIR%%/bbmap/tax/README.md
%%JAVAJARDIR%%/bbmap/tax/RenameGiToTaxid.class
%%JAVAJARDIR%%/bbmap/tax/RenameGiToTaxid.java
%%JAVAJARDIR%%/bbmap/tax/RenameIMG.class
%%JAVAJARDIR%%/bbmap/tax/RenameIMG.java
%%JAVAJARDIR%%/bbmap/tax/ShrinkAccession.class
%%JAVAJARDIR%%/bbmap/tax/ShrinkAccession.java
%%JAVAJARDIR%%/bbmap/tax/SplitByTaxa.class
%%JAVAJARDIR%%/bbmap/tax/SplitByTaxa.java
%%JAVAJARDIR%%/bbmap/tax/TaxApp$1.class
%%JAVAJARDIR%%/bbmap/tax/TaxApp.class
%%JAVAJARDIR%%/bbmap/tax/TaxApp.java
%%JAVAJARDIR%%/bbmap/tax/TaxClient.class
%%JAVAJARDIR%%/bbmap/tax/TaxClient.java
%%JAVAJARDIR%%/bbmap/tax/TaxFilter$1.class
%%JAVAJARDIR%%/bbmap/tax/TaxFilter.class
%%JAVAJARDIR%%/bbmap/tax/TaxFilter.java
%%JAVAJARDIR%%/bbmap/tax/TaxNode$CountComparator.class
%%JAVAJARDIR%%/bbmap/tax/TaxNode.class
%%JAVAJARDIR%%/bbmap/tax/TaxNode.java
%%JAVAJARDIR%%/bbmap/tax/TaxServer$CompareThread.class
%%JAVAJARDIR%%/bbmap/tax/TaxServer$HelpHandler.class
%%JAVAJARDIR%%/bbmap/tax/TaxServer$IconHandler.class
%%JAVAJARDIR%%/bbmap/tax/TaxServer$KillHandler.class
%%JAVAJARDIR%%/bbmap/tax/TaxServer$SketchHandler$SketchInstance.class
%%JAVAJARDIR%%/bbmap/tax/TaxServer$SketchHandler.class
%%JAVAJARDIR%%/bbmap/tax/TaxServer$StatsHandler.class
%%JAVAJARDIR%%/bbmap/tax/TaxServer$TaxHandler.class
%%JAVAJARDIR%%/bbmap/tax/TaxServer.class
%%JAVAJARDIR%%/bbmap/tax/TaxServer.java
%%JAVAJARDIR%%/bbmap/tax/TaxSize.class
%%JAVAJARDIR%%/bbmap/tax/TaxSize.java
%%JAVAJARDIR%%/bbmap/tax/TaxTree.class
%%JAVAJARDIR%%/bbmap/tax/TaxTree.java
%%JAVAJARDIR%%/bbmap/template/A_Sample.class
%%JAVAJARDIR%%/bbmap/template/A_Sample.java
%%JAVAJARDIR%%/bbmap/template/A_Sample2.class
%%JAVAJARDIR%%/bbmap/template/A_Sample2.java
%%JAVAJARDIR%%/bbmap/template/A_SampleBasic.class
%%JAVAJARDIR%%/bbmap/template/A_SampleBasic.java
%%JAVAJARDIR%%/bbmap/template/A_SampleBasic2.class
%%JAVAJARDIR%%/bbmap/template/A_SampleBasic2.java
%%JAVAJARDIR%%/bbmap/template/A_SampleByteFile.class
%%JAVAJARDIR%%/bbmap/template/A_SampleByteFile.java
%%JAVAJARDIR%%/bbmap/template/A_SampleByteFileMT$ProcessThread.class
%%JAVAJARDIR%%/bbmap/template/A_SampleByteFileMT.class
%%JAVAJARDIR%%/bbmap/template/A_SampleByteFileMT.java
%%JAVAJARDIR%%/bbmap/template/A_SampleD.class
%%JAVAJARDIR%%/bbmap/template/A_SampleD.java
%%JAVAJARDIR%%/bbmap/template/A_SampleMT$ProcessThread.class
%%JAVAJARDIR%%/bbmap/template/A_SampleMT.class
%%JAVAJARDIR%%/bbmap/template/A_SampleMT.java
%%JAVAJARDIR%%/bbmap/template/A_SampleMultipleInput.class
%%JAVAJARDIR%%/bbmap/template/A_SampleMultipleInput.java
%%JAVAJARDIR%%/bbmap/template/A_SampleSamStreamer$ProcessThread.class
%%JAVAJARDIR%%/bbmap/template/A_SampleSamStreamer.class
%%JAVAJARDIR%%/bbmap/template/A_SampleSamStreamer.java
%%JAVAJARDIR%%/bbmap/template/A_SampleStreamer.class
%%JAVAJARDIR%%/bbmap/template/A_SampleStreamer.java
%%JAVAJARDIR%%/bbmap/template/A_SampleStreamerMT$ProcessThread.class
%%JAVAJARDIR%%/bbmap/template/A_SampleStreamerMT.class
%%JAVAJARDIR%%/bbmap/template/A_SampleStreamerMT.java
%%JAVAJARDIR%%/bbmap/template/A_SampleSummary.class
%%JAVAJARDIR%%/bbmap/template/A_SampleSummary.java
%%JAVAJARDIR%%/bbmap/template/A_Sample_Generator$ProcessThread.class
%%JAVAJARDIR%%/bbmap/template/A_Sample_Generator.class
%%JAVAJARDIR%%/bbmap/template/A_Sample_Generator.java
%%JAVAJARDIR%%/bbmap/template/A_Sample_Unpaired.class
%%JAVAJARDIR%%/bbmap/template/A_Sample_Unpaired.java
%%JAVAJARDIR%%/bbmap/template/Accumulator.class
%%JAVAJARDIR%%/bbmap/template/Accumulator.java
%%JAVAJARDIR%%/bbmap/template/BBTool_ST.class
%%JAVAJARDIR%%/bbmap/template/BBTool_ST.java
%%JAVAJARDIR%%/bbmap/template/DoWorker.class
%%JAVAJARDIR%%/bbmap/template/DoWorker.java
%%JAVAJARDIR%%/bbmap/template/README.md
%%JAVAJARDIR%%/bbmap/template/ThreadPoolJob.class
%%JAVAJARDIR%%/bbmap/template/ThreadPoolJob.java
%%JAVAJARDIR%%/bbmap/template/ThreadWaiter.class
%%JAVAJARDIR%%/bbmap/template/ThreadWaiter.java
%%JAVAJARDIR%%/bbmap/tracker/AdapterTracker.class
%%JAVAJARDIR%%/bbmap/tracker/AdapterTracker.java
%%JAVAJARDIR%%/bbmap/tracker/CrisprTracker.class
%%JAVAJARDIR%%/bbmap/tracker/CrisprTracker.java
%%JAVAJARDIR%%/bbmap/tracker/EntropyTracker.class
%%JAVAJARDIR%%/bbmap/tracker/EntropyTracker.java
%%JAVAJARDIR%%/bbmap/tracker/KmerTracker.class
%%JAVAJARDIR%%/bbmap/tracker/KmerTracker.java
%%JAVAJARDIR%%/bbmap/tracker/PalindromeTracker.class
%%JAVAJARDIR%%/bbmap/tracker/PalindromeTracker.java
%%JAVAJARDIR%%/bbmap/tracker/PolymerTracker.class
%%JAVAJARDIR%%/bbmap/tracker/PolymerTracker.java
%%JAVAJARDIR%%/bbmap/tracker/QualityTracker.class
%%JAVAJARDIR%%/bbmap/tracker/QualityTracker.java
%%JAVAJARDIR%%/bbmap/tracker/ReadStats.class
%%JAVAJARDIR%%/bbmap/tracker/ReadStats.java
%%JAVAJARDIR%%/bbmap/tracker/SealStats$SealStatsLine.class
%%JAVAJARDIR%%/bbmap/tracker/SealStats.class
%%JAVAJARDIR%%/bbmap/tracker/SealStats.java
%%JAVAJARDIR%%/bbmap/ukmer/AbstractKmerTableU$AllocThread.class
%%JAVAJARDIR%%/bbmap/ukmer/AbstractKmerTableU.class
%%JAVAJARDIR%%/bbmap/ukmer/AbstractKmerTableU.java
%%JAVAJARDIR%%/bbmap/ukmer/DumpThreadU.class
%%JAVAJARDIR%%/bbmap/ukmer/DumpThreadU.java
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayU.class
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayU.java
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayU1D$WalkerU1D.class
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayU1D.class
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayU1D.java
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayU2D.class
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayU2D.java
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayUHybrid.class
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayUHybrid.java
%%JAVAJARDIR%%/bbmap/ukmer/HashBufferU.class
%%JAVAJARDIR%%/bbmap/ukmer/HashBufferU.java
%%JAVAJARDIR%%/bbmap/ukmer/HashForestU.class
%%JAVAJARDIR%%/bbmap/ukmer/HashForestU.java
%%JAVAJARDIR%%/bbmap/ukmer/HistogramMakerU$FillThread.class
%%JAVAJARDIR%%/bbmap/ukmer/HistogramMakerU.class
%%JAVAJARDIR%%/bbmap/ukmer/HistogramMakerU.java
%%JAVAJARDIR%%/bbmap/ukmer/Kmer.class
%%JAVAJARDIR%%/bbmap/ukmer/Kmer.java
%%JAVAJARDIR%%/bbmap/ukmer/KmerBufferU.class
%%JAVAJARDIR%%/bbmap/ukmer/KmerBufferU.java
%%JAVAJARDIR%%/bbmap/ukmer/KmerNodeU.class
%%JAVAJARDIR%%/bbmap/ukmer/KmerNodeU.java
%%JAVAJARDIR%%/bbmap/ukmer/KmerNodeU1D.class
%%JAVAJARDIR%%/bbmap/ukmer/KmerNodeU1D.java
%%JAVAJARDIR%%/bbmap/ukmer/KmerNodeU2D.class
%%JAVAJARDIR%%/bbmap/ukmer/KmerNodeU2D.java
%%JAVAJARDIR%%/bbmap/ukmer/KmerTableSetU$LoadThread.class
%%JAVAJARDIR%%/bbmap/ukmer/KmerTableSetU$WalkerKSTU.class
%%JAVAJARDIR%%/bbmap/ukmer/KmerTableSetU.class
%%JAVAJARDIR%%/bbmap/ukmer/KmerTableSetU.java
%%JAVAJARDIR%%/bbmap/ukmer/OwnershipThread.class
%%JAVAJARDIR%%/bbmap/ukmer/OwnershipThread.java
%%JAVAJARDIR%%/bbmap/ukmer/README.md
%%JAVAJARDIR%%/bbmap/ukmer/WalkerU.class
%%JAVAJARDIR%%/bbmap/ukmer/WalkerU.java
%%JAVAJARDIR%%/bbmap/var/ApplyVarsToReference$1.class
%%JAVAJARDIR%%/bbmap/var/ApplyVarsToReference.class
%%JAVAJARDIR%%/bbmap/var/ApplyVarsToReference.java
%%JAVAJARDIR%%/bbmap/var/GenerateConsensusVariations$1.class
%%JAVAJARDIR%%/bbmap/var/GenerateConsensusVariations.class
%%JAVAJARDIR%%/bbmap/var/GenerateConsensusVariations.java
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets$ProcessThread.class
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets.class
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets.java
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets2$1.class
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets2$ProcessThread.class
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets2.class
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets2.java
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets3$1.class
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets3$ProcessThread.class
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets3.class
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets3.java
%%JAVAJARDIR%%/bbmap/var/README.md
%%JAVAJARDIR%%/bbmap/var/StackVariations$1.class
%%JAVAJARDIR%%/bbmap/var/StackVariations$SVThread.class
%%JAVAJARDIR%%/bbmap/var/StackVariations.class
%%JAVAJARDIR%%/bbmap/var/StackVariations.java
%%JAVAJARDIR%%/bbmap/var/StackVariations2$1.class
%%JAVAJARDIR%%/bbmap/var/StackVariations2$SVThread.class
%%JAVAJARDIR%%/bbmap/var/StackVariations2.class
%%JAVAJARDIR%%/bbmap/var/StackVariations2.java
%%JAVAJARDIR%%/bbmap/var/VarLine.class
%%JAVAJARDIR%%/bbmap/var/VarLine.java
%%JAVAJARDIR%%/bbmap/var/Variation.class
%%JAVAJARDIR%%/bbmap/var/Variation.java
%%JAVAJARDIR%%/bbmap/var/Varlet.class
%%JAVAJARDIR%%/bbmap/var/Varlet.java
%%JAVAJARDIR%%/bbmap/var2/AnalyzeVars.class
%%JAVAJARDIR%%/bbmap/var2/AnalyzeVars.java
%%JAVAJARDIR%%/bbmap/var2/ApplyVariants.class
%%JAVAJARDIR%%/bbmap/var2/ApplyVariants.java
%%JAVAJARDIR%%/bbmap/var2/BalanceVectors.class
%%JAVAJARDIR%%/bbmap/var2/BalanceVectors.java
%%JAVAJARDIR%%/bbmap/var2/BedMask$1.class
%%JAVAJARDIR%%/bbmap/var2/BedMask.class
%%JAVAJARDIR%%/bbmap/var2/BedMask.java
%%JAVAJARDIR%%/bbmap/var2/BedSet$1.class
%%JAVAJARDIR%%/bbmap/var2/BedSet$2.class
%%JAVAJARDIR%%/bbmap/var2/BedSet$Bed.class
%%JAVAJARDIR%%/bbmap/var2/BedSet.class
%%JAVAJARDIR%%/bbmap/var2/BedSet.java
%%JAVAJARDIR%%/bbmap/var2/CVOutputWriter.class
%%JAVAJARDIR%%/bbmap/var2/CVOutputWriter.java
%%JAVAJARDIR%%/bbmap/var2/CallVariants$ProcessThread.class
%%JAVAJARDIR%%/bbmap/var2/CallVariants.class
%%JAVAJARDIR%%/bbmap/var2/CallVariants.java
%%JAVAJARDIR%%/bbmap/var2/CallVariants2$Sample$ProcessThread.class
%%JAVAJARDIR%%/bbmap/var2/CallVariants2$Sample.class
%%JAVAJARDIR%%/bbmap/var2/CallVariants2.class
%%JAVAJARDIR%%/bbmap/var2/CallVariants2.java
%%JAVAJARDIR%%/bbmap/var2/CompareVCF.class
%%JAVAJARDIR%%/bbmap/var2/CompareVCF.java
%%JAVAJARDIR%%/bbmap/var2/FeatureVectorMaker.class
%%JAVAJARDIR%%/bbmap/var2/FeatureVectorMaker.java
%%JAVAJARDIR%%/bbmap/var2/FilterSam$ProcessThread.class
%%JAVAJARDIR%%/bbmap/var2/FilterSam.class
%%JAVAJARDIR%%/bbmap/var2/FilterSam.java
%%JAVAJARDIR%%/bbmap/var2/FilterVCF$ProcessThread.class
%%JAVAJARDIR%%/bbmap/var2/FilterVCF.class
%%JAVAJARDIR%%/bbmap/var2/FilterVCF.java
%%JAVAJARDIR%%/bbmap/var2/GradeVCF$ProcessThread.class
%%JAVAJARDIR%%/bbmap/var2/GradeVCF.class
%%JAVAJARDIR%%/bbmap/var2/GradeVCF.java
%%JAVAJARDIR%%/bbmap/var2/InvertVCF.class
%%JAVAJARDIR%%/bbmap/var2/InvertVCF.java
%%JAVAJARDIR%%/bbmap/var2/LabelVCF.class
%%JAVAJARDIR%%/bbmap/var2/LabelVCF.java
%%JAVAJARDIR%%/bbmap/var2/MergeSamples$MergeThread.class
%%JAVAJARDIR%%/bbmap/var2/MergeSamples.class
%%JAVAJARDIR%%/bbmap/var2/MergeSamples.java
%%JAVAJARDIR%%/bbmap/var2/NNChooser$NetEntry.class
%%JAVAJARDIR%%/bbmap/var2/NNChooser.class
%%JAVAJARDIR%%/bbmap/var2/NNChooser.java
%%JAVAJARDIR%%/bbmap/var2/README.md
%%JAVAJARDIR%%/bbmap/var2/Realign$ProcessThread.class
%%JAVAJARDIR%%/bbmap/var2/Realign.class
%%JAVAJARDIR%%/bbmap/var2/Realign.java
%%JAVAJARDIR%%/bbmap/var2/Realigner.class
%%JAVAJARDIR%%/bbmap/var2/Realigner.java
%%JAVAJARDIR%%/bbmap/var2/RestoreBases$1.class
%%JAVAJARDIR%%/bbmap/var2/RestoreBases.class
%%JAVAJARDIR%%/bbmap/var2/RestoreBases.java
%%JAVAJARDIR%%/bbmap/var2/SamFilter.class
%%JAVAJARDIR%%/bbmap/var2/SamFilter.java
%%JAVAJARDIR%%/bbmap/var2/ScafMap.class
%%JAVAJARDIR%%/bbmap/var2/ScafMap.java
%%JAVAJARDIR%%/bbmap/var2/ScafMapNameTest.class
%%JAVAJARDIR%%/bbmap/var2/ScafMapNameTest.java
%%JAVAJARDIR%%/bbmap/var2/Scaffold.class
%%JAVAJARDIR%%/bbmap/var2/Scaffold.java
%%JAVAJARDIR%%/bbmap/var2/SoftClipper.class
%%JAVAJARDIR%%/bbmap/var2/SoftClipper.java
%%JAVAJARDIR%%/bbmap/var2/TransferLabels.class
%%JAVAJARDIR%%/bbmap/var2/TransferLabels.java
%%JAVAJARDIR%%/bbmap/var2/VCFFile$1.class
%%JAVAJARDIR%%/bbmap/var2/VCFFile.class
%%JAVAJARDIR%%/bbmap/var2/VCFFile.java
%%JAVAJARDIR%%/bbmap/var2/VCFLine.class
%%JAVAJARDIR%%/bbmap/var2/VCFLine.java
%%JAVAJARDIR%%/bbmap/var2/Var.class
%%JAVAJARDIR%%/bbmap/var2/Var.java
%%JAVAJARDIR%%/bbmap/var2/VarFilter.class
%%JAVAJARDIR%%/bbmap/var2/VarFilter.java
%%JAVAJARDIR%%/bbmap/var2/VarHelper.class
%%JAVAJARDIR%%/bbmap/var2/VarHelper.java
%%JAVAJARDIR%%/bbmap/var2/VarKey.class
%%JAVAJARDIR%%/bbmap/var2/VarKey.java
%%JAVAJARDIR%%/bbmap/var2/VarM.class
%%JAVAJARDIR%%/bbmap/var2/VarM.java
%%JAVAJARDIR%%/bbmap/var2/VarMap$ProcessThread.class
%%JAVAJARDIR%%/bbmap/var2/VarMap$VarMapIterator.class
%%JAVAJARDIR%%/bbmap/var2/VarMap.class
%%JAVAJARDIR%%/bbmap/var2/VarMap.java
%%JAVAJARDIR%%/bbmap/var2/VarProb.class
%%JAVAJARDIR%%/bbmap/var2/VarProb.java
%%JAVAJARDIR%%/bbmap/var2/VcfLoader$ProcessThread.class
%%JAVAJARDIR%%/bbmap/var2/VcfLoader.class
%%JAVAJARDIR%%/bbmap/var2/VcfLoader.java
%%JAVAJARDIR%%/bbmap/var2/VcfToTrainingVectors.class
%%JAVAJARDIR%%/bbmap/var2/VcfToTrainingVectors.java
%%JAVAJARDIR%%/bbmap/var2/VcfToVar.class
%%JAVAJARDIR%%/bbmap/var2/VcfToVar.java
%%JAVAJARDIR%%/bbmap/var2/VcfWriter$ProcessThread.class
%%JAVAJARDIR%%/bbmap/var2/VcfWriter.class
%%JAVAJARDIR%%/bbmap/var2/VcfWriter.java
%%JAVAJARDIR%%/bbmap/var2/VectorDonovan$QuantileTransformer.class
%%JAVAJARDIR%%/bbmap/var2/VectorDonovan.class
%%JAVAJARDIR%%/bbmap/var2/VectorDonovan.java
%%JAVAJARDIR%%/bbmap/var2/VectorElba$ElbaMinMaxValues.class
%%JAVAJARDIR%%/bbmap/var2/VectorElba.class
%%JAVAJARDIR%%/bbmap/var2/VectorElba.java
%%JAVAJARDIR%%/bbmap/var2/VectorUMP45.class
%%JAVAJARDIR%%/bbmap/var2/VectorUMP45.java
%%JAVAJARDIR%%/bbmap/var2/VectorsFromLabeledVCF.class
%%JAVAJARDIR%%/bbmap/var2/VectorsFromLabeledVCF.java
