bin/bbduk.sh
bin/bbmap.sh
bin/bbmerge.sh
bin/bbnorm.sh
bin/bloomfilter.sh
bin/dedupe.sh
bin/reformat.sh
bin/tadpole.sh
libexec/bbmap/a_sample_mt.sh
libexec/bbmap/addadapters.sh
libexec/bbmap/addssu.sh
libexec/bbmap/adjusthomopolymers.sh
libexec/bbmap/alltoall.sh
libexec/bbmap/analyzeaccession.sh
libexec/bbmap/analyzegenes.sh
libexec/bbmap/analyzesketchresults.sh
libexec/bbmap/applyvariants.sh
libexec/bbmap/bbcms.sh
libexec/bbmap/bbcountunique.sh
libexec/bbmap/bbduk.sh
libexec/bbmap/bbest.sh
libexec/bbmap/bbfakereads.sh
libexec/bbmap/bbmap.sh
libexec/bbmap/bbmapskimmer.sh
libexec/bbmap/bbmask.sh
libexec/bbmap/bbmerge-auto.sh
libexec/bbmap/bbmerge.sh
libexec/bbmap/bbnorm.sh
libexec/bbmap/bbrealign.sh
libexec/bbmap/bbrename.sh
libexec/bbmap/bbsketch.sh
libexec/bbmap/bbsplit.sh
libexec/bbmap/bbsplitpairs.sh
libexec/bbmap/bbstats.sh
libexec/bbmap/bbversion.sh
libexec/bbmap/bbwrap.sh
libexec/bbmap/bloomfilter.sh
libexec/bbmap/calcmem.sh
libexec/bbmap/calctruequality.sh
libexec/bbmap/callgenes.sh
libexec/bbmap/callpeaks.sh
libexec/bbmap/callvariants.sh
libexec/bbmap/callvariants2.sh
libexec/bbmap/clumpify.sh
libexec/bbmap/commonkmers.sh
libexec/bbmap/comparegff.sh
libexec/bbmap/comparesketch.sh
libexec/bbmap/comparessu.sh
libexec/bbmap/comparevcf.sh
libexec/bbmap/consect.sh
libexec/bbmap/consensus.sh
libexec/bbmap/countbarcodes.sh
libexec/bbmap/countgc.sh
libexec/bbmap/countsharedlines.sh
libexec/bbmap/crossblock.sh
libexec/bbmap/crosscontaminate.sh
libexec/bbmap/cutgff.sh
libexec/bbmap/cutprimers.sh
libexec/bbmap/decontaminate.sh
libexec/bbmap/dedupe.sh
libexec/bbmap/dedupe2.sh
libexec/bbmap/dedupebymapping.sh
libexec/bbmap/demuxbyname.sh
libexec/bbmap/diskbench.sh
libexec/bbmap/estherfilter.sh
libexec/bbmap/explodetree.sh
libexec/bbmap/fetchproks.sh
libexec/bbmap/filterassemblysummary.sh
libexec/bbmap/filterbarcodes.sh
libexec/bbmap/filterbycoverage.sh
libexec/bbmap/filterbyname.sh
libexec/bbmap/filterbysequence.sh
libexec/bbmap/filterbytaxa.sh
libexec/bbmap/filterbytile.sh
libexec/bbmap/filterlines.sh
libexec/bbmap/filterqc.sh
libexec/bbmap/filtersam.sh
libexec/bbmap/filtersilva.sh
libexec/bbmap/filtersubs.sh
libexec/bbmap/filtervcf.sh
libexec/bbmap/fixgaps.sh
libexec/bbmap/fungalrelease.sh
libexec/bbmap/fuse.sh
libexec/bbmap/gbff2gff.sh
libexec/bbmap/getreads.sh
libexec/bbmap/gi2ancestors.sh
libexec/bbmap/gi2taxid.sh
libexec/bbmap/gitable.sh
libexec/bbmap/grademerge.sh
libexec/bbmap/gradesam.sh
libexec/bbmap/icecreamfinder.sh
libexec/bbmap/icecreamgrader.sh
libexec/bbmap/icecreammaker.sh
libexec/bbmap/idmatrix.sh
libexec/bbmap/idtree.sh
libexec/bbmap/invertkey.sh
libexec/bbmap/kapastats.sh
libexec/bbmap/kcompress.sh
libexec/bbmap/keepbestcopy.sh
libexec/bbmap/khist.sh
libexec/bbmap/kmercountexact.sh
libexec/bbmap/kmercountmulti.sh
libexec/bbmap/kmercoverage.sh
libexec/bbmap/kmerfilterset.sh
libexec/bbmap/kmerlimit.sh
libexec/bbmap/kmerlimit2.sh
libexec/bbmap/kmerposition.sh
libexec/bbmap/kmutate.sh
libexec/bbmap/lilypad.sh
libexec/bbmap/loadreads.sh
libexec/bbmap/loglog.sh
libexec/bbmap/makechimeras.sh
libexec/bbmap/makecontaminatedgenomes.sh
libexec/bbmap/makepolymers.sh
libexec/bbmap/mapPacBio.sh
libexec/bbmap/matrixtocolumns.sh
libexec/bbmap/mergeOTUs.sh
libexec/bbmap/mergebarcodes.sh
libexec/bbmap/mergepgm.sh
libexec/bbmap/mergeribo.sh
libexec/bbmap/mergesam.sh
libexec/bbmap/mergesketch.sh
libexec/bbmap/mergesorted.sh
libexec/bbmap/msa.sh
libexec/bbmap/mutate.sh
libexec/bbmap/muxbyname.sh
libexec/bbmap/partition.sh
libexec/bbmap/phylip2fasta.sh
libexec/bbmap/pileup.sh
libexec/bbmap/plotflowcell.sh
libexec/bbmap/plotgc.sh
libexec/bbmap/postfilter.sh
libexec/bbmap/printtime.sh
libexec/bbmap/processfrag.sh
libexec/bbmap/processhi-c.sh
libexec/bbmap/processspeed.sh
libexec/bbmap/randomgenome.sh
libexec/bbmap/randomreads.sh
libexec/bbmap/readlength.sh
libexec/bbmap/readqc.sh
libexec/bbmap/reducesilva.sh
libexec/bbmap/reformat.sh
libexec/bbmap/reformatpb.sh
libexec/bbmap/removebadbarcodes.sh
libexec/bbmap/removecatdogmousehuman.sh
libexec/bbmap/removehuman.sh
libexec/bbmap/removehuman2.sh
libexec/bbmap/removemicrobes.sh
libexec/bbmap/removesmartbell.sh
libexec/bbmap/rename.sh
libexec/bbmap/renameimg.sh
libexec/bbmap/repair.sh
libexec/bbmap/replaceheaders.sh
libexec/bbmap/representative.sh
libexec/bbmap/rqcfilter.sh
libexec/bbmap/rqcfilter2.sh
libexec/bbmap/runhmm.sh
libexec/bbmap/samtoroc.sh
libexec/bbmap/seal.sh
libexec/bbmap/sendsketch.sh
libexec/bbmap/shred.sh
libexec/bbmap/shrinkaccession.sh
libexec/bbmap/shuffle.sh
libexec/bbmap/shuffle2.sh
libexec/bbmap/sketch.sh
libexec/bbmap/sketchblacklist.sh
libexec/bbmap/sketchblacklist2.sh
libexec/bbmap/sortbyname.sh
libexec/bbmap/splitbytaxa.sh
libexec/bbmap/splitnextera.sh
libexec/bbmap/splitribo.sh
libexec/bbmap/splitsam.sh
libexec/bbmap/splitsam4way.sh
libexec/bbmap/splitsam6way.sh
libexec/bbmap/stats.sh
libexec/bbmap/statswrapper.sh
libexec/bbmap/streamsam.sh
libexec/bbmap/subsketch.sh
libexec/bbmap/summarizecontam.sh
libexec/bbmap/summarizecoverage.sh
libexec/bbmap/summarizecrossblock.sh
libexec/bbmap/summarizemerge.sh
libexec/bbmap/summarizequast.sh
libexec/bbmap/summarizescafstats.sh
libexec/bbmap/summarizeseal.sh
libexec/bbmap/summarizesketch.sh
libexec/bbmap/synthmda.sh
libexec/bbmap/tadpipe.sh
libexec/bbmap/tadpole.sh
libexec/bbmap/tadwrapper.sh
libexec/bbmap/taxonomy.sh
libexec/bbmap/taxserver.sh
libexec/bbmap/taxsize.sh
libexec/bbmap/taxtree.sh
libexec/bbmap/testfilesystem.sh
libexec/bbmap/testformat.sh
libexec/bbmap/testformat2.sh
libexec/bbmap/tetramerfreq.sh
libexec/bbmap/textfile.sh
libexec/bbmap/translate6frames.sh
libexec/bbmap/unicode2ascii.sh
libexec/bbmap/unzip.sh
libexec/bbmap/vcf2gff.sh
libexec/bbmap/webcheck.sh
%%JAVAJARDIR%%/bbmap/align2/AbstractIndex.class
%%JAVAJARDIR%%/bbmap/align2/AbstractIndex.java
%%JAVAJARDIR%%/bbmap/align2/AbstractMapThread.class
%%JAVAJARDIR%%/bbmap/align2/AbstractMapThread.java
%%JAVAJARDIR%%/bbmap/align2/AbstractMapper.class
%%JAVAJARDIR%%/bbmap/align2/AbstractMapper.java
%%JAVAJARDIR%%/bbmap/align2/BBIndex.class
%%JAVAJARDIR%%/bbmap/align2/BBIndex.java
%%JAVAJARDIR%%/bbmap/align2/BBIndex5.class
%%JAVAJARDIR%%/bbmap/align2/BBIndex5.java
%%JAVAJARDIR%%/bbmap/align2/BBIndexAcc.class
%%JAVAJARDIR%%/bbmap/align2/BBIndexAcc.java
%%JAVAJARDIR%%/bbmap/align2/BBIndexPacBio.class
%%JAVAJARDIR%%/bbmap/align2/BBIndexPacBio.java
%%JAVAJARDIR%%/bbmap/align2/BBIndexPacBioSkimmer.class
%%JAVAJARDIR%%/bbmap/align2/BBIndexPacBioSkimmer.java
%%JAVAJARDIR%%/bbmap/align2/BBMap.class
%%JAVAJARDIR%%/bbmap/align2/BBMap.java
%%JAVAJARDIR%%/bbmap/align2/BBMap5.class
%%JAVAJARDIR%%/bbmap/align2/BBMap5.java
%%JAVAJARDIR%%/bbmap/align2/BBMapAcc.class
%%JAVAJARDIR%%/bbmap/align2/BBMapAcc.java
%%JAVAJARDIR%%/bbmap/align2/BBMapPacBio.class
%%JAVAJARDIR%%/bbmap/align2/BBMapPacBio.java
%%JAVAJARDIR%%/bbmap/align2/BBMapPacBioSkimmer.class
%%JAVAJARDIR%%/bbmap/align2/BBMapPacBioSkimmer.java
%%JAVAJARDIR%%/bbmap/align2/BBMapThread$1.class
%%JAVAJARDIR%%/bbmap/align2/BBMapThread.class
%%JAVAJARDIR%%/bbmap/align2/BBMapThread.java
%%JAVAJARDIR%%/bbmap/align2/BBMapThread5$1.class
%%JAVAJARDIR%%/bbmap/align2/BBMapThread5.class
%%JAVAJARDIR%%/bbmap/align2/BBMapThread5.java
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadAcc$1.class
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadAcc.class
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadAcc.java
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadPacBio$1.class
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadPacBio.class
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadPacBio.java
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadPacBioSkimmer.class
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadPacBioSkimmer.java
%%JAVAJARDIR%%/bbmap/align2/BBSplitter$1.class
%%JAVAJARDIR%%/bbmap/align2/BBSplitter$SetCount.class
%%JAVAJARDIR%%/bbmap/align2/BBSplitter.class
%%JAVAJARDIR%%/bbmap/align2/BBSplitter.java
%%JAVAJARDIR%%/bbmap/align2/BBWrap.class
%%JAVAJARDIR%%/bbmap/align2/BBWrap.java
%%JAVAJARDIR%%/bbmap/align2/BandedAligner.class
%%JAVAJARDIR%%/bbmap/align2/BandedAligner.java
%%JAVAJARDIR%%/bbmap/align2/BandedAlignerConcrete.class
%%JAVAJARDIR%%/bbmap/align2/BandedAlignerConcrete.java
%%JAVAJARDIR%%/bbmap/align2/BandedAlignerJNI.class
%%JAVAJARDIR%%/bbmap/align2/BandedAlignerJNI.java
%%JAVAJARDIR%%/bbmap/align2/Blacklist.class
%%JAVAJARDIR%%/bbmap/align2/Blacklist.java
%%JAVAJARDIR%%/bbmap/align2/Block.class
%%JAVAJARDIR%%/bbmap/align2/Block.java
%%JAVAJARDIR%%/bbmap/align2/ChromLoadThread.class
%%JAVAJARDIR%%/bbmap/align2/ChromLoadThread.java
%%JAVAJARDIR%%/bbmap/align2/CompareSamFiles$1.class
%%JAVAJARDIR%%/bbmap/align2/CompareSamFiles.class
%%JAVAJARDIR%%/bbmap/align2/CompareSamFiles.java
%%JAVAJARDIR%%/bbmap/align2/CompressString.class
%%JAVAJARDIR%%/bbmap/align2/CompressString.java
%%JAVAJARDIR%%/bbmap/align2/GapTools$Range.class
%%JAVAJARDIR%%/bbmap/align2/GapTools.class
%%JAVAJARDIR%%/bbmap/align2/GapTools.java
%%JAVAJARDIR%%/bbmap/align2/GradeSamFile$1.class
%%JAVAJARDIR%%/bbmap/align2/GradeSamFile.class
%%JAVAJARDIR%%/bbmap/align2/GradeSamFile.java
%%JAVAJARDIR%%/bbmap/align2/Index.class
%%JAVAJARDIR%%/bbmap/align2/Index.java
%%JAVAJARDIR%%/bbmap/align2/IndexMaker4$BlockMaker$CountThread.class
%%JAVAJARDIR%%/bbmap/align2/IndexMaker4$BlockMaker.class
%%JAVAJARDIR%%/bbmap/align2/IndexMaker4.class
%%JAVAJARDIR%%/bbmap/align2/IndexMaker4.java
%%JAVAJARDIR%%/bbmap/align2/IndexMaker5$BlockMaker$CountThread.class
%%JAVAJARDIR%%/bbmap/align2/IndexMaker5$BlockMaker.class
%%JAVAJARDIR%%/bbmap/align2/IndexMaker5.class
%%JAVAJARDIR%%/bbmap/align2/IndexMaker5.java
%%JAVAJARDIR%%/bbmap/align2/KeyRing.class
%%JAVAJARDIR%%/bbmap/align2/KeyRing.java
%%JAVAJARDIR%%/bbmap/align2/MSA.class
%%JAVAJARDIR%%/bbmap/align2/MSA.java
%%JAVAJARDIR%%/bbmap/align2/MakeQualityHistogram.class
%%JAVAJARDIR%%/bbmap/align2/MakeQualityHistogram.java
%%JAVAJARDIR%%/bbmap/align2/MakeRocCurve$1.class
%%JAVAJARDIR%%/bbmap/align2/MakeRocCurve.class
%%JAVAJARDIR%%/bbmap/align2/MakeRocCurve.java
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner10ts.class
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner10ts.java
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner11ts.class
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner11ts.java
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner11tsJNI.class
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner11tsJNI.java
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9Flat.class
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9Flat.java
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9PacBio.class
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9PacBio.java
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9XFlat.class
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9XFlat.java
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9ts.class
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9ts.java
%%JAVAJARDIR%%/bbmap/align2/NeedlemanWunsch.class
%%JAVAJARDIR%%/bbmap/align2/NeedlemanWunsch.java
%%JAVAJARDIR%%/bbmap/align2/PackedHeap.class
%%JAVAJARDIR%%/bbmap/align2/PackedHeap.java
%%JAVAJARDIR%%/bbmap/align2/Pointer.class
%%JAVAJARDIR%%/bbmap/align2/Pointer.java
%%JAVAJARDIR%%/bbmap/align2/PrintTime.class
%%JAVAJARDIR%%/bbmap/align2/PrintTime.java
%%JAVAJARDIR%%/bbmap/align2/Quad.class
%%JAVAJARDIR%%/bbmap/align2/Quad.java
%%JAVAJARDIR%%/bbmap/align2/Quad64.class
%%JAVAJARDIR%%/bbmap/align2/Quad64.java
%%JAVAJARDIR%%/bbmap/align2/Quad64Heap.class
%%JAVAJARDIR%%/bbmap/align2/Quad64Heap.java
%%JAVAJARDIR%%/bbmap/align2/QuadHeap.class
%%JAVAJARDIR%%/bbmap/align2/QuadHeap.java
%%JAVAJARDIR%%/bbmap/align2/QualityTools.class
%%JAVAJARDIR%%/bbmap/align2/QualityTools.java
%%JAVAJARDIR%%/bbmap/align2/RandomReads3$1.class
%%JAVAJARDIR%%/bbmap/align2/RandomReads3.class
%%JAVAJARDIR%%/bbmap/align2/RandomReads3.java
%%JAVAJARDIR%%/bbmap/align2/RefToIndex.class
%%JAVAJARDIR%%/bbmap/align2/RefToIndex.java
%%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput.class
%%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput.java
%%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput2.class
%%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput2.java
%%JAVAJARDIR%%/bbmap/align2/Solver.class
%%JAVAJARDIR%%/bbmap/align2/Solver.java
%%JAVAJARDIR%%/bbmap/align2/SplitMappedReads.class
%%JAVAJARDIR%%/bbmap/align2/SplitMappedReads.java
%%JAVAJARDIR%%/bbmap/align2/TranslateColorspaceRead.class
%%JAVAJARDIR%%/bbmap/align2/TranslateColorspaceRead.java
%%JAVAJARDIR%%/bbmap/aligner/Aligner.class
%%JAVAJARDIR%%/bbmap/aligner/Aligner.java
%%JAVAJARDIR%%/bbmap/aligner/Alignment.class
%%JAVAJARDIR%%/bbmap/aligner/Alignment.java
%%JAVAJARDIR%%/bbmap/aligner/AlignmentResult.class
%%JAVAJARDIR%%/bbmap/aligner/AlignmentResult.java
%%JAVAJARDIR%%/bbmap/aligner/AllToAll$ProcessThread.class
%%JAVAJARDIR%%/bbmap/aligner/AllToAll.class
%%JAVAJARDIR%%/bbmap/aligner/AllToAll.java
%%JAVAJARDIR%%/bbmap/aligner/FlatAligner.class
%%JAVAJARDIR%%/bbmap/aligner/FlatAligner.java
%%JAVAJARDIR%%/bbmap/aligner/FlatAligner2.class
%%JAVAJARDIR%%/bbmap/aligner/FlatAligner2.java
%%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter.class
%%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter.java
%%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter2.class
%%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter2.java
%%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter3.class
%%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter3.java
%%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.class
%%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.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$BuildThread.class
%%JAVAJARDIR%%/bbmap/assemble/KmerCompressor.class
%%JAVAJARDIR%%/bbmap/assemble/KmerCompressor.java
%%JAVAJARDIR%%/bbmap/assemble/Postfilter.class
%%JAVAJARDIR%%/bbmap/assemble/Postfilter.java
%%JAVAJARDIR%%/bbmap/assemble/Rollback.class
%%JAVAJARDIR%%/bbmap/assemble/Rollback.java
%%JAVAJARDIR%%/bbmap/assemble/ShaveObject.class
%%JAVAJARDIR%%/bbmap/assemble/ShaveObject.java
%%JAVAJARDIR%%/bbmap/assemble/Shaver.class
%%JAVAJARDIR%%/bbmap/assemble/Shaver.java
%%JAVAJARDIR%%/bbmap/assemble/Shaver1$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/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$1.class
%%JAVAJARDIR%%/bbmap/bloom/ErrorCorrect.class
%%JAVAJARDIR%%/bbmap/bloom/ErrorCorrect.java
%%JAVAJARDIR%%/bbmap/bloom/KCountArray$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/KmerCount6MT$CountThread.class
%%JAVAJARDIR%%/bbmap/bloom/KmerCount6MT.class
%%JAVAJARDIR%%/bbmap/bloom/KmerCount6MT.java
%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MT$CountThread.class
%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MT.class
%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MT.java
%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MTA$1.class
%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MTA$CountThread.class
%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MTA$CountThread2.class
%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MTA.class
%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MTA.java
%%JAVAJARDIR%%/bbmap/bloom/KmerCountAbstract.class
%%JAVAJARDIR%%/bbmap/bloom/KmerCountAbstract.java
%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount.class
%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount.java
%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount2.class
%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount2.java
%%JAVAJARDIR%%/bbmap/bloom/TestLargeKmer.class
%%JAVAJARDIR%%/bbmap/bloom/TestLargeKmer.java
%%JAVAJARDIR%%/bbmap/cardinality/BBLog.class
%%JAVAJARDIR%%/bbmap/cardinality/BBLog.java
%%JAVAJARDIR%%/bbmap/cardinality/BBLog_simple.class
%%JAVAJARDIR%%/bbmap/cardinality/BBLog_simple.java
%%JAVAJARDIR%%/bbmap/cardinality/CardinalityTracker.class
%%JAVAJARDIR%%/bbmap/cardinality/CardinalityTracker.java
%%JAVAJARDIR%%/bbmap/cardinality/LogLog.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog.java
%%JAVAJARDIR%%/bbmap/cardinality/LogLog16.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog16.java
%%JAVAJARDIR%%/bbmap/cardinality/LogLog2.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog2.java
%%JAVAJARDIR%%/bbmap/cardinality/LogLog8.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog8.java
%%JAVAJARDIR%%/bbmap/cardinality/LogLog8_simple.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog8_simple.java
%%JAVAJARDIR%%/bbmap/cardinality/LogLogWrapper$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$LogLogWrapper.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog_old.class
%%JAVAJARDIR%%/bbmap/cardinality/LogLog_old.java
%%JAVAJARDIR%%/bbmap/cardinality/MultiLogLog.class
%%JAVAJARDIR%%/bbmap/cardinality/MultiLogLog.java
%%JAVAJARDIR%%/bbmap/clump/Clump.class
%%JAVAJARDIR%%/bbmap/clump/Clump.java
%%JAVAJARDIR%%/bbmap/clump/ClumpList$ClumpThread.class
%%JAVAJARDIR%%/bbmap/clump/ClumpList$ProcessThread.class
%%JAVAJARDIR%%/bbmap/clump/ClumpList.class
%%JAVAJARDIR%%/bbmap/clump/ClumpList.java
%%JAVAJARDIR%%/bbmap/clump/ClumpTools.class
%%JAVAJARDIR%%/bbmap/clump/ClumpTools.java
%%JAVAJARDIR%%/bbmap/clump/Clumpify.class
%%JAVAJARDIR%%/bbmap/clump/Clumpify.java
%%JAVAJARDIR%%/bbmap/clump/KmerComparator$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/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/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/covid/SummarizeCoverage.class
%%JAVAJARDIR%%/bbmap/covid/SummarizeCoverage.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/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/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$ResultsLine.class
%%JAVAJARDIR%%/bbmap/driver/ParseCrossblockResults.class
%%JAVAJARDIR%%/bbmap/driver/ParseCrossblockResults.java
%%JAVAJARDIR%%/bbmap/driver/PlotGC.class
%%JAVAJARDIR%%/bbmap/driver/PlotGC.java
%%JAVAJARDIR%%/bbmap/driver/PrintEnv.class
%%JAVAJARDIR%%/bbmap/driver/PrintEnv.java
%%JAVAJARDIR%%/bbmap/driver/ProcessFragMerging.class
%%JAVAJARDIR%%/bbmap/driver/ProcessFragMerging.java
%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed.class
%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed.java
%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed2.class
%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed2.java
%%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.class
%%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.java
%%JAVAJARDIR%%/bbmap/driver/ReduceSilva.class
%%JAVAJARDIR%%/bbmap/driver/ReduceSilva.java
%%JAVAJARDIR%%/bbmap/driver/RenameAndMux$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$QuastSummary.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeQuast.class
%%JAVAJARDIR%%/bbmap/driver/SummarizeQuast.java
%%JAVAJARDIR%%/bbmap/driver/SummarizeSealStats$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/ByteFile2$BF1Thread.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile2.class
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile2.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/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/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$1.class
%%JAVAJARDIR%%/bbmap/fileIO/SummaryFile.class
%%JAVAJARDIR%%/bbmap/fileIO/SummaryFile.java
%%JAVAJARDIR%%/bbmap/fileIO/TextFile.class
%%JAVAJARDIR%%/bbmap/fileIO/TextFile.java
%%JAVAJARDIR%%/bbmap/fileIO/TextStreamWriter.class
%%JAVAJARDIR%%/bbmap/fileIO/TextStreamWriter.java
%%JAVAJARDIR%%/bbmap/fun/Calc.class
%%JAVAJARDIR%%/bbmap/fun/Calc.java
%%JAVAJARDIR%%/bbmap/fun/Chance.class
%%JAVAJARDIR%%/bbmap/fun/Chance.java
%%JAVAJARDIR%%/bbmap/fun/DiskBench$ReadThread.class
%%JAVAJARDIR%%/bbmap/fun/DiskBench$WriteThread.class
%%JAVAJARDIR%%/bbmap/fun/DiskBench.class
%%JAVAJARDIR%%/bbmap/fun/DiskBench.java
%%JAVAJARDIR%%/bbmap/fun/FindPath$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/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$1.class
%%JAVAJARDIR%%/bbmap/fun/MakeAdjacencyList.class
%%JAVAJARDIR%%/bbmap/fun/MakeAdjacencyList.java
%%JAVAJARDIR%%/bbmap/fun/Palindrome.class
%%JAVAJARDIR%%/bbmap/fun/Palindrome.java
%%JAVAJARDIR%%/bbmap/fun/ProbShared.class
%%JAVAJARDIR%%/bbmap/fun/ProbShared.java
%%JAVAJARDIR%%/bbmap/fun/ProbShared2.class
%%JAVAJARDIR%%/bbmap/fun/ProbShared2.java
%%JAVAJARDIR%%/bbmap/fun/ProbShared3.class
%%JAVAJARDIR%%/bbmap/fun/ProbShared3.java
%%JAVAJARDIR%%/bbmap/gff/CompareGff.class
%%JAVAJARDIR%%/bbmap/gff/CompareGff.java
%%JAVAJARDIR%%/bbmap/gff/CompareGff_old.class
%%JAVAJARDIR%%/bbmap/gff/CompareGff_old.java
%%JAVAJARDIR%%/bbmap/gff/CutGff$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/VcfToGff$1.class
%%JAVAJARDIR%%/bbmap/gff/VcfToGff.class
%%JAVAJARDIR%%/bbmap/gff/VcfToGff.java
%%JAVAJARDIR%%/bbmap/hiseq/AnalyzeFlowCell.class
%%JAVAJARDIR%%/bbmap/hiseq/AnalyzeFlowCell.java
%%JAVAJARDIR%%/bbmap/hiseq/CycleTracker.class
%%JAVAJARDIR%%/bbmap/hiseq/CycleTracker.java
%%JAVAJARDIR%%/bbmap/hiseq/FlowCell.class
%%JAVAJARDIR%%/bbmap/hiseq/FlowCell.java
%%JAVAJARDIR%%/bbmap/hiseq/FlowcellCoordinate.class
%%JAVAJARDIR%%/bbmap/hiseq/FlowcellCoordinate.java
%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser.class
%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser.java
%%JAVAJARDIR%%/bbmap/hiseq/Lane.class
%%JAVAJARDIR%%/bbmap/hiseq/Lane.java
%%JAVAJARDIR%%/bbmap/hiseq/MicroTile.class
%%JAVAJARDIR%%/bbmap/hiseq/MicroTile.java
%%JAVAJARDIR%%/bbmap/hiseq/PlotFlowCell.class
%%JAVAJARDIR%%/bbmap/hiseq/PlotFlowCell.java
%%JAVAJARDIR%%/bbmap/hiseq/Tile.class
%%JAVAJARDIR%%/bbmap/hiseq/Tile.java
%%JAVAJARDIR%%/bbmap/hmm/HMMSearchLine.class
%%JAVAJARDIR%%/bbmap/hmm/HMMSearchLine.java
%%JAVAJARDIR%%/bbmap/hmm/HMMSearchReport.class
%%JAVAJARDIR%%/bbmap/hmm/HMMSearchReport.java
%%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.class
%%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.java
%%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.class
%%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.java
%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJNI.class
%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJNI.java
%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJava.class
%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJava.java
%%JAVAJARDIR%%/bbmap/icecream/IceCreamFinder$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$ProcessThread.class
%%JAVAJARDIR%%/bbmap/icecream/IceCreamMaker.class
%%JAVAJARDIR%%/bbmap/icecream/IceCreamMaker.java
%%JAVAJARDIR%%/bbmap/icecream/PBHeader.class
%%JAVAJARDIR%%/bbmap/icecream/PBHeader.java
%%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.class
%%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.java
%%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.class
%%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.java
%%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio$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/jasper/Comparison.class
%%JAVAJARDIR%%/bbmap/jasper/Comparison.java
%%JAVAJARDIR%%/bbmap/jasper/DenseSimilarityMatrix.class
%%JAVAJARDIR%%/bbmap/jasper/DenseSimilarityMatrix.java
%%JAVAJARDIR%%/bbmap/jasper/DenseTree.class
%%JAVAJARDIR%%/bbmap/jasper/DenseTree.java
%%JAVAJARDIR%%/bbmap/jasper/DenseTreeValidate.class
%%JAVAJARDIR%%/bbmap/jasper/DenseTreeValidate.java
%%JAVAJARDIR%%/bbmap/jasper/KmerPosition.class
%%JAVAJARDIR%%/bbmap/jasper/KmerPosition.java
%%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.class
%%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.java
%%JAVAJARDIR%%/bbmap/jasper/NCBIComparison.class
%%JAVAJARDIR%%/bbmap/jasper/NCBIComparison.java
%%JAVAJARDIR%%/bbmap/jasper/NCBISparseSimilarityMatrix.class
%%JAVAJARDIR%%/bbmap/jasper/NCBISparseSimilarityMatrix.java
%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTree.class
%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTree.java
%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTreeValidate.class
%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTreeValidate.java
%%JAVAJARDIR%%/bbmap/jasper/NCBITreeNode.class
%%JAVAJARDIR%%/bbmap/jasper/NCBITreeNode.java
%%JAVAJARDIR%%/bbmap/jasper/Organism.class
%%JAVAJARDIR%%/bbmap/jasper/Organism.java
%%JAVAJARDIR%%/bbmap/jasper/SimilarityMatrix.class
%%JAVAJARDIR%%/bbmap/jasper/SimilarityMatrix.java
%%JAVAJARDIR%%/bbmap/jasper/SparseSimilarityMatrix.class
%%JAVAJARDIR%%/bbmap/jasper/SparseSimilarityMatrix.java
%%JAVAJARDIR%%/bbmap/jasper/SparseTree.class
%%JAVAJARDIR%%/bbmap/jasper/SparseTree.java
%%JAVAJARDIR%%/bbmap/jasper/SparseTreeValidate.class
%%JAVAJARDIR%%/bbmap/jasper/SparseTreeValidate.java
%%JAVAJARDIR%%/bbmap/jasper/TaxCompare.class
%%JAVAJARDIR%%/bbmap/jasper/TaxCompare.java
%%JAVAJARDIR%%/bbmap/jasper/TreeNode.class
%%JAVAJARDIR%%/bbmap/jasper/TreeNode.java
%%JAVAJARDIR%%/bbmap/jgi/AddAdapters.class
%%JAVAJARDIR%%/bbmap/jgi/AddAdapters.java
%%JAVAJARDIR%%/bbmap/jgi/AdjustHomopolymers.class
%%JAVAJARDIR%%/bbmap/jgi/AdjustHomopolymers.java
%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2$Triple.class
%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2.class
%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2.java
%%JAVAJARDIR%%/bbmap/jgi/AssemblyStatsWrapper.class
%%JAVAJARDIR%%/bbmap/jgi/AssemblyStatsWrapper.java
%%JAVAJARDIR%%/bbmap/jgi/BBDuk$LoadThread.class
%%JAVAJARDIR%%/bbmap/jgi/BBDuk$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/BBDuk.class
%%JAVAJARDIR%%/bbmap/jgi/BBDuk.java
%%JAVAJARDIR%%/bbmap/jgi/BBDuk2$LoadThread.class
%%JAVAJARDIR%%/bbmap/jgi/BBDuk2$ProcessThread.class
%%JAVAJARDIR%%/bbmap/jgi/BBDuk2.class
%%JAVAJARDIR%%/bbmap/jgi/BBDuk2.java
%%JAVAJARDIR%%/bbmap/jgi/BBMask$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/Consect.class
%%JAVAJARDIR%%/bbmap/jgi/Consect.java
%%JAVAJARDIR%%/bbmap/jgi/CorrelateBarcodes.class
%%JAVAJARDIR%%/bbmap/jgi/CorrelateBarcodes.java
%%JAVAJARDIR%%/bbmap/jgi/CountBarcodes.class
%%JAVAJARDIR%%/bbmap/jgi/CountBarcodes.java
%%JAVAJARDIR%%/bbmap/jgi/CountGC$1.class
%%JAVAJARDIR%%/bbmap/jgi/CountGC.class
%%JAVAJARDIR%%/bbmap/jgi/CountGC.java
%%JAVAJARDIR%%/bbmap/jgi/CountUniqueness.class
%%JAVAJARDIR%%/bbmap/jgi/CountUniqueness.java
%%JAVAJARDIR%%/bbmap/jgi/CovStatsLine.class
%%JAVAJARDIR%%/bbmap/jgi/CovStatsLine.java
%%JAVAJARDIR%%/bbmap/jgi/CoveragePileup.class
%%JAVAJARDIR%%/bbmap/jgi/CoveragePileup.java
%%JAVAJARDIR%%/bbmap/jgi/CrossContaminate$Vessel.class
%%JAVAJARDIR%%/bbmap/jgi/CrossContaminate.class
%%JAVAJARDIR%%/bbmap/jgi/CrossContaminate.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/FakeReads.class
%%JAVAJARDIR%%/bbmap/jgi/FakeReads.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/FindPrimers_old.class
%%JAVAJARDIR%%/bbmap/jgi/FindPrimers_old.java
%%JAVAJARDIR%%/bbmap/jgi/FindString.class
%%JAVAJARDIR%%/bbmap/jgi/FindString.java
%%JAVAJARDIR%%/bbmap/jgi/FungalRelease.class
%%JAVAJARDIR%%/bbmap/jgi/FungalRelease.java
%%JAVAJARDIR%%/bbmap/jgi/FuseSequence.class
%%JAVAJARDIR%%/bbmap/jgi/FuseSequence.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/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/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/MakeChimeras.class
%%JAVAJARDIR%%/bbmap/jgi/MakeChimeras.java
%%JAVAJARDIR%%/bbmap/jgi/MakeContaminatedGenomes.class
%%JAVAJARDIR%%/bbmap/jgi/MakeContaminatedGenomes.java
%%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram$1.class
%%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.class
%%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.java
%%JAVAJARDIR%%/bbmap/jgi/MakePolymers.class
%%JAVAJARDIR%%/bbmap/jgi/MakePolymers.java
%%JAVAJARDIR%%/bbmap/jgi/MergeBarcodes.class
%%JAVAJARDIR%%/bbmap/jgi/MergeBarcodes.java
%%JAVAJARDIR%%/bbmap/jgi/MergeSam.class
%%JAVAJARDIR%%/bbmap/jgi/MergeSam.java
%%JAVAJARDIR%%/bbmap/jgi/MutateGenome$SmallVar.class
%%JAVAJARDIR%%/bbmap/jgi/MutateGenome.class
%%JAVAJARDIR%%/bbmap/jgi/MutateGenome.java
%%JAVAJARDIR%%/bbmap/jgi/MutateGenome2$SmallVar.class
%%JAVAJARDIR%%/bbmap/jgi/MutateGenome2.class
%%JAVAJARDIR%%/bbmap/jgi/MutateGenome2.java
%%JAVAJARDIR%%/bbmap/jgi/Orf.class
%%JAVAJARDIR%%/bbmap/jgi/Orf.java
%%JAVAJARDIR%%/bbmap/jgi/PartitionReads.class
%%JAVAJARDIR%%/bbmap/jgi/PartitionReads.java
%%JAVAJARDIR%%/bbmap/jgi/PhylipToFasta.class
%%JAVAJARDIR%%/bbmap/jgi/PhylipToFasta.java
%%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.class
%%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.java
%%JAVAJARDIR%%/bbmap/jgi/RQCFilterStats.class
%%JAVAJARDIR%%/bbmap/jgi/RQCFilterStats.java
%%JAVAJARDIR%%/bbmap/jgi/RandomGenome.class
%%JAVAJARDIR%%/bbmap/jgi/RandomGenome.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/ReformatReads.class
%%JAVAJARDIR%%/bbmap/jgi/ReformatReads.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/Shred.class
%%JAVAJARDIR%%/bbmap/jgi/Shred.java
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$CountComparator.class
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$Kmer.class
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$NumComparator.class
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency.class
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency.java
%%JAVAJARDIR%%/bbmap/jgi/SplitNexteraLMP.class
%%JAVAJARDIR%%/bbmap/jgi/SplitNexteraLMP.java
%%JAVAJARDIR%%/bbmap/jgi/SplitPairsAndSingles.class
%%JAVAJARDIR%%/bbmap/jgi/SplitPairsAndSingles.java
%%JAVAJARDIR%%/bbmap/jgi/SplitSam4Way.class
%%JAVAJARDIR%%/bbmap/jgi/SplitSam4Way.java
%%JAVAJARDIR%%/bbmap/jgi/SplitSam6Way.class
%%JAVAJARDIR%%/bbmap/jgi/SplitSam6Way.java
%%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.class
%%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.java
%%JAVAJARDIR%%/bbmap/jgi/StringCount.class
%%JAVAJARDIR%%/bbmap/jgi/StringCount.java
%%JAVAJARDIR%%/bbmap/jgi/SynthMDA.class
%%JAVAJARDIR%%/bbmap/jgi/SynthMDA.java
%%JAVAJARDIR%%/bbmap/jgi/TestFilesystem$WriteThread.class
%%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.class
%%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.java
%%JAVAJARDIR%%/bbmap/jgi/TestFormat$Barcode.class
%%JAVAJARDIR%%/bbmap/jgi/TestFormat$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/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/kmer/AbstractKmerTable$AllocThread.class
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.class
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.java
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.class
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.java
%%JAVAJARDIR%%/bbmap/kmer/DumpThread.class
%%JAVAJARDIR%%/bbmap/kmer/DumpThread.java
%%JAVAJARDIR%%/bbmap/kmer/HashArray.class
%%JAVAJARDIR%%/bbmap/kmer/HashArray.java
%%JAVAJARDIR%%/bbmap/kmer/HashArray1D$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$FillThread.class
%%JAVAJARDIR%%/bbmap/kmer/HistogramMaker.class
%%JAVAJARDIR%%/bbmap/kmer/HistogramMaker.java
%%JAVAJARDIR%%/bbmap/kmer/KmerBuffer.class
%%JAVAJARDIR%%/bbmap/kmer/KmerBuffer.java
%%JAVAJARDIR%%/bbmap/kmer/KmerLink.class
%%JAVAJARDIR%%/bbmap/kmer/KmerLink.java
%%JAVAJARDIR%%/bbmap/kmer/KmerNode.class
%%JAVAJARDIR%%/bbmap/kmer/KmerNode.java
%%JAVAJARDIR%%/bbmap/kmer/KmerNode1D.class
%%JAVAJARDIR%%/bbmap/kmer/KmerNode1D.java
%%JAVAJARDIR%%/bbmap/kmer/KmerNode2D.class
%%JAVAJARDIR%%/bbmap/kmer/KmerNode2D.java
%%JAVAJARDIR%%/bbmap/kmer/KmerTable.class
%%JAVAJARDIR%%/bbmap/kmer/KmerTable.java
%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet$LoadThread.class
%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet$WalkerKST.class
%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet.class
%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet.java
%%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.class
%%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.java
%%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.class
%%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.java
%%JAVAJARDIR%%/bbmap/kmer/TableLoaderLockFree$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/ml/ProcessBBMergeHeaders$Header.class
%%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders.class
%%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders.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/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/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/Feature$FeatureComparatorScore.class
%%JAVAJARDIR%%/bbmap/prok/Feature.class
%%JAVAJARDIR%%/bbmap/prok/Feature.java
%%JAVAJARDIR%%/bbmap/prok/FetchProks$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/PGMTools$1.class
%%JAVAJARDIR%%/bbmap/prok/PGMTools.class
%%JAVAJARDIR%%/bbmap/prok/PGMTools.java
%%JAVAJARDIR%%/bbmap/prok/ProkObject.class
%%JAVAJARDIR%%/bbmap/prok/ProkObject.java
%%JAVAJARDIR%%/bbmap/prok/RiboMaker$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$ProcessThread.class
%%JAVAJARDIR%%/bbmap/prok/SplitRibo.class
%%JAVAJARDIR%%/bbmap/prok/SplitRibo.java
%%JAVAJARDIR%%/bbmap/prok/StatsContainer.class
%%JAVAJARDIR%%/bbmap/prok/StatsContainer.java
%%JAVAJARDIR%%/bbmap/server/PercentEncoding.class
%%JAVAJARDIR%%/bbmap/server/PercentEncoding.java
%%JAVAJARDIR%%/bbmap/server/ServerTools.class
%%JAVAJARDIR%%/bbmap/server/ServerTools.java
%%JAVAJARDIR%%/bbmap/server/SimpleHttpServer$GetHandler.class
%%JAVAJARDIR%%/bbmap/server/SimpleHttpServer.class
%%JAVAJARDIR%%/bbmap/server/SimpleHttpServer.java
%%JAVAJARDIR%%/bbmap/shared/Colors.class
%%JAVAJARDIR%%/bbmap/shared/Colors.java
%%JAVAJARDIR%%/bbmap/shared/KillSwitch.class
%%JAVAJARDIR%%/bbmap/shared/KillSwitch.java
%%JAVAJARDIR%%/bbmap/shared/MetadataWriter.class
%%JAVAJARDIR%%/bbmap/shared/MetadataWriter.java
%%JAVAJARDIR%%/bbmap/shared/Parse.class
%%JAVAJARDIR%%/bbmap/shared/Parse.java
%%JAVAJARDIR%%/bbmap/shared/Parser.class
%%JAVAJARDIR%%/bbmap/shared/Parser.java
%%JAVAJARDIR%%/bbmap/shared/PreParser.class
%%JAVAJARDIR%%/bbmap/shared/PreParser.java
%%JAVAJARDIR%%/bbmap/shared/Primes.class
%%JAVAJARDIR%%/bbmap/shared/Primes.java
%%JAVAJARDIR%%/bbmap/shared/ReadStats.class
%%JAVAJARDIR%%/bbmap/shared/ReadStats.java
%%JAVAJARDIR%%/bbmap/shared/Shared.class
%%JAVAJARDIR%%/bbmap/shared/Shared.java
%%JAVAJARDIR%%/bbmap/shared/Timer.class
%%JAVAJARDIR%%/bbmap/shared/Timer.java
%%JAVAJARDIR%%/bbmap/shared/Tools.class
%%JAVAJARDIR%%/bbmap/shared/Tools.java
%%JAVAJARDIR%%/bbmap/shared/TrimRead.class
%%JAVAJARDIR%%/bbmap/shared/TrimRead.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/GlocalAligner.class
%%JAVAJARDIR%%/bbmap/sketch/GlocalAligner.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/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$SketchResultsSummary.class
%%JAVAJARDIR%%/bbmap/sketch/SummarizeSketchStats.class
%%JAVAJARDIR%%/bbmap/sketch/SummarizeSketchStats.java
%%JAVAJARDIR%%/bbmap/sketch/Whitelist.class
%%JAVAJARDIR%%/bbmap/sketch/Whitelist.java
%%JAVAJARDIR%%/bbmap/sort/ContigLengthComparator.class
%%JAVAJARDIR%%/bbmap/sort/ContigLengthComparator.java
%%JAVAJARDIR%%/bbmap/sort/MergeSorted.class
%%JAVAJARDIR%%/bbmap/sort/MergeSorted.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparator.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparator.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorFlowcell.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorFlowcell.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorID.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorID.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorList.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorList.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorMapping.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorMapping.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorName.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorName.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorPosition.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorPosition.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorRandom.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorRandom.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTaxa.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTaxa.java
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological.class
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological.java
%%JAVAJARDIR%%/bbmap/sort/ReadErrorComparator.class
%%JAVAJARDIR%%/bbmap/sort/ReadErrorComparator.java
%%JAVAJARDIR%%/bbmap/sort/ReadLengthComparator.class
%%JAVAJARDIR%%/bbmap/sort/ReadLengthComparator.java
%%JAVAJARDIR%%/bbmap/sort/ReadQualityComparator.class
%%JAVAJARDIR%%/bbmap/sort/ReadQualityComparator.java
%%JAVAJARDIR%%/bbmap/sort/Shuffle$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/sort/SortReadsByID$1.class
%%JAVAJARDIR%%/bbmap/sort/SortReadsByID$Block.class
%%JAVAJARDIR%%/bbmap/sort/SortReadsByID.class
%%JAVAJARDIR%%/bbmap/sort/SortReadsByID.java
%%JAVAJARDIR%%/bbmap/star/Ship.class
%%JAVAJARDIR%%/bbmap/star/Ship.java
%%JAVAJARDIR%%/bbmap/star/Simulate.class
%%JAVAJARDIR%%/bbmap/star/Simulate.java
%%JAVAJARDIR%%/bbmap/star/Weapon.class
%%JAVAJARDIR%%/bbmap/star/Weapon.java
%%JAVAJARDIR%%/bbmap/stream/ArrayListSet$Pack.class
%%JAVAJARDIR%%/bbmap/stream/ArrayListSet.class
%%JAVAJARDIR%%/bbmap/stream/ArrayListSet.java
%%JAVAJARDIR%%/bbmap/stream/BufferedMultiCros.class
%%JAVAJARDIR%%/bbmap/stream/BufferedMultiCros.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$ListenThread.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStreamD.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStreamD.java
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadStreamInterface.class
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadStreamInterface.java
%%JAVAJARDIR%%/bbmap/stream/CrisContainer.class
%%JAVAJARDIR%%/bbmap/stream/CrisContainer.java
%%JAVAJARDIR%%/bbmap/stream/CrisWrapper.class
%%JAVAJARDIR%%/bbmap/stream/CrisWrapper.java
%%JAVAJARDIR%%/bbmap/stream/DualCris.class
%%JAVAJARDIR%%/bbmap/stream/DualCris.java
%%JAVAJARDIR%%/bbmap/stream/EmblReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/EmblReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/FASTQ.class
%%JAVAJARDIR%%/bbmap/stream/FASTQ.java
%%JAVAJARDIR%%/bbmap/stream/FastaQualReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/FastaQualReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/FastaReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/FastaReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/FastaShredInputStream.class
%%JAVAJARDIR%%/bbmap/stream/FastaShredInputStream.java
%%JAVAJARDIR%%/bbmap/stream/FastqReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/FastqReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/GbkReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/GbkReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/Header.class
%%JAVAJARDIR%%/bbmap/stream/Header.java
%%JAVAJARDIR%%/bbmap/stream/HeaderInputStream.class
%%JAVAJARDIR%%/bbmap/stream/HeaderInputStream.java
%%JAVAJARDIR%%/bbmap/stream/MDWalker.class
%%JAVAJARDIR%%/bbmap/stream/MDWalker.java
%%JAVAJARDIR%%/bbmap/stream/MultiCros.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros.java
%%JAVAJARDIR%%/bbmap/stream/MultiCros2$Buffer.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros2.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros2.java
%%JAVAJARDIR%%/bbmap/stream/MultiCros3$Buffer.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros3.class
%%JAVAJARDIR%%/bbmap/stream/MultiCros3.java
%%JAVAJARDIR%%/bbmap/stream/NullOutputStream.class
%%JAVAJARDIR%%/bbmap/stream/NullOutputStream.java
%%JAVAJARDIR%%/bbmap/stream/OnelineReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/OnelineReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/RTextInputStream.class
%%JAVAJARDIR%%/bbmap/stream/RTextInputStream.java
%%JAVAJARDIR%%/bbmap/stream/RandomReadInputStream3.class
%%JAVAJARDIR%%/bbmap/stream/RandomReadInputStream3.java
%%JAVAJARDIR%%/bbmap/stream/Read.class
%%JAVAJARDIR%%/bbmap/stream/Read.java
%%JAVAJARDIR%%/bbmap/stream/ReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/ReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/ReadStreamByteWriter.class
%%JAVAJARDIR%%/bbmap/stream/ReadStreamByteWriter.java
%%JAVAJARDIR%%/bbmap/stream/ReadStreamWriter$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/SamLine.class
%%JAVAJARDIR%%/bbmap/stream/SamLine.java
%%JAVAJARDIR%%/bbmap/stream/SamLineStreamer$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/SamLineStreamer.class
%%JAVAJARDIR%%/bbmap/stream/SamLineStreamer.java
%%JAVAJARDIR%%/bbmap/stream/SamReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/SamReadInputStream.java
%%JAVAJARDIR%%/bbmap/stream/SamReadStreamer$ProcessThread.class
%%JAVAJARDIR%%/bbmap/stream/SamReadStreamer.class
%%JAVAJARDIR%%/bbmap/stream/SamReadStreamer.java
%%JAVAJARDIR%%/bbmap/stream/SamStreamer.class
%%JAVAJARDIR%%/bbmap/stream/SamStreamer.java
%%JAVAJARDIR%%/bbmap/stream/SamStreamerMF.class
%%JAVAJARDIR%%/bbmap/stream/SamStreamerMF.java
%%JAVAJARDIR%%/bbmap/stream/SamStreamerWrapper.class
%%JAVAJARDIR%%/bbmap/stream/SamStreamerWrapper.java
%%JAVAJARDIR%%/bbmap/stream/ScaffoldCoordinates.class
%%JAVAJARDIR%%/bbmap/stream/ScaffoldCoordinates.java
%%JAVAJARDIR%%/bbmap/stream/ScarfReadInputStream.class
%%JAVAJARDIR%%/bbmap/stream/ScarfReadInputStream.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/structures/AbstractBitSet.class
%%JAVAJARDIR%%/bbmap/structures/AbstractBitSet.java
%%JAVAJARDIR%%/bbmap/structures/AbstractIntHashMap.class
%%JAVAJARDIR%%/bbmap/structures/AbstractIntHashMap.java
%%JAVAJARDIR%%/bbmap/structures/AtomicBitSet.class
%%JAVAJARDIR%%/bbmap/structures/AtomicBitSet.java
%%JAVAJARDIR%%/bbmap/structures/ByteBuilder.class
%%JAVAJARDIR%%/bbmap/structures/ByteBuilder.java
%%JAVAJARDIR%%/bbmap/structures/CoverageArray.class
%%JAVAJARDIR%%/bbmap/structures/CoverageArray.java
%%JAVAJARDIR%%/bbmap/structures/CoverageArray2.class
%%JAVAJARDIR%%/bbmap/structures/CoverageArray2.java
%%JAVAJARDIR%%/bbmap/structures/CoverageArray3.class
%%JAVAJARDIR%%/bbmap/structures/CoverageArray3.java
%%JAVAJARDIR%%/bbmap/structures/CoverageArray3A.class
%%JAVAJARDIR%%/bbmap/structures/CoverageArray3A.java
%%JAVAJARDIR%%/bbmap/structures/DoubleList.class
%%JAVAJARDIR%%/bbmap/structures/DoubleList.java
%%JAVAJARDIR%%/bbmap/structures/EntropyTracker.class
%%JAVAJARDIR%%/bbmap/structures/EntropyTracker.java
%%JAVAJARDIR%%/bbmap/structures/FloatList.class
%%JAVAJARDIR%%/bbmap/structures/FloatList.java
%%JAVAJARDIR%%/bbmap/structures/Heap.class
%%JAVAJARDIR%%/bbmap/structures/Heap.java
%%JAVAJARDIR%%/bbmap/structures/IntHashMap.class
%%JAVAJARDIR%%/bbmap/structures/IntHashMap.java
%%JAVAJARDIR%%/bbmap/structures/IntHashMapBinary.class
%%JAVAJARDIR%%/bbmap/structures/IntHashMapBinary.java
%%JAVAJARDIR%%/bbmap/structures/IntHashSet.class
%%JAVAJARDIR%%/bbmap/structures/IntHashSet.java
%%JAVAJARDIR%%/bbmap/structures/IntHashSetList.class
%%JAVAJARDIR%%/bbmap/structures/IntHashSetList.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/ListNum.class
%%JAVAJARDIR%%/bbmap/structures/ListNum.java
%%JAVAJARDIR%%/bbmap/structures/LongHashMap.class
%%JAVAJARDIR%%/bbmap/structures/LongHashMap.java
%%JAVAJARDIR%%/bbmap/structures/LongHashSet.class
%%JAVAJARDIR%%/bbmap/structures/LongHashSet.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/LongListSet$LongListSetIterator.class
%%JAVAJARDIR%%/bbmap/structures/LongListSet.class
%%JAVAJARDIR%%/bbmap/structures/LongListSet.java
%%JAVAJARDIR%%/bbmap/structures/LongLongHashMap.class
%%JAVAJARDIR%%/bbmap/structures/LongLongHashMap.java
%%JAVAJARDIR%%/bbmap/structures/LongM.class
%%JAVAJARDIR%%/bbmap/structures/LongM.java
%%JAVAJARDIR%%/bbmap/structures/LongPair.class
%%JAVAJARDIR%%/bbmap/structures/LongPair.java
%%JAVAJARDIR%%/bbmap/structures/MultiBitSet.class
%%JAVAJARDIR%%/bbmap/structures/MultiBitSet.java
%%JAVAJARDIR%%/bbmap/structures/PolymerTracker.class
%%JAVAJARDIR%%/bbmap/structures/PolymerTracker.java
%%JAVAJARDIR%%/bbmap/structures/Quantizer.class
%%JAVAJARDIR%%/bbmap/structures/Quantizer.java
%%JAVAJARDIR%%/bbmap/structures/Range.class
%%JAVAJARDIR%%/bbmap/structures/Range.java
%%JAVAJARDIR%%/bbmap/structures/RawBitSet.class
%%JAVAJARDIR%%/bbmap/structures/RawBitSet.java
%%JAVAJARDIR%%/bbmap/structures/StringNum.class
%%JAVAJARDIR%%/bbmap/structures/StringNum.java
%%JAVAJARDIR%%/bbmap/structures/StringPair.class
%%JAVAJARDIR%%/bbmap/structures/StringPair.java
%%JAVAJARDIR%%/bbmap/structures/SuperLongList.class
%%JAVAJARDIR%%/bbmap/structures/SuperLongList.java
%%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid$HashThread.class
%%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid.class
%%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid.java
%%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid_old$HashThread.class
%%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid_old.class
%%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid_old.java
%%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession$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/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/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/PrintTaxonomy.class
%%JAVAJARDIR%%/bbmap/tax/PrintTaxonomy.java
%%JAVAJARDIR%%/bbmap/tax/Query.class
%%JAVAJARDIR%%/bbmap/tax/Query.java
%%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$TaxHandler.class
%%JAVAJARDIR%%/bbmap/tax/TaxServer.class
%%JAVAJARDIR%%/bbmap/tax/TaxServer.java
%%JAVAJARDIR%%/bbmap/tax/TaxSize.class
%%JAVAJARDIR%%/bbmap/tax/TaxSize.java
%%JAVAJARDIR%%/bbmap/tax/TaxTree.class
%%JAVAJARDIR%%/bbmap/tax/TaxTree.java
%%JAVAJARDIR%%/bbmap/template/A_Sample.class
%%JAVAJARDIR%%/bbmap/template/A_Sample.java
%%JAVAJARDIR%%/bbmap/template/A_Sample2.class
%%JAVAJARDIR%%/bbmap/template/A_Sample2.java
%%JAVAJARDIR%%/bbmap/template/A_SampleBasic.class
%%JAVAJARDIR%%/bbmap/template/A_SampleBasic.java
%%JAVAJARDIR%%/bbmap/template/A_SampleBasic2.class
%%JAVAJARDIR%%/bbmap/template/A_SampleBasic2.java
%%JAVAJARDIR%%/bbmap/template/A_SampleByteFile.class
%%JAVAJARDIR%%/bbmap/template/A_SampleByteFile.java
%%JAVAJARDIR%%/bbmap/template/A_SampleD.class
%%JAVAJARDIR%%/bbmap/template/A_SampleD.java
%%JAVAJARDIR%%/bbmap/template/A_SampleMT$ProcessThread.class
%%JAVAJARDIR%%/bbmap/template/A_SampleMT.class
%%JAVAJARDIR%%/bbmap/template/A_SampleMT.java
%%JAVAJARDIR%%/bbmap/template/A_SampleSamStreamer$ProcessThread.class
%%JAVAJARDIR%%/bbmap/template/A_SampleSamStreamer.class
%%JAVAJARDIR%%/bbmap/template/A_SampleSamStreamer.java
%%JAVAJARDIR%%/bbmap/template/A_SampleSummary.class
%%JAVAJARDIR%%/bbmap/template/A_SampleSummary.java
%%JAVAJARDIR%%/bbmap/template/A_Sample_Generator$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/ThreadPoolJob.class
%%JAVAJARDIR%%/bbmap/template/ThreadPoolJob.java
%%JAVAJARDIR%%/bbmap/template/ThreadWaiter.class
%%JAVAJARDIR%%/bbmap/template/ThreadWaiter.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/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/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/ApplyVariants.class
%%JAVAJARDIR%%/bbmap/var2/ApplyVariants.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/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/MergeSamples$MergeThread.class
%%JAVAJARDIR%%/bbmap/var2/MergeSamples.class
%%JAVAJARDIR%%/bbmap/var2/MergeSamples.java
%%JAVAJARDIR%%/bbmap/var2/Realign$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/SamFilter.class
%%JAVAJARDIR%%/bbmap/var2/SamFilter.java
%%JAVAJARDIR%%/bbmap/var2/ScafMap.class
%%JAVAJARDIR%%/bbmap/var2/ScafMap.java
%%JAVAJARDIR%%/bbmap/var2/Scaffold.class
%%JAVAJARDIR%%/bbmap/var2/Scaffold.java
%%JAVAJARDIR%%/bbmap/var2/SoftClipper.class
%%JAVAJARDIR%%/bbmap/var2/SoftClipper.java
%%JAVAJARDIR%%/bbmap/var2/VCFFile$1.class
%%JAVAJARDIR%%/bbmap/var2/VCFFile.class
%%JAVAJARDIR%%/bbmap/var2/VCFFile.java
%%JAVAJARDIR%%/bbmap/var2/VCFLine.class
%%JAVAJARDIR%%/bbmap/var2/VCFLine.java
%%JAVAJARDIR%%/bbmap/var2/Var.class
%%JAVAJARDIR%%/bbmap/var2/Var.java
%%JAVAJARDIR%%/bbmap/var2/VarFilter.class
%%JAVAJARDIR%%/bbmap/var2/VarFilter.java
%%JAVAJARDIR%%/bbmap/var2/VarKey.class
%%JAVAJARDIR%%/bbmap/var2/VarKey.java
%%JAVAJARDIR%%/bbmap/var2/VarMap$ProcessThread.class
%%JAVAJARDIR%%/bbmap/var2/VarMap$VarMapIterator.class
%%JAVAJARDIR%%/bbmap/var2/VarMap.class
%%JAVAJARDIR%%/bbmap/var2/VarMap.java
%%JAVAJARDIR%%/bbmap/var2/VcfLoader$ProcessThread.class
%%JAVAJARDIR%%/bbmap/var2/VcfLoader.class
%%JAVAJARDIR%%/bbmap/var2/VcfLoader.java
%%JAVAJARDIR%%/bbmap/var2/VcfWriter$ProcessThread.class
%%JAVAJARDIR%%/bbmap/var2/VcfWriter.class
%%JAVAJARDIR%%/bbmap/var2/VcfWriter.java