bin/Xcalcmem.sh
bin/a_sample_mt.sh
bin/addadapters.sh
bin/addssu.sh
bin/adjusthomopolymers.sh
bin/alltoall.sh
bin/analyzeaccession.sh
bin/analyzegenes.sh
bin/analyzesketchresults.sh
bin/applyvariants.sh
bin/bbcms.sh
bin/bbcountunique.sh
bin/bbcrisprfinder.sh
bin/bbduk.sh
bin/bbest.sh
bin/bbfakereads.sh
bin/bbmap.sh
bin/bbmapskimmer.sh
bin/bbmask.sh
bin/bbmerge-auto.sh
bin/bbmerge.sh
bin/bbnorm.sh
bin/bbrealign.sh
bin/bbrename.sh
bin/bbsketch.sh
bin/bbsort.sh
bin/bbsplit.sh
bin/bbsplitpairs.sh
bin/bbstats.sh
bin/bbversion.sh
bin/bbwrap.sh
bin/bloomfilter.sh
bin/bloomfilterparser.sh
bin/build_env_setup.sh
bin/calcmem.sh
bin/calctruequality.sh
bin/callgenes.sh
bin/callpeaks.sh
bin/callvariants.sh
bin/callvariants2.sh
bin/cg2illumina.sh
bin/checkstrand.sh
bin/clumpify.sh
bin/commonkmers.sh
bin/comparegff.sh
bin/comparelabels.sh
bin/comparesketch.sh
bin/comparessu.sh
bin/comparevcf.sh
bin/conda_build.sh
bin/consect.sh
bin/consensus.sh
bin/copyfile.sh
bin/countbarcodes.sh
bin/countbarcodes2.sh
bin/countduplicates.sh
bin/countgc.sh
bin/countsharedlines.sh
bin/crossblock.sh
bin/crosscontaminate.sh
bin/cutgff.sh
bin/cutprimers.sh
bin/decontaminate.sh
bin/dedupe.sh
bin/dedupe2.sh
bin/dedupebymapping.sh
bin/demuxbyname.sh
bin/demuxserver.sh
bin/diskbench.sh
bin/estherfilter.sh
bin/explodetree.sh
bin/fetchproks.sh
bin/filterassemblysummary.sh
bin/filterbarcodes.sh
bin/filterbycoverage.sh
bin/filterbyname.sh
bin/filterbysequence.sh
bin/filterbytaxa.sh
bin/filterbytile.sh
bin/filterlines.sh
bin/filterqc.sh
bin/filtersam.sh
bin/filtersilva.sh
bin/filtersubs.sh
bin/filtervcf.sh
bin/findrepeats.sh
bin/fixgaps.sh
bin/fungalrelease.sh
bin/fuse.sh
bin/gbff2gff.sh
bin/getreads.sh
bin/gi2ancestors.sh
bin/gi2taxid.sh
bin/gitable.sh
bin/grademerge.sh
bin/gradesam.sh
bin/icecreamfinder.sh
bin/icecreamgrader.sh
bin/icecreammaker.sh
bin/idmatrix.sh
bin/idtree.sh
bin/invertkey.sh
bin/kapastats.sh
bin/kcompress.sh
bin/keepbestcopy.sh
bin/khist.sh
bin/kmercountexact.sh
bin/kmercountmulti.sh
bin/kmercoverage.sh
bin/kmerfilterset.sh
bin/kmerlimit.sh
bin/kmerlimit2.sh
bin/kmerposition.sh
bin/kmutate.sh
bin/lilypad.sh
bin/loadreads.sh
bin/loglog.sh
bin/makechimeras.sh
bin/makecontaminatedgenomes.sh
bin/makepolymers.sh
bin/mapPacBio.sh
bin/matrixtocolumns.sh
bin/mergeOTUs.sh
bin/mergebarcodes.sh
bin/mergepgm.sh
bin/mergeribo.sh
bin/mergesam.sh
bin/mergesketch.sh
bin/mergesorted.sh
bin/msa.sh
bin/mutate.sh
bin/muxbyname.sh
bin/netfilter.sh
bin/novademux.sh
bin/partition.sh
bin/phylip2fasta.sh
bin/pileup.sh
bin/pileup2.sh
bin/plotflowcell.sh
bin/plotgc.sh
bin/plotreadposition.sh
bin/postfilter.sh
bin/printtime.sh
bin/processfrag.sh
bin/processhi-c.sh
bin/processspeed.sh
bin/randomgenome.sh
bin/randomreads.sh
bin/readlength.sh
bin/readqc.sh
bin/reducesilva.sh
bin/reformat.sh
bin/reformatpb.sh
bin/removebadbarcodes.sh
bin/removecatdogmousehuman.sh
bin/removehuman.sh
bin/removehuman2.sh
bin/removemicrobes.sh
bin/removesmartbell.sh
bin/rename.sh
bin/renameimg.sh
bin/repair.sh
bin/replaceheaders.sh
bin/representative.sh
bin/rqcfilter.sh
bin/rqcfilter2.sh
bin/runhmm.sh
bin/samtoroc.sh
bin/scoresequence.sh
bin/seal.sh
bin/sendsketch.sh
bin/seqtovec.sh
bin/shred.sh
bin/shrinkaccession.sh
bin/shuffle.sh
bin/shuffle2.sh
bin/sketch.sh
bin/sketchblacklist.sh
bin/sketchblacklist2.sh
bin/sortbyname.sh
bin/splitbytaxa.sh
bin/splitnextera.sh
bin/splitribo.sh
bin/splitsam.sh
bin/splitsam4way.sh
bin/splitsam6way.sh
bin/stats.sh
bin/statswrapper.sh
bin/streamsam.sh
bin/subsketch.sh
bin/summarizecontam.sh
bin/summarizecoverage.sh
bin/summarizecrossblock.sh
bin/summarizemerge.sh
bin/summarizequast.sh
bin/summarizescafstats.sh
bin/summarizeseal.sh
bin/summarizesketch.sh
bin/synthmda.sh
bin/tadpipe.sh
bin/tadpole.sh
bin/tadwrapper.sh
bin/tagandmerge.sh
bin/taxonomy.sh
bin/taxserver.sh
bin/taxsize.sh
bin/taxtree.sh
bin/testfilesystem.sh
bin/testformat.sh
bin/testformat2.sh
bin/tetramerfreq.sh
bin/textfile.sh
bin/train.sh
bin/translate6frames.sh
bin/unicode2ascii.sh
bin/unzip.sh
bin/vcf2gff.sh
bin/webcheck.sh
opt/bbmap-39.08-0/README.md
opt/bbmap-39.08-0/Xcalcmem.sh
opt/bbmap-39.08-0/a_sample_mt.sh
opt/bbmap-39.08-0/addadapters.sh
opt/bbmap-39.08-0/addssu.sh
opt/bbmap-39.08-0/adjusthomopolymers.sh
opt/bbmap-39.08-0/alltoall.sh
opt/bbmap-39.08-0/analyzeaccession.sh
opt/bbmap-39.08-0/analyzegenes.sh
opt/bbmap-39.08-0/analyzesketchresults.sh
opt/bbmap-39.08-0/applyvariants.sh
opt/bbmap-39.08-0/bbcms.sh
opt/bbmap-39.08-0/bbcountunique.sh
opt/bbmap-39.08-0/bbcrisprfinder.sh
opt/bbmap-39.08-0/bbduk.sh
opt/bbmap-39.08-0/bbest.sh
opt/bbmap-39.08-0/bbfakereads.sh
opt/bbmap-39.08-0/bbmap.sh
opt/bbmap-39.08-0/bbmapskimmer.sh
opt/bbmap-39.08-0/bbmask.sh
opt/bbmap-39.08-0/bbmerge-auto.sh
opt/bbmap-39.08-0/bbmerge.sh
opt/bbmap-39.08-0/bbnorm.sh
opt/bbmap-39.08-0/bbrealign.sh
opt/bbmap-39.08-0/bbrename.sh
opt/bbmap-39.08-0/bbsketch.sh
opt/bbmap-39.08-0/bbsort.sh
opt/bbmap-39.08-0/bbsplit.sh
opt/bbmap-39.08-0/bbsplitpairs.sh
opt/bbmap-39.08-0/bbstats.sh
opt/bbmap-39.08-0/bbversion.sh
opt/bbmap-39.08-0/bbwrap.sh
opt/bbmap-39.08-0/bitbucket-pipelines.yml
opt/bbmap-39.08-0/bloomfilter.sh
opt/bbmap-39.08-0/bloomfilterparser.sh
opt/bbmap-39.08-0/build_env_setup.sh
opt/bbmap-39.08-0/calcmem.sh
opt/bbmap-39.08-0/calctruequality.sh
opt/bbmap-39.08-0/callgenes.sh
opt/bbmap-39.08-0/callpeaks.sh
opt/bbmap-39.08-0/callvariants.sh
opt/bbmap-39.08-0/callvariants2.sh
opt/bbmap-39.08-0/cg2illumina.sh
opt/bbmap-39.08-0/checkstrand.sh
opt/bbmap-39.08-0/clumpify.sh
opt/bbmap-39.08-0/commonkmers.sh
opt/bbmap-39.08-0/comparegff.sh
opt/bbmap-39.08-0/comparelabels.sh
opt/bbmap-39.08-0/comparesketch.sh
opt/bbmap-39.08-0/comparessu.sh
opt/bbmap-39.08-0/comparevcf.sh
opt/bbmap-39.08-0/conda_build.sh
opt/bbmap-39.08-0/config/cluster16s.txt
opt/bbmap-39.08-0/config/filter16s.txt
opt/bbmap-39.08-0/config/histograms.txt
opt/bbmap-39.08-0/config/recalibrate.txt
opt/bbmap-39.08-0/config/rnaseq.txt
opt/bbmap-39.08-0/config/trimadapters.txt
opt/bbmap-39.08-0/consect.sh
opt/bbmap-39.08-0/consensus.sh
opt/bbmap-39.08-0/copyfile.sh
opt/bbmap-39.08-0/countbarcodes.sh
opt/bbmap-39.08-0/countbarcodes2.sh
opt/bbmap-39.08-0/countduplicates.sh
opt/bbmap-39.08-0/countgc.sh
opt/bbmap-39.08-0/countsharedlines.sh
opt/bbmap-39.08-0/crossblock.sh
opt/bbmap-39.08-0/crosscontaminate.sh
opt/bbmap-39.08-0/current/align2/AbstractIndex.class
opt/bbmap-39.08-0/current/align2/AbstractIndex.java
opt/bbmap-39.08-0/current/align2/AbstractMapThread.class
opt/bbmap-39.08-0/current/align2/AbstractMapThread.java
opt/bbmap-39.08-0/current/align2/AbstractMapper.class
opt/bbmap-39.08-0/current/align2/AbstractMapper.java
opt/bbmap-39.08-0/current/align2/BBIndex.class
opt/bbmap-39.08-0/current/align2/BBIndex.java
opt/bbmap-39.08-0/current/align2/BBIndex5.class
opt/bbmap-39.08-0/current/align2/BBIndex5.java
opt/bbmap-39.08-0/current/align2/BBIndexAcc.class
opt/bbmap-39.08-0/current/align2/BBIndexAcc.java
opt/bbmap-39.08-0/current/align2/BBIndexPacBio.class
opt/bbmap-39.08-0/current/align2/BBIndexPacBio.java
opt/bbmap-39.08-0/current/align2/BBIndexPacBioSkimmer.class
opt/bbmap-39.08-0/current/align2/BBIndexPacBioSkimmer.java
opt/bbmap-39.08-0/current/align2/BBMap.class
opt/bbmap-39.08-0/current/align2/BBMap.java
opt/bbmap-39.08-0/current/align2/BBMap5.class
opt/bbmap-39.08-0/current/align2/BBMap5.java
opt/bbmap-39.08-0/current/align2/BBMapAcc.class
opt/bbmap-39.08-0/current/align2/BBMapAcc.java
opt/bbmap-39.08-0/current/align2/BBMapPacBio.class
opt/bbmap-39.08-0/current/align2/BBMapPacBio.java
opt/bbmap-39.08-0/current/align2/BBMapPacBioSkimmer.class
opt/bbmap-39.08-0/current/align2/BBMapPacBioSkimmer.java
opt/bbmap-39.08-0/current/align2/BBMapThread$1.class
opt/bbmap-39.08-0/current/align2/BBMapThread.class
opt/bbmap-39.08-0/current/align2/BBMapThread.java
opt/bbmap-39.08-0/current/align2/BBMapThread5$1.class
opt/bbmap-39.08-0/current/align2/BBMapThread5.class
opt/bbmap-39.08-0/current/align2/BBMapThread5.java
opt/bbmap-39.08-0/current/align2/BBMapThreadAcc$1.class
opt/bbmap-39.08-0/current/align2/BBMapThreadAcc.class
opt/bbmap-39.08-0/current/align2/BBMapThreadAcc.java
opt/bbmap-39.08-0/current/align2/BBMapThreadPacBio$1.class
opt/bbmap-39.08-0/current/align2/BBMapThreadPacBio.class
opt/bbmap-39.08-0/current/align2/BBMapThreadPacBio.java
opt/bbmap-39.08-0/current/align2/BBMapThreadPacBioSkimmer.class
opt/bbmap-39.08-0/current/align2/BBMapThreadPacBioSkimmer.java
opt/bbmap-39.08-0/current/align2/BBSplitter$1.class
opt/bbmap-39.08-0/current/align2/BBSplitter$SetCount.class
opt/bbmap-39.08-0/current/align2/BBSplitter.class
opt/bbmap-39.08-0/current/align2/BBSplitter.java
opt/bbmap-39.08-0/current/align2/BBWrap.class
opt/bbmap-39.08-0/current/align2/BBWrap.java
opt/bbmap-39.08-0/current/align2/BandedAligner.class
opt/bbmap-39.08-0/current/align2/BandedAligner.java
opt/bbmap-39.08-0/current/align2/BandedAlignerConcrete.class
opt/bbmap-39.08-0/current/align2/BandedAlignerConcrete.java
opt/bbmap-39.08-0/current/align2/BandedAlignerJNI.class
opt/bbmap-39.08-0/current/align2/BandedAlignerJNI.java
opt/bbmap-39.08-0/current/align2/Blacklist.class
opt/bbmap-39.08-0/current/align2/Blacklist.java
opt/bbmap-39.08-0/current/align2/Block.class
opt/bbmap-39.08-0/current/align2/Block.java
opt/bbmap-39.08-0/current/align2/ChromLoadThread.class
opt/bbmap-39.08-0/current/align2/ChromLoadThread.java
opt/bbmap-39.08-0/current/align2/CompareSamFiles$1.class
opt/bbmap-39.08-0/current/align2/CompareSamFiles.class
opt/bbmap-39.08-0/current/align2/CompareSamFiles.java
opt/bbmap-39.08-0/current/align2/CompressString.class
opt/bbmap-39.08-0/current/align2/CompressString.java
opt/bbmap-39.08-0/current/align2/GapTools$Range.class
opt/bbmap-39.08-0/current/align2/GapTools.class
opt/bbmap-39.08-0/current/align2/GapTools.java
opt/bbmap-39.08-0/current/align2/GradeSamFile$1.class
opt/bbmap-39.08-0/current/align2/GradeSamFile.class
opt/bbmap-39.08-0/current/align2/GradeSamFile.java
opt/bbmap-39.08-0/current/align2/Index.class
opt/bbmap-39.08-0/current/align2/Index.java
opt/bbmap-39.08-0/current/align2/IndexMaker4$BlockMaker$CountThread.class
opt/bbmap-39.08-0/current/align2/IndexMaker4$BlockMaker.class
opt/bbmap-39.08-0/current/align2/IndexMaker4.class
opt/bbmap-39.08-0/current/align2/IndexMaker4.java
opt/bbmap-39.08-0/current/align2/IndexMaker5$BlockMaker$CountThread.class
opt/bbmap-39.08-0/current/align2/IndexMaker5$BlockMaker.class
opt/bbmap-39.08-0/current/align2/IndexMaker5.class
opt/bbmap-39.08-0/current/align2/IndexMaker5.java
opt/bbmap-39.08-0/current/align2/KeyRing.class
opt/bbmap-39.08-0/current/align2/KeyRing.java
opt/bbmap-39.08-0/current/align2/MSA.class
opt/bbmap-39.08-0/current/align2/MSA.java
opt/bbmap-39.08-0/current/align2/MakeQualityHistogram.class
opt/bbmap-39.08-0/current/align2/MakeQualityHistogram.java
opt/bbmap-39.08-0/current/align2/MakeRocCurve$1.class
opt/bbmap-39.08-0/current/align2/MakeRocCurve.class
opt/bbmap-39.08-0/current/align2/MakeRocCurve.java
opt/bbmap-39.08-0/current/align2/MultiStateAligner10ts.class
opt/bbmap-39.08-0/current/align2/MultiStateAligner10ts.java
opt/bbmap-39.08-0/current/align2/MultiStateAligner11ts.class
opt/bbmap-39.08-0/current/align2/MultiStateAligner11ts.java
opt/bbmap-39.08-0/current/align2/MultiStateAligner11tsJNI.class
opt/bbmap-39.08-0/current/align2/MultiStateAligner11tsJNI.java
opt/bbmap-39.08-0/current/align2/MultiStateAligner9Flat.class
opt/bbmap-39.08-0/current/align2/MultiStateAligner9Flat.java
opt/bbmap-39.08-0/current/align2/MultiStateAligner9PacBio.class
opt/bbmap-39.08-0/current/align2/MultiStateAligner9PacBio.java
opt/bbmap-39.08-0/current/align2/MultiStateAligner9XFlat.class
opt/bbmap-39.08-0/current/align2/MultiStateAligner9XFlat.java
opt/bbmap-39.08-0/current/align2/MultiStateAligner9ts.class
opt/bbmap-39.08-0/current/align2/MultiStateAligner9ts.java
opt/bbmap-39.08-0/current/align2/NeedlemanWunsch.class
opt/bbmap-39.08-0/current/align2/NeedlemanWunsch.java
opt/bbmap-39.08-0/current/align2/PackedHeap.class
opt/bbmap-39.08-0/current/align2/PackedHeap.java
opt/bbmap-39.08-0/current/align2/Pointer.class
opt/bbmap-39.08-0/current/align2/Pointer.java
opt/bbmap-39.08-0/current/align2/PrintTime.class
opt/bbmap-39.08-0/current/align2/PrintTime.java
opt/bbmap-39.08-0/current/align2/Quad.class
opt/bbmap-39.08-0/current/align2/Quad.java
opt/bbmap-39.08-0/current/align2/Quad64.class
opt/bbmap-39.08-0/current/align2/Quad64.java
opt/bbmap-39.08-0/current/align2/Quad64Heap.class
opt/bbmap-39.08-0/current/align2/Quad64Heap.java
opt/bbmap-39.08-0/current/align2/QuadHeap.class
opt/bbmap-39.08-0/current/align2/QuadHeap.java
opt/bbmap-39.08-0/current/align2/QualityTools.class
opt/bbmap-39.08-0/current/align2/QualityTools.java
opt/bbmap-39.08-0/current/align2/RandomReads3$1.class
opt/bbmap-39.08-0/current/align2/RandomReads3.class
opt/bbmap-39.08-0/current/align2/RandomReads3.java
opt/bbmap-39.08-0/current/align2/RefToIndex.class
opt/bbmap-39.08-0/current/align2/RefToIndex.java
opt/bbmap-39.08-0/current/align2/ReformatBatchOutput.class
opt/bbmap-39.08-0/current/align2/ReformatBatchOutput.java
opt/bbmap-39.08-0/current/align2/ReformatBatchOutput2.class
opt/bbmap-39.08-0/current/align2/ReformatBatchOutput2.java
opt/bbmap-39.08-0/current/align2/Solver.class
opt/bbmap-39.08-0/current/align2/Solver.java
opt/bbmap-39.08-0/current/align2/SplitMappedReads.class
opt/bbmap-39.08-0/current/align2/SplitMappedReads.java
opt/bbmap-39.08-0/current/align2/TranslateColorspaceRead.class
opt/bbmap-39.08-0/current/align2/TranslateColorspaceRead.java
opt/bbmap-39.08-0/current/aligner/Aligner.class
opt/bbmap-39.08-0/current/aligner/Aligner.java
opt/bbmap-39.08-0/current/aligner/Alignment.class
opt/bbmap-39.08-0/current/aligner/Alignment.java
opt/bbmap-39.08-0/current/aligner/AlignmentResult.class
opt/bbmap-39.08-0/current/aligner/AlignmentResult.java
opt/bbmap-39.08-0/current/aligner/AllToAll$ProcessThread.class
opt/bbmap-39.08-0/current/aligner/AllToAll.class
opt/bbmap-39.08-0/current/aligner/AllToAll.java
opt/bbmap-39.08-0/current/aligner/FlatAligner.class
opt/bbmap-39.08-0/current/aligner/FlatAligner.java
opt/bbmap-39.08-0/current/aligner/FlatAligner2.class
opt/bbmap-39.08-0/current/aligner/FlatAligner2.java
opt/bbmap-39.08-0/current/aligner/MicroAligner.class
opt/bbmap-39.08-0/current/aligner/MicroAligner.java
opt/bbmap-39.08-0/current/aligner/MicroAligner2.class
opt/bbmap-39.08-0/current/aligner/MicroAligner2.java
opt/bbmap-39.08-0/current/aligner/MultiStateAligner9PacBioAdapter.class
opt/bbmap-39.08-0/current/aligner/MultiStateAligner9PacBioAdapter.java
opt/bbmap-39.08-0/current/aligner/MultiStateAligner9PacBioAdapter2.class
opt/bbmap-39.08-0/current/aligner/MultiStateAligner9PacBioAdapter2.java
opt/bbmap-39.08-0/current/aligner/MultiStateAligner9PacBioAdapter3.class
opt/bbmap-39.08-0/current/aligner/MultiStateAligner9PacBioAdapter3.java
opt/bbmap-39.08-0/current/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.class
opt/bbmap-39.08-0/current/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.java
opt/bbmap-39.08-0/current/aligner/SingleStateAlignerFlat.class
opt/bbmap-39.08-0/current/aligner/SingleStateAlignerFlat.java
opt/bbmap-39.08-0/current/aligner/SingleStateAlignerFlat2.class
opt/bbmap-39.08-0/current/aligner/SingleStateAlignerFlat2.java
opt/bbmap-39.08-0/current/aligner/SingleStateAlignerFlat2Amino.class
opt/bbmap-39.08-0/current/aligner/SingleStateAlignerFlat2Amino.java
opt/bbmap-39.08-0/current/aligner/SingleStateAlignerFlat2_1D.class
opt/bbmap-39.08-0/current/aligner/SingleStateAlignerFlat2_1D.java
opt/bbmap-39.08-0/current/aligner/SingleStateAlignerFlat3.class
opt/bbmap-39.08-0/current/aligner/SingleStateAlignerFlat3.java
opt/bbmap-39.08-0/current/aligner/SingleStateAlignerFlatFloat.class
opt/bbmap-39.08-0/current/aligner/SingleStateAlignerFlatFloat.java
opt/bbmap-39.08-0/current/aligner/SingleStateAlignerPacBioAdapter.class
opt/bbmap-39.08-0/current/aligner/SingleStateAlignerPacBioAdapter.java
opt/bbmap-39.08-0/current/assemble/AbstractBuildThread.class
opt/bbmap-39.08-0/current/assemble/AbstractBuildThread.java
opt/bbmap-39.08-0/current/assemble/AbstractExploreThread.class
opt/bbmap-39.08-0/current/assemble/AbstractExploreThread.java
opt/bbmap-39.08-0/current/assemble/AbstractProcessContigThread.class
opt/bbmap-39.08-0/current/assemble/AbstractProcessContigThread.java
opt/bbmap-39.08-0/current/assemble/AbstractRemoveThread$RemoveThread1.class
opt/bbmap-39.08-0/current/assemble/AbstractRemoveThread$RemoveThread2.class
opt/bbmap-39.08-0/current/assemble/AbstractRemoveThread.class
opt/bbmap-39.08-0/current/assemble/AbstractRemoveThread.java
opt/bbmap-39.08-0/current/assemble/AbstractShaveThread.class
opt/bbmap-39.08-0/current/assemble/AbstractShaveThread.java
opt/bbmap-39.08-0/current/assemble/BubblePopper.class
opt/bbmap-39.08-0/current/assemble/BubblePopper.java
opt/bbmap-39.08-0/current/assemble/Contig.class
opt/bbmap-39.08-0/current/assemble/Contig.java
opt/bbmap-39.08-0/current/assemble/Edge.class
opt/bbmap-39.08-0/current/assemble/Edge.java
opt/bbmap-39.08-0/current/assemble/ErrorTracker.class
opt/bbmap-39.08-0/current/assemble/ErrorTracker.java
opt/bbmap-39.08-0/current/assemble/KmerCompressor$BuildThread.class
opt/bbmap-39.08-0/current/assemble/KmerCompressor.class
opt/bbmap-39.08-0/current/assemble/KmerCompressor.java
opt/bbmap-39.08-0/current/assemble/Postfilter.class
opt/bbmap-39.08-0/current/assemble/Postfilter.java
opt/bbmap-39.08-0/current/assemble/Rollback.class
opt/bbmap-39.08-0/current/assemble/Rollback.java
opt/bbmap-39.08-0/current/assemble/ShaveObject.class
opt/bbmap-39.08-0/current/assemble/ShaveObject.java
opt/bbmap-39.08-0/current/assemble/Shaver.class
opt/bbmap-39.08-0/current/assemble/Shaver.java
opt/bbmap-39.08-0/current/assemble/Shaver1$ExploreThread.class
opt/bbmap-39.08-0/current/assemble/Shaver1$ShaveThread.class
opt/bbmap-39.08-0/current/assemble/Shaver1.class
opt/bbmap-39.08-0/current/assemble/Shaver1.java
opt/bbmap-39.08-0/current/assemble/Shaver2$ExploreThread.class
opt/bbmap-39.08-0/current/assemble/Shaver2$ShaveThread.class
opt/bbmap-39.08-0/current/assemble/Shaver2.class
opt/bbmap-39.08-0/current/assemble/Shaver2.java
opt/bbmap-39.08-0/current/assemble/TadPipe.class
opt/bbmap-39.08-0/current/assemble/TadPipe.java
opt/bbmap-39.08-0/current/assemble/Tadpole$DumpKmersThread.class
opt/bbmap-39.08-0/current/assemble/Tadpole$ExtendThread.class
opt/bbmap-39.08-0/current/assemble/Tadpole$MakeKhistThread.class
opt/bbmap-39.08-0/current/assemble/Tadpole.class
opt/bbmap-39.08-0/current/assemble/Tadpole.java
opt/bbmap-39.08-0/current/assemble/Tadpole1$BuildThread.class
opt/bbmap-39.08-0/current/assemble/Tadpole1$ProcessContigThread.class
opt/bbmap-39.08-0/current/assemble/Tadpole1.class
opt/bbmap-39.08-0/current/assemble/Tadpole1.java
opt/bbmap-39.08-0/current/assemble/Tadpole2$BuildThread.class
opt/bbmap-39.08-0/current/assemble/Tadpole2$ProcessContigThread.class
opt/bbmap-39.08-0/current/assemble/Tadpole2.class
opt/bbmap-39.08-0/current/assemble/Tadpole2.java
opt/bbmap-39.08-0/current/assemble/TadpoleWrapper$1.class
opt/bbmap-39.08-0/current/assemble/TadpoleWrapper$Record.class
opt/bbmap-39.08-0/current/assemble/TadpoleWrapper.class
opt/bbmap-39.08-0/current/assemble/TadpoleWrapper.java
opt/bbmap-39.08-0/current/barcode/AnalyzeBarcodes.class
opt/bbmap-39.08-0/current/barcode/AnalyzeBarcodes.java
opt/bbmap-39.08-0/current/barcode/Barcode.class
opt/bbmap-39.08-0/current/barcode/Barcode.java
opt/bbmap-39.08-0/current/barcode/BarcodeCounter.class
opt/bbmap-39.08-0/current/barcode/BarcodeCounter.java
opt/bbmap-39.08-0/current/barcode/BarcodeMappingStats.class
opt/bbmap-39.08-0/current/barcode/BarcodeMappingStats.java
opt/bbmap-39.08-0/current/barcode/BarcodeStats.class
opt/bbmap-39.08-0/current/barcode/BarcodeStats.java
opt/bbmap-39.08-0/current/barcode/CompareLabels$Label.class
opt/bbmap-39.08-0/current/barcode/CompareLabels.class
opt/bbmap-39.08-0/current/barcode/CompareLabels.java
opt/bbmap-39.08-0/current/barcode/CorrelateBarcodes.class
opt/bbmap-39.08-0/current/barcode/CorrelateBarcodes.java
opt/bbmap-39.08-0/current/barcode/CountBarcodes.class
opt/bbmap-39.08-0/current/barcode/CountBarcodes.java
opt/bbmap-39.08-0/current/barcode/CountBarcodes2.class
opt/bbmap-39.08-0/current/barcode/CountBarcodes2.java
opt/bbmap-39.08-0/current/barcode/DemuxClient.class
opt/bbmap-39.08-0/current/barcode/DemuxClient.java
opt/bbmap-39.08-0/current/barcode/DemuxData.class
opt/bbmap-39.08-0/current/barcode/DemuxData.java
opt/bbmap-39.08-0/current/barcode/DemuxServer$BaseHandler.class
opt/bbmap-39.08-0/current/barcode/DemuxServer$DemuxHandler.class
opt/bbmap-39.08-0/current/barcode/DemuxServer$IconHandler.class
opt/bbmap-39.08-0/current/barcode/DemuxServer$KillHandler.class
opt/bbmap-39.08-0/current/barcode/DemuxServer$Pair.class
opt/bbmap-39.08-0/current/barcode/DemuxServer$StatsHandler.class
opt/bbmap-39.08-0/current/barcode/DemuxServer.class
opt/bbmap-39.08-0/current/barcode/DemuxServer.java
opt/bbmap-39.08-0/current/barcode/LegacyFileWriter$QTag.class
opt/bbmap-39.08-0/current/barcode/LegacyFileWriter.class
opt/bbmap-39.08-0/current/barcode/LegacyFileWriter.java
opt/bbmap-39.08-0/current/barcode/NovaDemux.class
opt/bbmap-39.08-0/current/barcode/NovaDemux.java
opt/bbmap-39.08-0/current/barcode/PCRMatrix$MapLine.class
opt/bbmap-39.08-0/current/barcode/PCRMatrix.class
opt/bbmap-39.08-0/current/barcode/PCRMatrix.java
opt/bbmap-39.08-0/current/barcode/PCRMatrixHDist$PopThread.class
opt/bbmap-39.08-0/current/barcode/PCRMatrixHDist.class
opt/bbmap-39.08-0/current/barcode/PCRMatrixHDist.java
opt/bbmap-39.08-0/current/barcode/PCRMatrixHDist_old$PopThread.class
opt/bbmap-39.08-0/current/barcode/PCRMatrixHDist_old.class
opt/bbmap-39.08-0/current/barcode/PCRMatrixHDist_old.java
opt/bbmap-39.08-0/current/barcode/TagAndMerge.class
opt/bbmap-39.08-0/current/barcode/TagAndMerge.java
opt/bbmap-39.08-0/current/barcode/Transition.class
opt/bbmap-39.08-0/current/barcode/Transition.java
opt/bbmap-39.08-0/current/barcode/prob/PCRMatrixProb.class
opt/bbmap-39.08-0/current/barcode/prob/PCRMatrixProb.java
opt/bbmap-39.08-0/current/barcode/prob/PCRMatrixProbAbstract.class
opt/bbmap-39.08-0/current/barcode/prob/PCRMatrixProbAbstract.java
opt/bbmap-39.08-0/current/barcode/prob/PCRMatrixTile.class
opt/bbmap-39.08-0/current/barcode/prob/PCRMatrixTile.java
opt/bbmap-39.08-0/current/bbmin/LongHashSet.class
opt/bbmap-39.08-0/current/bbmin/LongHashSet.java
opt/bbmap-39.08-0/current/bbmin/LongList.class
opt/bbmap-39.08-0/current/bbmin/LongList.java
opt/bbmap-39.08-0/current/bbmin/Minimizer.class
opt/bbmap-39.08-0/current/bbmin/Minimizer.java
opt/bbmap-39.08-0/current/bloom/BloomFilter.class
opt/bbmap-39.08-0/current/bloom/BloomFilter.java
opt/bbmap-39.08-0/current/bloom/BloomFilterCorrector.class
opt/bbmap-39.08-0/current/bloom/BloomFilterCorrector.java
opt/bbmap-39.08-0/current/bloom/BloomFilterCorrectorWrapper$ProcessThread.class
opt/bbmap-39.08-0/current/bloom/BloomFilterCorrectorWrapper.class
opt/bbmap-39.08-0/current/bloom/BloomFilterCorrectorWrapper.java
opt/bbmap-39.08-0/current/bloom/BloomFilterWrapper$ProcessThread.class
opt/bbmap-39.08-0/current/bloom/BloomFilterWrapper.class
opt/bbmap-39.08-0/current/bloom/BloomFilterWrapper.java
opt/bbmap-39.08-0/current/bloom/ErrorCorrect$1.class
opt/bbmap-39.08-0/current/bloom/ErrorCorrect.class
opt/bbmap-39.08-0/current/bloom/ErrorCorrect.java
opt/bbmap-39.08-0/current/bloom/IndexCounter$CountThread.class
opt/bbmap-39.08-0/current/bloom/IndexCounter.class
opt/bbmap-39.08-0/current/bloom/IndexCounter.java
opt/bbmap-39.08-0/current/bloom/KCountArray$AllocThread.class
opt/bbmap-39.08-0/current/bloom/KCountArray.class
opt/bbmap-39.08-0/current/bloom/KCountArray.java
opt/bbmap-39.08-0/current/bloom/KCountArray2.class
opt/bbmap-39.08-0/current/bloom/KCountArray2.java
opt/bbmap-39.08-0/current/bloom/KCountArray3.class
opt/bbmap-39.08-0/current/bloom/KCountArray3.java
opt/bbmap-39.08-0/current/bloom/KCountArray4.class
opt/bbmap-39.08-0/current/bloom/KCountArray4.java
opt/bbmap-39.08-0/current/bloom/KCountArray4MT$WriteThread.class
opt/bbmap-39.08-0/current/bloom/KCountArray4MT.class
opt/bbmap-39.08-0/current/bloom/KCountArray4MT.java
opt/bbmap-39.08-0/current/bloom/KCountArray5MT$WriteThread.class
opt/bbmap-39.08-0/current/bloom/KCountArray5MT.class
opt/bbmap-39.08-0/current/bloom/KCountArray5MT.java
opt/bbmap-39.08-0/current/bloom/KCountArray6MT$WriteThread.class
opt/bbmap-39.08-0/current/bloom/KCountArray6MT.class
opt/bbmap-39.08-0/current/bloom/KCountArray6MT.java
opt/bbmap-39.08-0/current/bloom/KCountArray7MT$WriteThread.class
opt/bbmap-39.08-0/current/bloom/KCountArray7MT.class
opt/bbmap-39.08-0/current/bloom/KCountArray7MT.java
opt/bbmap-39.08-0/current/bloom/KCountArray7MTA$CountUsedThread.class
opt/bbmap-39.08-0/current/bloom/KCountArray7MTA.class
opt/bbmap-39.08-0/current/bloom/KCountArray7MTA.java
opt/bbmap-39.08-0/current/bloom/KCountArray8MT$WriteThread.class
opt/bbmap-39.08-0/current/bloom/KCountArray8MT.class
opt/bbmap-39.08-0/current/bloom/KCountArray8MT.java
opt/bbmap-39.08-0/current/bloom/KmerCount3.class
opt/bbmap-39.08-0/current/bloom/KmerCount3.java
opt/bbmap-39.08-0/current/bloom/KmerCount4.class
opt/bbmap-39.08-0/current/bloom/KmerCount4.java
opt/bbmap-39.08-0/current/bloom/KmerCount5.class
opt/bbmap-39.08-0/current/bloom/KmerCount5.java
opt/bbmap-39.08-0/current/bloom/KmerCount6.class
opt/bbmap-39.08-0/current/bloom/KmerCount6.java
opt/bbmap-39.08-0/current/bloom/KmerCountAbstract.class
opt/bbmap-39.08-0/current/bloom/KmerCountAbstract.java
opt/bbmap-39.08-0/current/bloom/LargeKmerCount.class
opt/bbmap-39.08-0/current/bloom/LargeKmerCount.java
opt/bbmap-39.08-0/current/bloom/LargeKmerCount2.class
opt/bbmap-39.08-0/current/bloom/LargeKmerCount2.java
opt/bbmap-39.08-0/current/bloom/ParseBloomFilter.class
opt/bbmap-39.08-0/current/bloom/ParseBloomFilter.java
opt/bbmap-39.08-0/current/bloom/ReadCounter$1.class
opt/bbmap-39.08-0/current/bloom/ReadCounter$CountThread.class
opt/bbmap-39.08-0/current/bloom/ReadCounter.class
opt/bbmap-39.08-0/current/bloom/ReadCounter.java
opt/bbmap-39.08-0/current/bloom/ReadCounter_old$1.class
opt/bbmap-39.08-0/current/bloom/ReadCounter_old$CountThread.class
opt/bbmap-39.08-0/current/bloom/ReadCounter_old.class
opt/bbmap-39.08-0/current/bloom/ReadCounter_old.java
opt/bbmap-39.08-0/current/bloom/TestLargeKmer.class
opt/bbmap-39.08-0/current/bloom/TestLargeKmer.java
opt/bbmap-39.08-0/current/cardinality/BBLog.class
opt/bbmap-39.08-0/current/cardinality/BBLog.java
opt/bbmap-39.08-0/current/cardinality/BBLog_simple.class
opt/bbmap-39.08-0/current/cardinality/BBLog_simple.java
opt/bbmap-39.08-0/current/cardinality/CardinalityTracker.class
opt/bbmap-39.08-0/current/cardinality/CardinalityTracker.java
opt/bbmap-39.08-0/current/cardinality/LogLog.class
opt/bbmap-39.08-0/current/cardinality/LogLog.java
opt/bbmap-39.08-0/current/cardinality/LogLog16.class
opt/bbmap-39.08-0/current/cardinality/LogLog16.java
opt/bbmap-39.08-0/current/cardinality/LogLog2.class
opt/bbmap-39.08-0/current/cardinality/LogLog2.java
opt/bbmap-39.08-0/current/cardinality/LogLog8.class
opt/bbmap-39.08-0/current/cardinality/LogLog8.java
opt/bbmap-39.08-0/current/cardinality/LogLog8_simple.class
opt/bbmap-39.08-0/current/cardinality/LogLog8_simple.java
opt/bbmap-39.08-0/current/cardinality/LogLogWrapper$LogLogThread.class
opt/bbmap-39.08-0/current/cardinality/LogLogWrapper.class
opt/bbmap-39.08-0/current/cardinality/LogLogWrapper.java
opt/bbmap-39.08-0/current/cardinality/LogLog_old$LogLogWrapper$LogLogThread.class
opt/bbmap-39.08-0/current/cardinality/LogLog_old$LogLogWrapper.class
opt/bbmap-39.08-0/current/cardinality/LogLog_old.class
opt/bbmap-39.08-0/current/cardinality/LogLog_old.java
opt/bbmap-39.08-0/current/cardinality/MultiLogLog.class
opt/bbmap-39.08-0/current/cardinality/MultiLogLog.java
opt/bbmap-39.08-0/current/clump/Clump.class
opt/bbmap-39.08-0/current/clump/Clump.java
opt/bbmap-39.08-0/current/clump/ClumpList$ClumpThread.class
opt/bbmap-39.08-0/current/clump/ClumpList$ProcessThread.class
opt/bbmap-39.08-0/current/clump/ClumpList.class
opt/bbmap-39.08-0/current/clump/ClumpList.java
opt/bbmap-39.08-0/current/clump/ClumpTools.class
opt/bbmap-39.08-0/current/clump/ClumpTools.java
opt/bbmap-39.08-0/current/clump/Clumpify.class
opt/bbmap-39.08-0/current/clump/Clumpify.java
opt/bbmap-39.08-0/current/clump/Hasher.class
opt/bbmap-39.08-0/current/clump/Hasher.java
opt/bbmap-39.08-0/current/clump/KmerComparator$HashThread.class
opt/bbmap-39.08-0/current/clump/KmerComparator.class
opt/bbmap-39.08-0/current/clump/KmerComparator.java
opt/bbmap-39.08-0/current/clump/KmerComparator2.class
opt/bbmap-39.08-0/current/clump/KmerComparator2.java
opt/bbmap-39.08-0/current/clump/KmerComparatorX.class
opt/bbmap-39.08-0/current/clump/KmerComparatorX.java
opt/bbmap-39.08-0/current/clump/KmerComparatorY.class
opt/bbmap-39.08-0/current/clump/KmerComparatorY.java
opt/bbmap-39.08-0/current/clump/KmerReduce$HashThread.class
opt/bbmap-39.08-0/current/clump/KmerReduce.class
opt/bbmap-39.08-0/current/clump/KmerReduce.java
opt/bbmap-39.08-0/current/clump/KmerSort$FetchThread1.class
opt/bbmap-39.08-0/current/clump/KmerSort$HashSplitThread.class
opt/bbmap-39.08-0/current/clump/KmerSort.class
opt/bbmap-39.08-0/current/clump/KmerSort.java
opt/bbmap-39.08-0/current/clump/KmerSort1.class
opt/bbmap-39.08-0/current/clump/KmerSort1.java
opt/bbmap-39.08-0/current/clump/KmerSort2.class
opt/bbmap-39.08-0/current/clump/KmerSort2.java
opt/bbmap-39.08-0/current/clump/KmerSort3$FetchThread3$FetchSubThread.class
opt/bbmap-39.08-0/current/clump/KmerSort3$FetchThread3.class
opt/bbmap-39.08-0/current/clump/KmerSort3.class
opt/bbmap-39.08-0/current/clump/KmerSort3.java
opt/bbmap-39.08-0/current/clump/KmerSplit$HashThread.class
opt/bbmap-39.08-0/current/clump/KmerSplit.class
opt/bbmap-39.08-0/current/clump/KmerSplit.java
opt/bbmap-39.08-0/current/clump/PivotSet$HashThread.class
opt/bbmap-39.08-0/current/clump/PivotSet.class
opt/bbmap-39.08-0/current/clump/PivotSet.java
opt/bbmap-39.08-0/current/clump/ReadKey.class
opt/bbmap-39.08-0/current/clump/ReadKey.java
opt/bbmap-39.08-0/current/clump/Splitter.class
opt/bbmap-39.08-0/current/clump/Splitter.java
opt/bbmap-39.08-0/current/clump/StreamToOutput.class
opt/bbmap-39.08-0/current/clump/StreamToOutput.java
opt/bbmap-39.08-0/current/cluster/Cluster.class
opt/bbmap-39.08-0/current/cluster/Cluster.java
opt/bbmap-39.08-0/current/cluster/ClusterTools.class
opt/bbmap-39.08-0/current/cluster/ClusterTools.java
opt/bbmap-39.08-0/current/cluster/MergeReadHeaders.class
opt/bbmap-39.08-0/current/cluster/MergeReadHeaders.java
opt/bbmap-39.08-0/current/cluster/ReadTag.class
opt/bbmap-39.08-0/current/cluster/ReadTag.java
opt/bbmap-39.08-0/current/cluster/ReclusterByKmer$ClusterThread.class
opt/bbmap-39.08-0/current/cluster/ReclusterByKmer.class
opt/bbmap-39.08-0/current/cluster/ReclusterByKmer.java
opt/bbmap-39.08-0/current/consensus/BaseGraph.class
opt/bbmap-39.08-0/current/consensus/BaseGraph.java
opt/bbmap-39.08-0/current/consensus/BaseGraphPart.class
opt/bbmap-39.08-0/current/consensus/BaseGraphPart.java
opt/bbmap-39.08-0/current/consensus/BaseNode.class
opt/bbmap-39.08-0/current/consensus/BaseNode.java
opt/bbmap-39.08-0/current/consensus/ConsensusMaker$ProcessThread.class
opt/bbmap-39.08-0/current/consensus/ConsensusMaker.class
opt/bbmap-39.08-0/current/consensus/ConsensusMaker.java
opt/bbmap-39.08-0/current/consensus/ConsensusObject.class
opt/bbmap-39.08-0/current/consensus/ConsensusObject.java
opt/bbmap-39.08-0/current/consensus/FixScaffoldGaps$ProcessThread.class
opt/bbmap-39.08-0/current/consensus/FixScaffoldGaps$Scaffold.class
opt/bbmap-39.08-0/current/consensus/FixScaffoldGaps.class
opt/bbmap-39.08-0/current/consensus/FixScaffoldGaps.java
opt/bbmap-39.08-0/current/consensus/Lilypad$Contig.class
opt/bbmap-39.08-0/current/consensus/Lilypad$Edge.class
opt/bbmap-39.08-0/current/consensus/Lilypad$ProcessThread.class
opt/bbmap-39.08-0/current/consensus/Lilypad.class
opt/bbmap-39.08-0/current/consensus/Lilypad.java
opt/bbmap-39.08-0/current/covid/SummarizeCoverage.class
opt/bbmap-39.08-0/current/covid/SummarizeCoverage.java
opt/bbmap-39.08-0/current/dna/AminoAcid.class
opt/bbmap-39.08-0/current/dna/AminoAcid.java
opt/bbmap-39.08-0/current/dna/ChromArrayMaker.class
opt/bbmap-39.08-0/current/dna/ChromArrayMaker.java
opt/bbmap-39.08-0/current/dna/ChromToFasta$1.class
opt/bbmap-39.08-0/current/dna/ChromToFasta.class
opt/bbmap-39.08-0/current/dna/ChromToFasta.java
opt/bbmap-39.08-0/current/dna/ChromosomeArray.class
opt/bbmap-39.08-0/current/dna/ChromosomeArray.java
opt/bbmap-39.08-0/current/dna/Data.class
opt/bbmap-39.08-0/current/dna/Data.java
opt/bbmap-39.08-0/current/dna/Exon.class
opt/bbmap-39.08-0/current/dna/Exon.java
opt/bbmap-39.08-0/current/dna/FastaToChromArrays2$1.class
opt/bbmap-39.08-0/current/dna/FastaToChromArrays2.class
opt/bbmap-39.08-0/current/dna/FastaToChromArrays2.java
opt/bbmap-39.08-0/current/dna/Gene.class
opt/bbmap-39.08-0/current/dna/Gene.java
opt/bbmap-39.08-0/current/dna/GeneSet.class
opt/bbmap-39.08-0/current/dna/GeneSet.java
opt/bbmap-39.08-0/current/dna/Matrix.class
opt/bbmap-39.08-0/current/dna/Matrix.java
opt/bbmap-39.08-0/current/dna/Motif.class
opt/bbmap-39.08-0/current/dna/Motif.java
opt/bbmap-39.08-0/current/dna/MotifMulti.class
opt/bbmap-39.08-0/current/dna/MotifMulti.java
opt/bbmap-39.08-0/current/dna/MotifProbsN.class
opt/bbmap-39.08-0/current/dna/MotifProbsN.java
opt/bbmap-39.08-0/current/dna/MotifSimple.class
opt/bbmap-39.08-0/current/dna/MotifSimple.java
opt/bbmap-39.08-0/current/dna/ScafLoc.class
opt/bbmap-39.08-0/current/dna/ScafLoc.java
opt/bbmap-39.08-0/current/dna/Scaffold.class
opt/bbmap-39.08-0/current/dna/Scaffold.java
opt/bbmap-39.08-0/current/driver/BBVersion.class
opt/bbmap-39.08-0/current/driver/BBVersion.java
opt/bbmap-39.08-0/current/driver/ClearRam.class
opt/bbmap-39.08-0/current/driver/ClearRam.java
opt/bbmap-39.08-0/current/driver/CollateSpikeIn.class
opt/bbmap-39.08-0/current/driver/CollateSpikeIn.java
opt/bbmap-39.08-0/current/driver/CompareReferenceGenomes.class
opt/bbmap-39.08-0/current/driver/CompareReferenceGenomes.java
opt/bbmap-39.08-0/current/driver/CompareSequences.class
opt/bbmap-39.08-0/current/driver/CompareSequences.java
opt/bbmap-39.08-0/current/driver/ConcatenateFiles.class
opt/bbmap-39.08-0/current/driver/ConcatenateFiles.java
opt/bbmap-39.08-0/current/driver/ConcatenateTextFiles$1.class
opt/bbmap-39.08-0/current/driver/ConcatenateTextFiles$WriteThread.class
opt/bbmap-39.08-0/current/driver/ConcatenateTextFiles.class
opt/bbmap-39.08-0/current/driver/ConcatenateTextFiles.java
opt/bbmap-39.08-0/current/driver/Concatenator.class
opt/bbmap-39.08-0/current/driver/Concatenator.java
opt/bbmap-39.08-0/current/driver/ConvertSamToAln.class
opt/bbmap-39.08-0/current/driver/ConvertSamToAln.java
opt/bbmap-39.08-0/current/driver/CorrelateIdentity.class
opt/bbmap-39.08-0/current/driver/CorrelateIdentity.java
opt/bbmap-39.08-0/current/driver/CountRNAs.class
opt/bbmap-39.08-0/current/driver/CountRNAs.java
opt/bbmap-39.08-0/current/driver/CountSharedLines.class
opt/bbmap-39.08-0/current/driver/CountSharedLines.java
opt/bbmap-39.08-0/current/driver/EstherFilter.class
opt/bbmap-39.08-0/current/driver/EstherFilter.java
opt/bbmap-39.08-0/current/driver/FilterAssemblySummary.class
opt/bbmap-39.08-0/current/driver/FilterAssemblySummary.java
opt/bbmap-39.08-0/current/driver/FilterLines.class
opt/bbmap-39.08-0/current/driver/FilterLines.java
opt/bbmap-39.08-0/current/driver/FilterReadsByName.class
opt/bbmap-39.08-0/current/driver/FilterReadsByName.java
opt/bbmap-39.08-0/current/driver/FindMotifs.class
opt/bbmap-39.08-0/current/driver/FindMotifs.java
opt/bbmap-39.08-0/current/driver/FixChr.class
opt/bbmap-39.08-0/current/driver/FixChr.java
opt/bbmap-39.08-0/current/driver/FixDumbFile.class
opt/bbmap-39.08-0/current/driver/FixDumbFile.java
opt/bbmap-39.08-0/current/driver/GenerateNoCallsFromCoverage.class
opt/bbmap-39.08-0/current/driver/GenerateNoCallsFromCoverage.java
opt/bbmap-39.08-0/current/driver/GetSequence.class
opt/bbmap-39.08-0/current/driver/GetSequence.java
opt/bbmap-39.08-0/current/driver/GetUniquePrefixes.class
opt/bbmap-39.08-0/current/driver/GetUniquePrefixes.java
opt/bbmap-39.08-0/current/driver/Grep.class
opt/bbmap-39.08-0/current/driver/Grep.java
opt/bbmap-39.08-0/current/driver/Life.class
opt/bbmap-39.08-0/current/driver/Life.java
opt/bbmap-39.08-0/current/driver/LineCount.class
opt/bbmap-39.08-0/current/driver/LineCount.java
opt/bbmap-39.08-0/current/driver/LoadReads.class
opt/bbmap-39.08-0/current/driver/LoadReads.java
opt/bbmap-39.08-0/current/driver/LookAtID.class
opt/bbmap-39.08-0/current/driver/LookAtID.java
opt/bbmap-39.08-0/current/driver/MakeTestScript.class
opt/bbmap-39.08-0/current/driver/MakeTestScript.java
opt/bbmap-39.08-0/current/driver/MakeTestScriptScoreOnly.class
opt/bbmap-39.08-0/current/driver/MakeTestScriptScoreOnly.java
opt/bbmap-39.08-0/current/driver/MeasureGene.class
opt/bbmap-39.08-0/current/driver/MeasureGene.java
opt/bbmap-39.08-0/current/driver/MergeBigelow.class
opt/bbmap-39.08-0/current/driver/MergeBigelow.java
opt/bbmap-39.08-0/current/driver/MergeCoverageOTU.class
opt/bbmap-39.08-0/current/driver/MergeCoverageOTU.java
opt/bbmap-39.08-0/current/driver/MergeTextFiles.class
opt/bbmap-39.08-0/current/driver/MergeTextFiles.java
opt/bbmap-39.08-0/current/driver/MergeTextFiles2.class
opt/bbmap-39.08-0/current/driver/MergeTextFiles2.java
opt/bbmap-39.08-0/current/driver/MoveFiles.class
opt/bbmap-39.08-0/current/driver/MoveFiles.java
opt/bbmap-39.08-0/current/driver/ParseCrossblockResults$ResultsLine.class
opt/bbmap-39.08-0/current/driver/ParseCrossblockResults.class
opt/bbmap-39.08-0/current/driver/ParseCrossblockResults.java
opt/bbmap-39.08-0/current/driver/PlotGC.class
opt/bbmap-39.08-0/current/driver/PlotGC.java
opt/bbmap-39.08-0/current/driver/PrintEnv.class
opt/bbmap-39.08-0/current/driver/PrintEnv.java
opt/bbmap-39.08-0/current/driver/ProcessFragMerging.class
opt/bbmap-39.08-0/current/driver/ProcessFragMerging.java
opt/bbmap-39.08-0/current/driver/ProcessSpeed.class
opt/bbmap-39.08-0/current/driver/ProcessSpeed.java
opt/bbmap-39.08-0/current/driver/ProcessSpeed2.class
opt/bbmap-39.08-0/current/driver/ProcessSpeed2.java
opt/bbmap-39.08-0/current/driver/ProcessWebcheck.class
opt/bbmap-39.08-0/current/driver/ProcessWebcheck.java
opt/bbmap-39.08-0/current/driver/ReduceSilva.class
opt/bbmap-39.08-0/current/driver/ReduceSilva.java
opt/bbmap-39.08-0/current/driver/RenameAndMux$MuxThread.class
opt/bbmap-39.08-0/current/driver/RenameAndMux.class
opt/bbmap-39.08-0/current/driver/RenameAndMux.java
opt/bbmap-39.08-0/current/driver/RenameByHeader.class
opt/bbmap-39.08-0/current/driver/RenameByHeader.java
opt/bbmap-39.08-0/current/driver/RenameNcbiToTid.class
opt/bbmap-39.08-0/current/driver/RenameNcbiToTid.java
opt/bbmap-39.08-0/current/driver/RenameRefseqFiles.class
opt/bbmap-39.08-0/current/driver/RenameRefseqFiles.java
opt/bbmap-39.08-0/current/driver/Sample.class
opt/bbmap-39.08-0/current/driver/Sample.java
opt/bbmap-39.08-0/current/driver/Search.class
opt/bbmap-39.08-0/current/driver/Search.java
opt/bbmap-39.08-0/current/driver/SelectReads.class
opt/bbmap-39.08-0/current/driver/SelectReads.java
opt/bbmap-39.08-0/current/driver/SniffSplices.class
opt/bbmap-39.08-0/current/driver/SniffSplices.java
opt/bbmap-39.08-0/current/driver/SummarizeContamReport$ComparatorA.class
opt/bbmap-39.08-0/current/driver/SummarizeContamReport$ComparatorB.class
opt/bbmap-39.08-0/current/driver/SummarizeContamReport$StringLongLong.class
opt/bbmap-39.08-0/current/driver/SummarizeContamReport.class
opt/bbmap-39.08-0/current/driver/SummarizeContamReport.java
opt/bbmap-39.08-0/current/driver/SummarizeCoverage.class
opt/bbmap-39.08-0/current/driver/SummarizeCoverage.java
opt/bbmap-39.08-0/current/driver/SummarizeCrossblock.class
opt/bbmap-39.08-0/current/driver/SummarizeCrossblock.java
opt/bbmap-39.08-0/current/driver/SummarizeMSDIN.class
opt/bbmap-39.08-0/current/driver/SummarizeMSDIN.java
opt/bbmap-39.08-0/current/driver/SummarizeQuast$Entry.class
opt/bbmap-39.08-0/current/driver/SummarizeQuast$QuastSummary.class
opt/bbmap-39.08-0/current/driver/SummarizeQuast.class
opt/bbmap-39.08-0/current/driver/SummarizeQuast.java
opt/bbmap-39.08-0/current/driver/SummarizeSealCrosstalk$Result.class
opt/bbmap-39.08-0/current/driver/SummarizeSealCrosstalk.class
opt/bbmap-39.08-0/current/driver/SummarizeSealCrosstalk.java
opt/bbmap-39.08-0/current/driver/SummarizeSealStats$SealSummary.class
opt/bbmap-39.08-0/current/driver/SummarizeSealStats.class
opt/bbmap-39.08-0/current/driver/SummarizeSealStats.java
opt/bbmap-39.08-0/current/driver/TestCompressionSpeed.class
opt/bbmap-39.08-0/current/driver/TestCompressionSpeed.java
opt/bbmap-39.08-0/current/driver/TestLockSpeed$1.class
opt/bbmap-39.08-0/current/driver/TestLockSpeed$AtomBox.class
opt/bbmap-39.08-0/current/driver/TestLockSpeed$CountBox.class
opt/bbmap-39.08-0/current/driver/TestLockSpeed$CountThread.class
opt/bbmap-39.08-0/current/driver/TestLockSpeed$LockBox.class
opt/bbmap-39.08-0/current/driver/TestLockSpeed$VolatileBox.class
opt/bbmap-39.08-0/current/driver/TestLockSpeed.class
opt/bbmap-39.08-0/current/driver/TestLockSpeed.java
opt/bbmap-39.08-0/current/driver/Translator.class
opt/bbmap-39.08-0/current/driver/Translator.java
opt/bbmap-39.08-0/current/driver/Translator2.class
opt/bbmap-39.08-0/current/driver/Translator2.java
opt/bbmap-39.08-0/current/driver/TransposeTextFile.class
opt/bbmap-39.08-0/current/driver/TransposeTextFile.java
opt/bbmap-39.08-0/current/driver/TrimSamFile.class
opt/bbmap-39.08-0/current/driver/TrimSamFile.java
opt/bbmap-39.08-0/current/fileIO/ArrayFile.class
opt/bbmap-39.08-0/current/fileIO/ArrayFile.java
opt/bbmap-39.08-0/current/fileIO/ByteFile.class
opt/bbmap-39.08-0/current/fileIO/ByteFile.java
opt/bbmap-39.08-0/current/fileIO/ByteFile1.class
opt/bbmap-39.08-0/current/fileIO/ByteFile1.java
opt/bbmap-39.08-0/current/fileIO/ByteFile2$BF1Thread.class
opt/bbmap-39.08-0/current/fileIO/ByteFile2.class
opt/bbmap-39.08-0/current/fileIO/ByteFile2.java
opt/bbmap-39.08-0/current/fileIO/ByteStreamWriter.class
opt/bbmap-39.08-0/current/fileIO/ByteStreamWriter.java
opt/bbmap-39.08-0/current/fileIO/ChainBlock.class
opt/bbmap-39.08-0/current/fileIO/ChainBlock.java
opt/bbmap-39.08-0/current/fileIO/ChainLine.class
opt/bbmap-39.08-0/current/fileIO/ChainLine.java
opt/bbmap-39.08-0/current/fileIO/CompressFiles.class
opt/bbmap-39.08-0/current/fileIO/CompressFiles.java
opt/bbmap-39.08-0/current/fileIO/CopyFile$1.class
opt/bbmap-39.08-0/current/fileIO/CopyFile.class
opt/bbmap-39.08-0/current/fileIO/CopyFile.java
opt/bbmap-39.08-0/current/fileIO/CopyFiles.class
opt/bbmap-39.08-0/current/fileIO/CopyFiles.java
opt/bbmap-39.08-0/current/fileIO/CopyFiles2.class
opt/bbmap-39.08-0/current/fileIO/CopyFiles2.java
opt/bbmap-39.08-0/current/fileIO/FileFormat.class
opt/bbmap-39.08-0/current/fileIO/FileFormat.java
opt/bbmap-39.08-0/current/fileIO/FindFiles.class
opt/bbmap-39.08-0/current/fileIO/FindFiles.java
opt/bbmap-39.08-0/current/fileIO/GenericTextFile.class
opt/bbmap-39.08-0/current/fileIO/GenericTextFile.java
opt/bbmap-39.08-0/current/fileIO/LoadThread.class
opt/bbmap-39.08-0/current/fileIO/LoadThread.java
opt/bbmap-39.08-0/current/fileIO/MatrixFile.class
opt/bbmap-39.08-0/current/fileIO/MatrixFile.java
opt/bbmap-39.08-0/current/fileIO/OpenFile.class
opt/bbmap-39.08-0/current/fileIO/OpenFile.java
opt/bbmap-39.08-0/current/fileIO/PipeThread.class
opt/bbmap-39.08-0/current/fileIO/PipeThread.java
opt/bbmap-39.08-0/current/fileIO/QuickFile.class
opt/bbmap-39.08-0/current/fileIO/QuickFile.java
opt/bbmap-39.08-0/current/fileIO/ReadWrite$1.class
opt/bbmap-39.08-0/current/fileIO/ReadWrite$WriteObjectThread.class
opt/bbmap-39.08-0/current/fileIO/ReadWrite$WriteStringThread.class
opt/bbmap-39.08-0/current/fileIO/ReadWrite.class
opt/bbmap-39.08-0/current/fileIO/ReadWrite.java
opt/bbmap-39.08-0/current/fileIO/SummaryFile$1.class
opt/bbmap-39.08-0/current/fileIO/SummaryFile.class
opt/bbmap-39.08-0/current/fileIO/SummaryFile.java
opt/bbmap-39.08-0/current/fileIO/TextFile.class
opt/bbmap-39.08-0/current/fileIO/TextFile.java
opt/bbmap-39.08-0/current/fileIO/TextStreamWriter.class
opt/bbmap-39.08-0/current/fileIO/TextStreamWriter.java
opt/bbmap-39.08-0/current/fun/Calc.class
opt/bbmap-39.08-0/current/fun/Calc.java
opt/bbmap-39.08-0/current/fun/Chance.class
opt/bbmap-39.08-0/current/fun/Chance.java
opt/bbmap-39.08-0/current/fun/Crunch.class
opt/bbmap-39.08-0/current/fun/Crunch.java
opt/bbmap-39.08-0/current/fun/DiskBench$ReadThread.class
opt/bbmap-39.08-0/current/fun/DiskBench$WriteThread.class
opt/bbmap-39.08-0/current/fun/DiskBench.class
opt/bbmap-39.08-0/current/fun/DiskBench.java
opt/bbmap-39.08-0/current/fun/Dongle.class
opt/bbmap-39.08-0/current/fun/Dongle.java
opt/bbmap-39.08-0/current/fun/FindPath$Edge.class
opt/bbmap-39.08-0/current/fun/FindPath$Node.class
opt/bbmap-39.08-0/current/fun/FindPath$Path.class
opt/bbmap-39.08-0/current/fun/FindPath.class
opt/bbmap-39.08-0/current/fun/FindPath.java
opt/bbmap-39.08-0/current/fun/Foo.class
opt/bbmap-39.08-0/current/fun/Foo.java
opt/bbmap-39.08-0/current/fun/Foo2.class
opt/bbmap-39.08-0/current/fun/Foo2.java
opt/bbmap-39.08-0/current/fun/Foo3$LongList.class
opt/bbmap-39.08-0/current/fun/Foo3$Pair.class
opt/bbmap-39.08-0/current/fun/Foo3.class
opt/bbmap-39.08-0/current/fun/Foo3.java
opt/bbmap-39.08-0/current/fun/Foo4$Pair.class
opt/bbmap-39.08-0/current/fun/Foo4.class
opt/bbmap-39.08-0/current/fun/Foo4.java
opt/bbmap-39.08-0/current/fun/Foo5$LongList.class
opt/bbmap-39.08-0/current/fun/Foo5.class
opt/bbmap-39.08-0/current/fun/Foo5.java
opt/bbmap-39.08-0/current/fun/Foo6.class
opt/bbmap-39.08-0/current/fun/Foo6.java
opt/bbmap-39.08-0/current/fun/Foo7.class
opt/bbmap-39.08-0/current/fun/Foo7.java
opt/bbmap-39.08-0/current/fun/Genetic$Bug.class
opt/bbmap-39.08-0/current/fun/Genetic.class
opt/bbmap-39.08-0/current/fun/Genetic.java
opt/bbmap-39.08-0/current/fun/Life.class
opt/bbmap-39.08-0/current/fun/Life.java
opt/bbmap-39.08-0/current/fun/MakeAdjacencyList$1.class
opt/bbmap-39.08-0/current/fun/MakeAdjacencyList.class
opt/bbmap-39.08-0/current/fun/MakeAdjacencyList.java
opt/bbmap-39.08-0/current/fun/Merced$Person.class
opt/bbmap-39.08-0/current/fun/Merced.class
opt/bbmap-39.08-0/current/fun/Merced.java
opt/bbmap-39.08-0/current/fun/PalSim.class
opt/bbmap-39.08-0/current/fun/PalSim.java
opt/bbmap-39.08-0/current/fun/Palindrome.class
opt/bbmap-39.08-0/current/fun/Palindrome.java
opt/bbmap-39.08-0/current/fun/Palindrome2$Drome.class
opt/bbmap-39.08-0/current/fun/Palindrome2.class
opt/bbmap-39.08-0/current/fun/Palindrome2.java
opt/bbmap-39.08-0/current/fun/ProbShared.class
opt/bbmap-39.08-0/current/fun/ProbShared.java
opt/bbmap-39.08-0/current/fun/ProbShared2.class
opt/bbmap-39.08-0/current/fun/ProbShared2.java
opt/bbmap-39.08-0/current/fun/ProbShared3.class
opt/bbmap-39.08-0/current/fun/ProbShared3.java
opt/bbmap-39.08-0/current/gff/CompareGff.class
opt/bbmap-39.08-0/current/gff/CompareGff.java
opt/bbmap-39.08-0/current/gff/CompareGff_old.class
opt/bbmap-39.08-0/current/gff/CompareGff_old.java
opt/bbmap-39.08-0/current/gff/CutGff$ProcessThread.class
opt/bbmap-39.08-0/current/gff/CutGff.class
opt/bbmap-39.08-0/current/gff/CutGff.java
opt/bbmap-39.08-0/current/gff/CutGff_ST.class
opt/bbmap-39.08-0/current/gff/CutGff_ST.java
opt/bbmap-39.08-0/current/gff/GbffFeature.class
opt/bbmap-39.08-0/current/gff/GbffFeature.java
opt/bbmap-39.08-0/current/gff/GbffFile.class
opt/bbmap-39.08-0/current/gff/GbffFile.java
opt/bbmap-39.08-0/current/gff/GbffLocus.class
opt/bbmap-39.08-0/current/gff/GbffLocus.java
opt/bbmap-39.08-0/current/gff/GffLine.class
opt/bbmap-39.08-0/current/gff/GffLine.java
opt/bbmap-39.08-0/current/gff/ParseCrispr.class
opt/bbmap-39.08-0/current/gff/ParseCrispr.java
opt/bbmap-39.08-0/current/gff/VcfToGff$1.class
opt/bbmap-39.08-0/current/gff/VcfToGff.class
opt/bbmap-39.08-0/current/gff/VcfToGff.java
opt/bbmap-39.08-0/current/hiseq/AnalyzeFlowCell.class
opt/bbmap-39.08-0/current/hiseq/AnalyzeFlowCell.java
opt/bbmap-39.08-0/current/hiseq/BGI2Illumina.class
opt/bbmap-39.08-0/current/hiseq/BGI2Illumina.java
opt/bbmap-39.08-0/current/hiseq/BGIHeaderParser.class
opt/bbmap-39.08-0/current/hiseq/BGIHeaderParser.java
opt/bbmap-39.08-0/current/hiseq/BGIHeaderParser2.class
opt/bbmap-39.08-0/current/hiseq/BGIHeaderParser2.java
opt/bbmap-39.08-0/current/hiseq/CycleTracker.class
opt/bbmap-39.08-0/current/hiseq/CycleTracker.java
opt/bbmap-39.08-0/current/hiseq/FlowCell.class
opt/bbmap-39.08-0/current/hiseq/FlowCell.java
opt/bbmap-39.08-0/current/hiseq/FlowcellCoordinate.class
opt/bbmap-39.08-0/current/hiseq/FlowcellCoordinate.java
opt/bbmap-39.08-0/current/hiseq/IlluminaHeaderParser1.class
opt/bbmap-39.08-0/current/hiseq/IlluminaHeaderParser1.java
opt/bbmap-39.08-0/current/hiseq/IlluminaHeaderParser2.class
opt/bbmap-39.08-0/current/hiseq/IlluminaHeaderParser2.java
opt/bbmap-39.08-0/current/hiseq/Lane.class
opt/bbmap-39.08-0/current/hiseq/Lane.java
opt/bbmap-39.08-0/current/hiseq/MicroTile.class
opt/bbmap-39.08-0/current/hiseq/MicroTile.java
opt/bbmap-39.08-0/current/hiseq/PlotFlowCell$WorkerThread.class
opt/bbmap-39.08-0/current/hiseq/PlotFlowCell.class
opt/bbmap-39.08-0/current/hiseq/PlotFlowCell.java
opt/bbmap-39.08-0/current/hiseq/PlotReadPosition.class
opt/bbmap-39.08-0/current/hiseq/PlotReadPosition.java
opt/bbmap-39.08-0/current/hiseq/ReadHeaderParser.class
opt/bbmap-39.08-0/current/hiseq/ReadHeaderParser.java
opt/bbmap-39.08-0/current/hiseq/Tile.class
opt/bbmap-39.08-0/current/hiseq/Tile.java
opt/bbmap-39.08-0/current/hmm/HMMSearchLine.class
opt/bbmap-39.08-0/current/hmm/HMMSearchLine.java
opt/bbmap-39.08-0/current/hmm/HMMSearchReport.class
opt/bbmap-39.08-0/current/hmm/HMMSearchReport.java
opt/bbmap-39.08-0/current/hmm/ProteinSummary.class
opt/bbmap-39.08-0/current/hmm/ProteinSummary.java
opt/bbmap-39.08-0/current/icecream/IceCreamAligner.class
opt/bbmap-39.08-0/current/icecream/IceCreamAligner.java
opt/bbmap-39.08-0/current/icecream/IceCreamAlignerJNI.class
opt/bbmap-39.08-0/current/icecream/IceCreamAlignerJNI.java
opt/bbmap-39.08-0/current/icecream/IceCreamAlignerJava.class
opt/bbmap-39.08-0/current/icecream/IceCreamAlignerJava.java
opt/bbmap-39.08-0/current/icecream/IceCreamFinder$ProcessThread.class
opt/bbmap-39.08-0/current/icecream/IceCreamFinder.class
opt/bbmap-39.08-0/current/icecream/IceCreamFinder.java
opt/bbmap-39.08-0/current/icecream/IceCreamGrader.class
opt/bbmap-39.08-0/current/icecream/IceCreamGrader.java
opt/bbmap-39.08-0/current/icecream/IceCreamMaker$ProcessThread.class
opt/bbmap-39.08-0/current/icecream/IceCreamMaker.class
opt/bbmap-39.08-0/current/icecream/IceCreamMaker.java
opt/bbmap-39.08-0/current/icecream/PBHeader.class
opt/bbmap-39.08-0/current/icecream/PBHeader.java
opt/bbmap-39.08-0/current/icecream/PolymerTrimmer.class
opt/bbmap-39.08-0/current/icecream/PolymerTrimmer.java
opt/bbmap-39.08-0/current/icecream/ReadBuilder.class
opt/bbmap-39.08-0/current/icecream/ReadBuilder.java
opt/bbmap-39.08-0/current/icecream/ReformatPacBio$ProcessThread.class
opt/bbmap-39.08-0/current/icecream/ReformatPacBio.class
opt/bbmap-39.08-0/current/icecream/ReformatPacBio.java
opt/bbmap-39.08-0/current/icecream/ZMW.class
opt/bbmap-39.08-0/current/icecream/ZMW.java
opt/bbmap-39.08-0/current/icecream/ZMWStreamer.class
opt/bbmap-39.08-0/current/icecream/ZMWStreamer.java
opt/bbmap-39.08-0/current/jasper/Comparison.class
opt/bbmap-39.08-0/current/jasper/Comparison.java
opt/bbmap-39.08-0/current/jasper/DenseSimilarityMatrix.class
opt/bbmap-39.08-0/current/jasper/DenseSimilarityMatrix.java
opt/bbmap-39.08-0/current/jasper/DenseTree.class
opt/bbmap-39.08-0/current/jasper/DenseTree.java
opt/bbmap-39.08-0/current/jasper/DenseTreeValidate.class
opt/bbmap-39.08-0/current/jasper/DenseTreeValidate.java
opt/bbmap-39.08-0/current/jasper/KmerPosition.class
opt/bbmap-39.08-0/current/jasper/KmerPosition.java
opt/bbmap-39.08-0/current/jasper/KmerPosition3.class
opt/bbmap-39.08-0/current/jasper/KmerPosition3.java
opt/bbmap-39.08-0/current/jasper/NCBIComparison.class
opt/bbmap-39.08-0/current/jasper/NCBIComparison.java
opt/bbmap-39.08-0/current/jasper/NCBISparseSimilarityMatrix.class
opt/bbmap-39.08-0/current/jasper/NCBISparseSimilarityMatrix.java
opt/bbmap-39.08-0/current/jasper/NCBISparseTree.class
opt/bbmap-39.08-0/current/jasper/NCBISparseTree.java
opt/bbmap-39.08-0/current/jasper/NCBISparseTreeValidate.class
opt/bbmap-39.08-0/current/jasper/NCBISparseTreeValidate.java
opt/bbmap-39.08-0/current/jasper/NCBITreeNode.class
opt/bbmap-39.08-0/current/jasper/NCBITreeNode.java
opt/bbmap-39.08-0/current/jasper/Organism.class
opt/bbmap-39.08-0/current/jasper/Organism.java
opt/bbmap-39.08-0/current/jasper/SimilarityMatrix.class
opt/bbmap-39.08-0/current/jasper/SimilarityMatrix.java
opt/bbmap-39.08-0/current/jasper/SparseSimilarityMatrix.class
opt/bbmap-39.08-0/current/jasper/SparseSimilarityMatrix.java
opt/bbmap-39.08-0/current/jasper/SparseTree.class
opt/bbmap-39.08-0/current/jasper/SparseTree.java
opt/bbmap-39.08-0/current/jasper/SparseTreeValidate.class
opt/bbmap-39.08-0/current/jasper/SparseTreeValidate.java
opt/bbmap-39.08-0/current/jasper/TaxCompare.class
opt/bbmap-39.08-0/current/jasper/TaxCompare.java
opt/bbmap-39.08-0/current/jasper/TreeNode.class
opt/bbmap-39.08-0/current/jasper/TreeNode.java
opt/bbmap-39.08-0/current/jgi/AddAdapters.class
opt/bbmap-39.08-0/current/jgi/AddAdapters.java
opt/bbmap-39.08-0/current/jgi/AdjustHomopolymers.class
opt/bbmap-39.08-0/current/jgi/AdjustHomopolymers.java
opt/bbmap-39.08-0/current/jgi/AssemblyStats2$Triple.class
opt/bbmap-39.08-0/current/jgi/AssemblyStats2.class
opt/bbmap-39.08-0/current/jgi/AssemblyStats2.java
opt/bbmap-39.08-0/current/jgi/AssemblyStatsWrapper.class
opt/bbmap-39.08-0/current/jgi/AssemblyStatsWrapper.java
opt/bbmap-39.08-0/current/jgi/BBDuk$LoadThread.class
opt/bbmap-39.08-0/current/jgi/BBDuk$ProcessThread.class
opt/bbmap-39.08-0/current/jgi/BBDuk.class
opt/bbmap-39.08-0/current/jgi/BBDuk.java
opt/bbmap-39.08-0/current/jgi/BBDuk2$LoadThread.class
opt/bbmap-39.08-0/current/jgi/BBDuk2$ProcessThread.class
opt/bbmap-39.08-0/current/jgi/BBDuk2.class
opt/bbmap-39.08-0/current/jgi/BBDuk2.java
opt/bbmap-39.08-0/current/jgi/BBMask$MaskLowEntropyThread.class
opt/bbmap-39.08-0/current/jgi/BBMask$MaskRepeatThread.class
opt/bbmap-39.08-0/current/jgi/BBMask$MaskSamThread.class
opt/bbmap-39.08-0/current/jgi/BBMask.class
opt/bbmap-39.08-0/current/jgi/BBMask.java
opt/bbmap-39.08-0/current/jgi/BBMerge$MateThread.class
opt/bbmap-39.08-0/current/jgi/BBMerge.class
opt/bbmap-39.08-0/current/jgi/BBMerge.java
opt/bbmap-39.08-0/current/jgi/BBMergeOverlapper.class
opt/bbmap-39.08-0/current/jgi/BBMergeOverlapper.java
opt/bbmap-39.08-0/current/jgi/BBQC.class
opt/bbmap-39.08-0/current/jgi/BBQC.java
opt/bbmap-39.08-0/current/jgi/CalcTrueQuality$CountMatrixSet.class
opt/bbmap-39.08-0/current/jgi/CalcTrueQuality$GBMatrixSet.class
opt/bbmap-39.08-0/current/jgi/CalcTrueQuality$Worker.class
opt/bbmap-39.08-0/current/jgi/CalcTrueQuality.class
opt/bbmap-39.08-0/current/jgi/CalcTrueQuality.java
opt/bbmap-39.08-0/current/jgi/CalcUniqueness$Counter.class
opt/bbmap-39.08-0/current/jgi/CalcUniqueness.class
opt/bbmap-39.08-0/current/jgi/CalcUniqueness.java
opt/bbmap-39.08-0/current/jgi/CallPeaks$Peak.class
opt/bbmap-39.08-0/current/jgi/CallPeaks.class
opt/bbmap-39.08-0/current/jgi/CallPeaks.java
opt/bbmap-39.08-0/current/jgi/CheckStrand.class
opt/bbmap-39.08-0/current/jgi/CheckStrand.java
opt/bbmap-39.08-0/current/jgi/CheckStrand2$ProcessThread.class
opt/bbmap-39.08-0/current/jgi/CheckStrand2.class
opt/bbmap-39.08-0/current/jgi/CheckStrand2.java
opt/bbmap-39.08-0/current/jgi/Consect.class
opt/bbmap-39.08-0/current/jgi/Consect.java
opt/bbmap-39.08-0/current/jgi/CountDuplicates$ProcessThread.class
opt/bbmap-39.08-0/current/jgi/CountDuplicates.class
opt/bbmap-39.08-0/current/jgi/CountDuplicates.java
opt/bbmap-39.08-0/current/jgi/CountDuplicatesBuffered$ProcessThread.class
opt/bbmap-39.08-0/current/jgi/CountDuplicatesBuffered.class
opt/bbmap-39.08-0/current/jgi/CountDuplicatesBuffered.java
opt/bbmap-39.08-0/current/jgi/CountGC$1.class
opt/bbmap-39.08-0/current/jgi/CountGC.class
opt/bbmap-39.08-0/current/jgi/CountGC.java
opt/bbmap-39.08-0/current/jgi/CountUniqueness.class
opt/bbmap-39.08-0/current/jgi/CountUniqueness.java
opt/bbmap-39.08-0/current/jgi/CovStatsLine.class
opt/bbmap-39.08-0/current/jgi/CovStatsLine.java
opt/bbmap-39.08-0/current/jgi/CoveragePileup.class
opt/bbmap-39.08-0/current/jgi/CoveragePileup.java
opt/bbmap-39.08-0/current/jgi/CoveragePileupMT$LoadThread.class
opt/bbmap-39.08-0/current/jgi/CoveragePileupMT.class
opt/bbmap-39.08-0/current/jgi/CoveragePileupMT.java
opt/bbmap-39.08-0/current/jgi/CrisprFinder$1.class
opt/bbmap-39.08-0/current/jgi/CrisprFinder$Alignment.class
opt/bbmap-39.08-0/current/jgi/CrisprFinder$ProcessThread.class
opt/bbmap-39.08-0/current/jgi/CrisprFinder.class
opt/bbmap-39.08-0/current/jgi/CrisprFinder.java
opt/bbmap-39.08-0/current/jgi/CrossContaminate$Vessel.class
opt/bbmap-39.08-0/current/jgi/CrossContaminate.class
opt/bbmap-39.08-0/current/jgi/CrossContaminate.java
opt/bbmap-39.08-0/current/jgi/CutPrimers.class
opt/bbmap-39.08-0/current/jgi/CutPrimers.java
opt/bbmap-39.08-0/current/jgi/DecontaminateByNormalization.class
opt/bbmap-39.08-0/current/jgi/DecontaminateByNormalization.java
opt/bbmap-39.08-0/current/jgi/Dedupe$ClusterLengthComparator.class
opt/bbmap-39.08-0/current/jgi/Dedupe$ClusterThread.class
opt/bbmap-39.08-0/current/jgi/Dedupe$HashThread.class
opt/bbmap-39.08-0/current/jgi/Dedupe$MstThread.class
opt/bbmap-39.08-0/current/jgi/Dedupe$Overlap.class
opt/bbmap-39.08-0/current/jgi/Dedupe$Unit.class
opt/bbmap-39.08-0/current/jgi/Dedupe$UnitOffsetComparator.class
opt/bbmap-39.08-0/current/jgi/Dedupe.class
opt/bbmap-39.08-0/current/jgi/Dedupe.java
opt/bbmap-39.08-0/current/jgi/Dedupe2$ClusterLengthComparator.class
opt/bbmap-39.08-0/current/jgi/Dedupe2$ClusterThread.class
opt/bbmap-39.08-0/current/jgi/Dedupe2$HashThread.class
opt/bbmap-39.08-0/current/jgi/Dedupe2$MstThread.class
opt/bbmap-39.08-0/current/jgi/Dedupe2$Overlap.class
opt/bbmap-39.08-0/current/jgi/Dedupe2$Unit.class
opt/bbmap-39.08-0/current/jgi/Dedupe2$UnitOffsetComparator.class
opt/bbmap-39.08-0/current/jgi/Dedupe2.class
opt/bbmap-39.08-0/current/jgi/Dedupe2.java
opt/bbmap-39.08-0/current/jgi/DedupeByMapping$Quad.class
opt/bbmap-39.08-0/current/jgi/DedupeByMapping.class
opt/bbmap-39.08-0/current/jgi/DedupeByMapping.java
opt/bbmap-39.08-0/current/jgi/DedupeProtein$ClusterLengthComparator.class
opt/bbmap-39.08-0/current/jgi/DedupeProtein$ClusterThread.class
opt/bbmap-39.08-0/current/jgi/DedupeProtein$HashThread.class
opt/bbmap-39.08-0/current/jgi/DedupeProtein$MstThread.class
opt/bbmap-39.08-0/current/jgi/DedupeProtein$Overlap.class
opt/bbmap-39.08-0/current/jgi/DedupeProtein$Unit.class
opt/bbmap-39.08-0/current/jgi/DedupeProtein$UnitOffsetComparator.class
opt/bbmap-39.08-0/current/jgi/DedupeProtein.class
opt/bbmap-39.08-0/current/jgi/DedupeProtein.java
opt/bbmap-39.08-0/current/jgi/DemuxByName.class
opt/bbmap-39.08-0/current/jgi/DemuxByName.java
opt/bbmap-39.08-0/current/jgi/DemuxByName2.class
opt/bbmap-39.08-0/current/jgi/DemuxByName2.java
opt/bbmap-39.08-0/current/jgi/Difference.class
opt/bbmap-39.08-0/current/jgi/Difference.java
opt/bbmap-39.08-0/current/jgi/FakeReads.class
opt/bbmap-39.08-0/current/jgi/FakeReads.java
opt/bbmap-39.08-0/current/jgi/FilterByCoverage.class
opt/bbmap-39.08-0/current/jgi/FilterByCoverage.java
opt/bbmap-39.08-0/current/jgi/FilterBySequence$Code.class
opt/bbmap-39.08-0/current/jgi/FilterBySequence$LoadThread.class
opt/bbmap-39.08-0/current/jgi/FilterBySequence$ProcessThread.class
opt/bbmap-39.08-0/current/jgi/FilterBySequence.class
opt/bbmap-39.08-0/current/jgi/FilterBySequence.java
opt/bbmap-39.08-0/current/jgi/FilterReadsWithSubs.class
opt/bbmap-39.08-0/current/jgi/FilterReadsWithSubs.java
opt/bbmap-39.08-0/current/jgi/FindHiCJunctions.class
opt/bbmap-39.08-0/current/jgi/FindHiCJunctions.java
opt/bbmap-39.08-0/current/jgi/FindPrimers$ProcessThread.class
opt/bbmap-39.08-0/current/jgi/FindPrimers.class
opt/bbmap-39.08-0/current/jgi/FindPrimers.java
opt/bbmap-39.08-0/current/jgi/FindPrimers_old.class
opt/bbmap-39.08-0/current/jgi/FindPrimers_old.java
opt/bbmap-39.08-0/current/jgi/FindString.class
opt/bbmap-39.08-0/current/jgi/FindString.java
opt/bbmap-39.08-0/current/jgi/FungalRelease.class
opt/bbmap-39.08-0/current/jgi/FungalRelease.java
opt/bbmap-39.08-0/current/jgi/FuseSequence.class
opt/bbmap-39.08-0/current/jgi/FuseSequence.java
opt/bbmap-39.08-0/current/jgi/GatherKapaStats$KapaEntry.class
opt/bbmap-39.08-0/current/jgi/GatherKapaStats$Plate.class
opt/bbmap-39.08-0/current/jgi/GatherKapaStats$TagData.class
opt/bbmap-39.08-0/current/jgi/GatherKapaStats$Well.class
opt/bbmap-39.08-0/current/jgi/GatherKapaStats.class
opt/bbmap-39.08-0/current/jgi/GatherKapaStats.java
opt/bbmap-39.08-0/current/jgi/GetReads.class
opt/bbmap-39.08-0/current/jgi/GetReads.java
opt/bbmap-39.08-0/current/jgi/GradeMergedReads.class
opt/bbmap-39.08-0/current/jgi/GradeMergedReads.java
opt/bbmap-39.08-0/current/jgi/GreedyBarCodeFinder.class
opt/bbmap-39.08-0/current/jgi/GreedyBarCodeFinder.java
opt/bbmap-39.08-0/current/jgi/IdentityMatrix$ProcessThread.class
opt/bbmap-39.08-0/current/jgi/IdentityMatrix.class
opt/bbmap-39.08-0/current/jgi/IdentityMatrix.java
opt/bbmap-39.08-0/current/jgi/Info.class
opt/bbmap-39.08-0/current/jgi/Info.java
opt/bbmap-39.08-0/current/jgi/KExpand.class
opt/bbmap-39.08-0/current/jgi/KExpand.java
opt/bbmap-39.08-0/current/jgi/KeepBestCopy.class
opt/bbmap-39.08-0/current/jgi/KeepBestCopy.java
opt/bbmap-39.08-0/current/jgi/KmerCountExact$DumpKmersThread.class
opt/bbmap-39.08-0/current/jgi/KmerCountExact$MakeKhistThread.class
opt/bbmap-39.08-0/current/jgi/KmerCountExact.class
opt/bbmap-39.08-0/current/jgi/KmerCountExact.java
opt/bbmap-39.08-0/current/jgi/KmerCountMulti$ProcessThread.class
opt/bbmap-39.08-0/current/jgi/KmerCountMulti.class
opt/bbmap-39.08-0/current/jgi/KmerCountMulti.java
opt/bbmap-39.08-0/current/jgi/KmerCoverage$1.class
opt/bbmap-39.08-0/current/jgi/KmerCoverage$ProcessThread.class
opt/bbmap-39.08-0/current/jgi/KmerCoverage.class
opt/bbmap-39.08-0/current/jgi/KmerCoverage.java
opt/bbmap-39.08-0/current/jgi/KmerFilterSetMaker.class
opt/bbmap-39.08-0/current/jgi/KmerFilterSetMaker.java
opt/bbmap-39.08-0/current/jgi/KmerNormalize$1.class
opt/bbmap-39.08-0/current/jgi/KmerNormalize$ProcessThread.class
opt/bbmap-39.08-0/current/jgi/KmerNormalize.class
opt/bbmap-39.08-0/current/jgi/KmerNormalize.java
opt/bbmap-39.08-0/current/jgi/KmerSample.class
opt/bbmap-39.08-0/current/jgi/KmerSample.java
opt/bbmap-39.08-0/current/jgi/MakeChimeras.class
opt/bbmap-39.08-0/current/jgi/MakeChimeras.java
opt/bbmap-39.08-0/current/jgi/MakeContaminatedGenomes.class
opt/bbmap-39.08-0/current/jgi/MakeContaminatedGenomes.java
opt/bbmap-39.08-0/current/jgi/MakeLengthHistogram$1.class
opt/bbmap-39.08-0/current/jgi/MakeLengthHistogram.class
opt/bbmap-39.08-0/current/jgi/MakeLengthHistogram.java
opt/bbmap-39.08-0/current/jgi/MakePolymers.class
opt/bbmap-39.08-0/current/jgi/MakePolymers.java
opt/bbmap-39.08-0/current/jgi/MergeBarcodes.class
opt/bbmap-39.08-0/current/jgi/MergeBarcodes.java
opt/bbmap-39.08-0/current/jgi/MergeSam.class
opt/bbmap-39.08-0/current/jgi/MergeSam.java
opt/bbmap-39.08-0/current/jgi/MutateGenome$SmallVar.class
opt/bbmap-39.08-0/current/jgi/MutateGenome.class
opt/bbmap-39.08-0/current/jgi/MutateGenome.java
opt/bbmap-39.08-0/current/jgi/MutateGenome2$SmallVar.class
opt/bbmap-39.08-0/current/jgi/MutateGenome2.class
opt/bbmap-39.08-0/current/jgi/MutateGenome2.java
opt/bbmap-39.08-0/current/jgi/Orf.class
opt/bbmap-39.08-0/current/jgi/Orf.java
opt/bbmap-39.08-0/current/jgi/PartitionReads$Partition.class
opt/bbmap-39.08-0/current/jgi/PartitionReads.class
opt/bbmap-39.08-0/current/jgi/PartitionReads.java
opt/bbmap-39.08-0/current/jgi/PhylipToFasta.class
opt/bbmap-39.08-0/current/jgi/PhylipToFasta.java
opt/bbmap-39.08-0/current/jgi/RQCFilter2.class
opt/bbmap-39.08-0/current/jgi/RQCFilter2.java
opt/bbmap-39.08-0/current/jgi/RQCFilterStats.class
opt/bbmap-39.08-0/current/jgi/RQCFilterStats.java
opt/bbmap-39.08-0/current/jgi/RandomGenome.class
opt/bbmap-39.08-0/current/jgi/RandomGenome.java
opt/bbmap-39.08-0/current/jgi/ReadKmerDepthDistribution$1.class
opt/bbmap-39.08-0/current/jgi/ReadKmerDepthDistribution$ProcessThread.class
opt/bbmap-39.08-0/current/jgi/ReadKmerDepthDistribution.class
opt/bbmap-39.08-0/current/jgi/ReadKmerDepthDistribution.java
opt/bbmap-39.08-0/current/jgi/RedirectTest.class
opt/bbmap-39.08-0/current/jgi/RedirectTest.java
opt/bbmap-39.08-0/current/jgi/ReformatReads.class
opt/bbmap-39.08-0/current/jgi/ReformatReads.java
opt/bbmap-39.08-0/current/jgi/RemapQuality.class
opt/bbmap-39.08-0/current/jgi/RemapQuality.java
opt/bbmap-39.08-0/current/jgi/RemoveBadBarcodes.class
opt/bbmap-39.08-0/current/jgi/RemoveBadBarcodes.java
opt/bbmap-39.08-0/current/jgi/RenameReads.class
opt/bbmap-39.08-0/current/jgi/RenameReads.java
opt/bbmap-39.08-0/current/jgi/ReplaceHeaders.class
opt/bbmap-39.08-0/current/jgi/ReplaceHeaders.java
opt/bbmap-39.08-0/current/jgi/RepresentativeSet$Edge.class
opt/bbmap-39.08-0/current/jgi/RepresentativeSet$Node.class
opt/bbmap-39.08-0/current/jgi/RepresentativeSet.class
opt/bbmap-39.08-0/current/jgi/RepresentativeSet.java
opt/bbmap-39.08-0/current/jgi/SamToEst$1.class
opt/bbmap-39.08-0/current/jgi/SamToEst$EST.class
opt/bbmap-39.08-0/current/jgi/SamToEst.class
opt/bbmap-39.08-0/current/jgi/SamToEst.java
opt/bbmap-39.08-0/current/jgi/Seal$LoadThread.class
opt/bbmap-39.08-0/current/jgi/Seal$ProcessThread.class
opt/bbmap-39.08-0/current/jgi/Seal.class
opt/bbmap-39.08-0/current/jgi/Seal.java
opt/bbmap-39.08-0/current/jgi/SealRefInfo.class
opt/bbmap-39.08-0/current/jgi/SealRefInfo.java
opt/bbmap-39.08-0/current/jgi/Shred.class
opt/bbmap-39.08-0/current/jgi/Shred.java
opt/bbmap-39.08-0/current/jgi/SmallKmerFrequency$CountComparator.class
opt/bbmap-39.08-0/current/jgi/SmallKmerFrequency$Kmer.class
opt/bbmap-39.08-0/current/jgi/SmallKmerFrequency$NumComparator.class
opt/bbmap-39.08-0/current/jgi/SmallKmerFrequency.class
opt/bbmap-39.08-0/current/jgi/SmallKmerFrequency.java
opt/bbmap-39.08-0/current/jgi/SplitNexteraLMP.class
opt/bbmap-39.08-0/current/jgi/SplitNexteraLMP.java
opt/bbmap-39.08-0/current/jgi/SplitPairsAndSingles.class
opt/bbmap-39.08-0/current/jgi/SplitPairsAndSingles.java
opt/bbmap-39.08-0/current/jgi/SplitSam4Way.class
opt/bbmap-39.08-0/current/jgi/SplitSam4Way.java
opt/bbmap-39.08-0/current/jgi/SplitSam6Way.class
opt/bbmap-39.08-0/current/jgi/SplitSam6Way.java
opt/bbmap-39.08-0/current/jgi/SplitSamFile.class
opt/bbmap-39.08-0/current/jgi/SplitSamFile.java
opt/bbmap-39.08-0/current/jgi/StringCount.class
opt/bbmap-39.08-0/current/jgi/StringCount.java
opt/bbmap-39.08-0/current/jgi/SynthMDA.class
opt/bbmap-39.08-0/current/jgi/SynthMDA.java
opt/bbmap-39.08-0/current/jgi/TestFilesystem$WriteThread.class
opt/bbmap-39.08-0/current/jgi/TestFilesystem.class
opt/bbmap-39.08-0/current/jgi/TestFilesystem.java
opt/bbmap-39.08-0/current/jgi/TestFormat$TestThread.class
opt/bbmap-39.08-0/current/jgi/TestFormat.class
opt/bbmap-39.08-0/current/jgi/TestFormat.java
opt/bbmap-39.08-0/current/jgi/TetramerFrequencies$Line.class
opt/bbmap-39.08-0/current/jgi/TetramerFrequencies$PrintThread.class
opt/bbmap-39.08-0/current/jgi/TetramerFrequencies.class
opt/bbmap-39.08-0/current/jgi/TetramerFrequencies.java
opt/bbmap-39.08-0/current/jgi/TranslateSixFrames.class
opt/bbmap-39.08-0/current/jgi/TranslateSixFrames.java
opt/bbmap-39.08-0/current/jgi/UnicodeToAscii.class
opt/bbmap-39.08-0/current/jgi/UnicodeToAscii.java
opt/bbmap-39.08-0/current/jgi/Unzip.class
opt/bbmap-39.08-0/current/jgi/Unzip.java
opt/bbmap-39.08-0/current/json/JsonLiteral.class
opt/bbmap-39.08-0/current/json/JsonLiteral.java
opt/bbmap-39.08-0/current/json/JsonObject.class
opt/bbmap-39.08-0/current/json/JsonObject.java
opt/bbmap-39.08-0/current/json/JsonParser.class
opt/bbmap-39.08-0/current/json/JsonParser.java
opt/bbmap-39.08-0/current/kmer/AbstractKmerTable$AllocThread.class
opt/bbmap-39.08-0/current/kmer/AbstractKmerTable.class
opt/bbmap-39.08-0/current/kmer/AbstractKmerTable.java
opt/bbmap-39.08-0/current/kmer/AbstractKmerTableSet.class
opt/bbmap-39.08-0/current/kmer/AbstractKmerTableSet.java
opt/bbmap-39.08-0/current/kmer/DumpThread.class
opt/bbmap-39.08-0/current/kmer/DumpThread.java
opt/bbmap-39.08-0/current/kmer/HashArray.class
opt/bbmap-39.08-0/current/kmer/HashArray.java
opt/bbmap-39.08-0/current/kmer/HashArray1D$Walker1D.class
opt/bbmap-39.08-0/current/kmer/HashArray1D.class
opt/bbmap-39.08-0/current/kmer/HashArray1D.java
opt/bbmap-39.08-0/current/kmer/HashArray2D.class
opt/bbmap-39.08-0/current/kmer/HashArray2D.java
opt/bbmap-39.08-0/current/kmer/HashArrayHybrid.class
opt/bbmap-39.08-0/current/kmer/HashArrayHybrid.java
opt/bbmap-39.08-0/current/kmer/HashArrayHybridFast.class
opt/bbmap-39.08-0/current/kmer/HashArrayHybridFast.java
opt/bbmap-39.08-0/current/kmer/HashBuffer.class
opt/bbmap-39.08-0/current/kmer/HashBuffer.java
opt/bbmap-39.08-0/current/kmer/HashForest.class
opt/bbmap-39.08-0/current/kmer/HashForest.java
opt/bbmap-39.08-0/current/kmer/HistogramMaker$FillThread.class
opt/bbmap-39.08-0/current/kmer/HistogramMaker.class
opt/bbmap-39.08-0/current/kmer/HistogramMaker.java
opt/bbmap-39.08-0/current/kmer/KmerBuffer.class
opt/bbmap-39.08-0/current/kmer/KmerBuffer.java
opt/bbmap-39.08-0/current/kmer/KmerLink.class
opt/bbmap-39.08-0/current/kmer/KmerLink.java
opt/bbmap-39.08-0/current/kmer/KmerNode.class
opt/bbmap-39.08-0/current/kmer/KmerNode.java
opt/bbmap-39.08-0/current/kmer/KmerNode1D.class
opt/bbmap-39.08-0/current/kmer/KmerNode1D.java
opt/bbmap-39.08-0/current/kmer/KmerNode2D.class
opt/bbmap-39.08-0/current/kmer/KmerNode2D.java
opt/bbmap-39.08-0/current/kmer/KmerTable.class
opt/bbmap-39.08-0/current/kmer/KmerTable.java
opt/bbmap-39.08-0/current/kmer/KmerTableSet$LoadThread.class
opt/bbmap-39.08-0/current/kmer/KmerTableSet$WalkerKST.class
opt/bbmap-39.08-0/current/kmer/KmerTableSet.class
opt/bbmap-39.08-0/current/kmer/KmerTableSet.java
opt/bbmap-39.08-0/current/kmer/OwnershipThread.class
opt/bbmap-39.08-0/current/kmer/OwnershipThread.java
opt/bbmap-39.08-0/current/kmer/ScheduleMaker.class
opt/bbmap-39.08-0/current/kmer/ScheduleMaker.java
opt/bbmap-39.08-0/current/kmer/SimpleKmerTable.class
opt/bbmap-39.08-0/current/kmer/SimpleKmerTable.java
opt/bbmap-39.08-0/current/kmer/TableLoaderLockFree$LoadThread.class
opt/bbmap-39.08-0/current/kmer/TableLoaderLockFree.class
opt/bbmap-39.08-0/current/kmer/TableLoaderLockFree.java
opt/bbmap-39.08-0/current/kmer/TableReader.class
opt/bbmap-39.08-0/current/kmer/TableReader.java
opt/bbmap-39.08-0/current/kmer/Walker.class
opt/bbmap-39.08-0/current/kmer/Walker.java
opt/bbmap-39.08-0/current/ml/Bell.class
opt/bbmap-39.08-0/current/ml/Bell.java
opt/bbmap-39.08-0/current/ml/Cell.class
opt/bbmap-39.08-0/current/ml/Cell.java
opt/bbmap-39.08-0/current/ml/CellNet.class
opt/bbmap-39.08-0/current/ml/CellNet.java
opt/bbmap-39.08-0/current/ml/CellNetParser.class
opt/bbmap-39.08-0/current/ml/CellNetParser.java
opt/bbmap-39.08-0/current/ml/CellNetReverseComparator.class
opt/bbmap-39.08-0/current/ml/CellNetReverseComparator.java
opt/bbmap-39.08-0/current/ml/DataLoader$Pair.class
opt/bbmap-39.08-0/current/ml/DataLoader.class
opt/bbmap-39.08-0/current/ml/DataLoader.java
opt/bbmap-39.08-0/current/ml/ExtendedMSig.class
opt/bbmap-39.08-0/current/ml/ExtendedMSig.java
opt/bbmap-39.08-0/current/ml/ExtendedSigmoid.class
opt/bbmap-39.08-0/current/ml/ExtendedSigmoid.java
opt/bbmap-39.08-0/current/ml/Function.class
opt/bbmap-39.08-0/current/ml/Function.java
opt/bbmap-39.08-0/current/ml/Functions.class
opt/bbmap-39.08-0/current/ml/Functions.java
opt/bbmap-39.08-0/current/ml/JobData.class
opt/bbmap-39.08-0/current/ml/JobData.java
opt/bbmap-39.08-0/current/ml/JobResults.class
opt/bbmap-39.08-0/current/ml/JobResults.java
opt/bbmap-39.08-0/current/ml/MSig.class
opt/bbmap-39.08-0/current/ml/MSig.java
opt/bbmap-39.08-0/current/ml/Matrix.class
opt/bbmap-39.08-0/current/ml/Matrix.java
opt/bbmap-39.08-0/current/ml/NetFilter$ProcessThread.class
opt/bbmap-39.08-0/current/ml/NetFilter.class
opt/bbmap-39.08-0/current/ml/NetFilter.java
opt/bbmap-39.08-0/current/ml/ProcessBBMergeHeaders$Header.class
opt/bbmap-39.08-0/current/ml/ProcessBBMergeHeaders.class
opt/bbmap-39.08-0/current/ml/ProcessBBMergeHeaders.java
opt/bbmap-39.08-0/current/ml/Profiler.class
opt/bbmap-39.08-0/current/ml/Profiler.java
opt/bbmap-39.08-0/current/ml/RSLog.class
opt/bbmap-39.08-0/current/ml/RSLog.java
opt/bbmap-39.08-0/current/ml/Sample.class
opt/bbmap-39.08-0/current/ml/Sample.java
opt/bbmap-39.08-0/current/ml/SampleErrorComparator.class
opt/bbmap-39.08-0/current/ml/SampleErrorComparator.java
opt/bbmap-39.08-0/current/ml/SampleSet.class
opt/bbmap-39.08-0/current/ml/SampleSet.java
opt/bbmap-39.08-0/current/ml/SampleValueComparator.class
opt/bbmap-39.08-0/current/ml/SampleValueComparator.java
opt/bbmap-39.08-0/current/ml/ScannerThread$LaunchThread.class
opt/bbmap-39.08-0/current/ml/ScannerThread.class
opt/bbmap-39.08-0/current/ml/ScannerThread.java
opt/bbmap-39.08-0/current/ml/ScoreSequence.class
opt/bbmap-39.08-0/current/ml/ScoreSequence.java
opt/bbmap-39.08-0/current/ml/Seed.class
opt/bbmap-39.08-0/current/ml/Seed.java
opt/bbmap-39.08-0/current/ml/SequenceToVector$1.class
opt/bbmap-39.08-0/current/ml/SequenceToVector.class
opt/bbmap-39.08-0/current/ml/SequenceToVector.java
opt/bbmap-39.08-0/current/ml/Sigmoid.class
opt/bbmap-39.08-0/current/ml/Sigmoid.java
opt/bbmap-39.08-0/current/ml/Source.class
opt/bbmap-39.08-0/current/ml/Source.java
opt/bbmap-39.08-0/current/ml/Status.class
opt/bbmap-39.08-0/current/ml/Status.java
opt/bbmap-39.08-0/current/ml/Subset.class
opt/bbmap-39.08-0/current/ml/Subset.java
opt/bbmap-39.08-0/current/ml/Swish.class
opt/bbmap-39.08-0/current/ml/Swish.java
opt/bbmap-39.08-0/current/ml/Tanh.class
opt/bbmap-39.08-0/current/ml/Tanh.java
opt/bbmap-39.08-0/current/ml/Trainer.class
opt/bbmap-39.08-0/current/ml/Trainer.java
opt/bbmap-39.08-0/current/ml/TrainerThread$LaunchThread.class
opt/bbmap-39.08-0/current/ml/TrainerThread.class
opt/bbmap-39.08-0/current/ml/TrainerThread.java
opt/bbmap-39.08-0/current/ml/WorkerThread.class
opt/bbmap-39.08-0/current/ml/WorkerThread.java
opt/bbmap-39.08-0/current/pacbio/CalcCoverageFromSites$1.class
opt/bbmap-39.08-0/current/pacbio/CalcCoverageFromSites.class
opt/bbmap-39.08-0/current/pacbio/CalcCoverageFromSites.java
opt/bbmap-39.08-0/current/pacbio/GenerateMultiChrom.class
opt/bbmap-39.08-0/current/pacbio/GenerateMultiChrom.java
opt/bbmap-39.08-0/current/pacbio/MakePacBioScript.class
opt/bbmap-39.08-0/current/pacbio/MakePacBioScript.java
opt/bbmap-39.08-0/current/pacbio/MergeFastaContigs$1.class
opt/bbmap-39.08-0/current/pacbio/MergeFastaContigs.class
opt/bbmap-39.08-0/current/pacbio/MergeFastaContigs.java
opt/bbmap-39.08-0/current/pacbio/MergeReadsAndGenome$1.class
opt/bbmap-39.08-0/current/pacbio/MergeReadsAndGenome.class
opt/bbmap-39.08-0/current/pacbio/MergeReadsAndGenome.java
opt/bbmap-39.08-0/current/pacbio/PartitionFastaFile.class
opt/bbmap-39.08-0/current/pacbio/PartitionFastaFile.java
opt/bbmap-39.08-0/current/pacbio/PartitionReads$1.class
opt/bbmap-39.08-0/current/pacbio/PartitionReads.class
opt/bbmap-39.08-0/current/pacbio/PartitionReads.java
opt/bbmap-39.08-0/current/pacbio/ProcessStackedSitesNormalized$1.class
opt/bbmap-39.08-0/current/pacbio/ProcessStackedSitesNormalized$Buffer.class
opt/bbmap-39.08-0/current/pacbio/ProcessStackedSitesNormalized$Ssra.class
opt/bbmap-39.08-0/current/pacbio/ProcessStackedSitesNormalized.class
opt/bbmap-39.08-0/current/pacbio/ProcessStackedSitesNormalized.java
opt/bbmap-39.08-0/current/pacbio/RemoveAdapters2$1.class
opt/bbmap-39.08-0/current/pacbio/RemoveAdapters2$ProcessThread.class
opt/bbmap-39.08-0/current/pacbio/RemoveAdapters2.class
opt/bbmap-39.08-0/current/pacbio/RemoveAdapters2.java
opt/bbmap-39.08-0/current/pacbio/RemoveAdapters3$ProcessThread.class
opt/bbmap-39.08-0/current/pacbio/RemoveAdapters3.class
opt/bbmap-39.08-0/current/pacbio/RemoveAdapters3.java
opt/bbmap-39.08-0/current/pacbio/SiteR.class
opt/bbmap-39.08-0/current/pacbio/SiteR.java
opt/bbmap-39.08-0/current/pacbio/SortSites$1.class
opt/bbmap-39.08-0/current/pacbio/SortSites.class
opt/bbmap-39.08-0/current/pacbio/SortSites.java
opt/bbmap-39.08-0/current/pacbio/SplitOffPerfectContigs$1.class
opt/bbmap-39.08-0/current/pacbio/SplitOffPerfectContigs.class
opt/bbmap-39.08-0/current/pacbio/SplitOffPerfectContigs.java
opt/bbmap-39.08-0/current/pacbio/StackSites$1.class
opt/bbmap-39.08-0/current/pacbio/StackSites$Glob.class
opt/bbmap-39.08-0/current/pacbio/StackSites.class
opt/bbmap-39.08-0/current/pacbio/StackSites.java
opt/bbmap-39.08-0/current/pacbio/StackSites2$1.class
opt/bbmap-39.08-0/current/pacbio/StackSites2$Glob.class
opt/bbmap-39.08-0/current/pacbio/StackSites2.class
opt/bbmap-39.08-0/current/pacbio/StackSites2.java
opt/bbmap-39.08-0/current/prok/AnalyzeGenes$FileThread.class
opt/bbmap-39.08-0/current/prok/AnalyzeGenes.class
opt/bbmap-39.08-0/current/prok/AnalyzeGenes.java
opt/bbmap-39.08-0/current/prok/CallGenes$ProcessThread.class
opt/bbmap-39.08-0/current/prok/CallGenes.class
opt/bbmap-39.08-0/current/prok/CallGenes.java
opt/bbmap-39.08-0/current/prok/FetchProks$ProcessThread.class
opt/bbmap-39.08-0/current/prok/FetchProks$Stats.class
opt/bbmap-39.08-0/current/prok/FetchProks.class
opt/bbmap-39.08-0/current/prok/FetchProks.java
opt/bbmap-39.08-0/current/prok/FilterSilva.class
opt/bbmap-39.08-0/current/prok/FilterSilva.java
opt/bbmap-39.08-0/current/prok/FrameStats.class
opt/bbmap-39.08-0/current/prok/FrameStats.java
opt/bbmap-39.08-0/current/prok/GeneCaller.class
opt/bbmap-39.08-0/current/prok/GeneCaller.java
opt/bbmap-39.08-0/current/prok/GeneModel.class
opt/bbmap-39.08-0/current/prok/GeneModel.java
opt/bbmap-39.08-0/current/prok/GeneModelParser.class
opt/bbmap-39.08-0/current/prok/GeneModelParser.java
opt/bbmap-39.08-0/current/prok/MergeRibo$ListComparator.class
opt/bbmap-39.08-0/current/prok/MergeRibo$ProcessThread.class
opt/bbmap-39.08-0/current/prok/MergeRibo$Ribo.class
opt/bbmap-39.08-0/current/prok/MergeRibo.class
opt/bbmap-39.08-0/current/prok/MergeRibo.java
opt/bbmap-39.08-0/current/prok/MergeRibo_Fast$ProcessThread.class
opt/bbmap-39.08-0/current/prok/MergeRibo_Fast$Ribo.class
opt/bbmap-39.08-0/current/prok/MergeRibo_Fast.class
opt/bbmap-39.08-0/current/prok/MergeRibo_Fast.java
opt/bbmap-39.08-0/current/prok/Orf.class
opt/bbmap-39.08-0/current/prok/Orf.java
opt/bbmap-39.08-0/current/prok/PFeature$FeatureComparatorScore.class
opt/bbmap-39.08-0/current/prok/PFeature.class
opt/bbmap-39.08-0/current/prok/PFeature.java
opt/bbmap-39.08-0/current/prok/PGMTools$1.class
opt/bbmap-39.08-0/current/prok/PGMTools.class
opt/bbmap-39.08-0/current/prok/PGMTools.java
opt/bbmap-39.08-0/current/prok/ProkObject.class
opt/bbmap-39.08-0/current/prok/ProkObject.java
opt/bbmap-39.08-0/current/prok/RiboMaker$ProcessThread.class
opt/bbmap-39.08-0/current/prok/RiboMaker.class
opt/bbmap-39.08-0/current/prok/RiboMaker.java
opt/bbmap-39.08-0/current/prok/ScafData.class
opt/bbmap-39.08-0/current/prok/ScafData.java
opt/bbmap-39.08-0/current/prok/ScoreTracker.class
opt/bbmap-39.08-0/current/prok/ScoreTracker.java
opt/bbmap-39.08-0/current/prok/SplitRibo$ProcessThread.class
opt/bbmap-39.08-0/current/prok/SplitRibo.class
opt/bbmap-39.08-0/current/prok/SplitRibo.java
opt/bbmap-39.08-0/current/prok/StatsContainer.class
opt/bbmap-39.08-0/current/prok/StatsContainer.java
opt/bbmap-39.08-0/current/repeat/Palindrome.class
opt/bbmap-39.08-0/current/repeat/Palindrome.java
opt/bbmap-39.08-0/current/repeat/PalindromeFinder.class
opt/bbmap-39.08-0/current/repeat/PalindromeFinder.java
opt/bbmap-39.08-0/current/repeat/Repeat$PosComparator.class
opt/bbmap-39.08-0/current/repeat/Repeat$PosComparator2.class
opt/bbmap-39.08-0/current/repeat/Repeat.class
opt/bbmap-39.08-0/current/repeat/Repeat.java
opt/bbmap-39.08-0/current/repeat/RepeatFinder$ProcessThread.class
opt/bbmap-39.08-0/current/repeat/RepeatFinder.class
opt/bbmap-39.08-0/current/repeat/RepeatFinder.java
opt/bbmap-39.08-0/current/repeat/RepeatSet.class
opt/bbmap-39.08-0/current/repeat/RepeatSet.java
opt/bbmap-39.08-0/current/server/PercentEncoding.class
opt/bbmap-39.08-0/current/server/PercentEncoding.java
opt/bbmap-39.08-0/current/server/ServerTools.class
opt/bbmap-39.08-0/current/server/ServerTools.java
opt/bbmap-39.08-0/current/server/SimpleHttpServer$GetHandler.class
opt/bbmap-39.08-0/current/server/SimpleHttpServer.class
opt/bbmap-39.08-0/current/server/SimpleHttpServer.java
opt/bbmap-39.08-0/current/shared/Colors.class
opt/bbmap-39.08-0/current/shared/Colors.java
opt/bbmap-39.08-0/current/shared/KillSwitch.class
opt/bbmap-39.08-0/current/shared/KillSwitch.java
opt/bbmap-39.08-0/current/shared/LineParser.class
opt/bbmap-39.08-0/current/shared/LineParser.java
opt/bbmap-39.08-0/current/shared/LineParser1.class
opt/bbmap-39.08-0/current/shared/LineParser1.java
opt/bbmap-39.08-0/current/shared/LineParser2.class
opt/bbmap-39.08-0/current/shared/LineParser2.java
opt/bbmap-39.08-0/current/shared/LineParserS.class
opt/bbmap-39.08-0/current/shared/LineParserS.java
opt/bbmap-39.08-0/current/shared/LineParserS1.class
opt/bbmap-39.08-0/current/shared/LineParserS1.java
opt/bbmap-39.08-0/current/shared/LineParserS2.class
opt/bbmap-39.08-0/current/shared/LineParserS2.java
opt/bbmap-39.08-0/current/shared/LineParserS3.class
opt/bbmap-39.08-0/current/shared/LineParserS3.java
opt/bbmap-39.08-0/current/shared/LineParserS4.class
opt/bbmap-39.08-0/current/shared/LineParserS4.java
opt/bbmap-39.08-0/current/shared/LineParserS4Reverse.class
opt/bbmap-39.08-0/current/shared/LineParserS4Reverse.java
opt/bbmap-39.08-0/current/shared/LineParserSimple.class
opt/bbmap-39.08-0/current/shared/LineParserSimple.java
opt/bbmap-39.08-0/current/shared/MetadataWriter.class
opt/bbmap-39.08-0/current/shared/MetadataWriter.java
opt/bbmap-39.08-0/current/shared/Parse.class
opt/bbmap-39.08-0/current/shared/Parse.java
opt/bbmap-39.08-0/current/shared/Parser.class
opt/bbmap-39.08-0/current/shared/Parser.java
opt/bbmap-39.08-0/current/shared/PreParser.class
opt/bbmap-39.08-0/current/shared/PreParser.java
opt/bbmap-39.08-0/current/shared/Primes.class
opt/bbmap-39.08-0/current/shared/Primes.java
opt/bbmap-39.08-0/current/shared/SIMD.class
opt/bbmap-39.08-0/current/shared/SIMD.java
opt/bbmap-39.08-0/current/shared/Shared.class
opt/bbmap-39.08-0/current/shared/Shared.java
opt/bbmap-39.08-0/current/shared/Timer.class
opt/bbmap-39.08-0/current/shared/Timer.java
opt/bbmap-39.08-0/current/shared/Tools$1.class
opt/bbmap-39.08-0/current/shared/Tools.class
opt/bbmap-39.08-0/current/shared/Tools.java
opt/bbmap-39.08-0/current/shared/TrimRead.class
opt/bbmap-39.08-0/current/shared/TrimRead.java
opt/bbmap-39.08-0/current/shared/Vector.class
opt/bbmap-39.08-0/current/shared/Vector.java
opt/bbmap-39.08-0/current/sketch/AddSSU$SketchHeader.class
opt/bbmap-39.08-0/current/sketch/AddSSU.class
opt/bbmap-39.08-0/current/sketch/AddSSU.java
opt/bbmap-39.08-0/current/sketch/AlignmentJob.class
opt/bbmap-39.08-0/current/sketch/AlignmentJob.java
opt/bbmap-39.08-0/current/sketch/AlignmentThreadPool$AlignmentThread.class
opt/bbmap-39.08-0/current/sketch/AlignmentThreadPool.class
opt/bbmap-39.08-0/current/sketch/AlignmentThreadPool.java
opt/bbmap-39.08-0/current/sketch/AnalyzeSketchResults$SSUThread.class
opt/bbmap-39.08-0/current/sketch/AnalyzeSketchResults.class
opt/bbmap-39.08-0/current/sketch/AnalyzeSketchResults.java
opt/bbmap-39.08-0/current/sketch/Blacklist.class
opt/bbmap-39.08-0/current/sketch/Blacklist.java
opt/bbmap-39.08-0/current/sketch/BlacklistMaker$ProcessThread.class
opt/bbmap-39.08-0/current/sketch/BlacklistMaker.class
opt/bbmap-39.08-0/current/sketch/BlacklistMaker.java
opt/bbmap-39.08-0/current/sketch/BlacklistMaker2$KeyPair.class
opt/bbmap-39.08-0/current/sketch/BlacklistMaker2$ProcessThread.class
opt/bbmap-39.08-0/current/sketch/BlacklistMaker2.class
opt/bbmap-39.08-0/current/sketch/BlacklistMaker2.java
opt/bbmap-39.08-0/current/sketch/CompareBuffer.class
opt/bbmap-39.08-0/current/sketch/CompareBuffer.java
opt/bbmap-39.08-0/current/sketch/CompareSSU$ProcessThread.class
opt/bbmap-39.08-0/current/sketch/CompareSSU.class
opt/bbmap-39.08-0/current/sketch/CompareSSU.java
opt/bbmap-39.08-0/current/sketch/CompareSketch$CompareThread.class
opt/bbmap-39.08-0/current/sketch/CompareSketch.class
opt/bbmap-39.08-0/current/sketch/CompareSketch.java
opt/bbmap-39.08-0/current/sketch/Comparison$Depth2Comparator.class
opt/bbmap-39.08-0/current/sketch/Comparison$DepthComparator.class
opt/bbmap-39.08-0/current/sketch/Comparison$HitsComparator.class
opt/bbmap-39.08-0/current/sketch/Comparison$KIDComparator.class
opt/bbmap-39.08-0/current/sketch/Comparison$SSUComparator.class
opt/bbmap-39.08-0/current/sketch/Comparison$ScoreComparator.class
opt/bbmap-39.08-0/current/sketch/Comparison$VolumeComparator.class
opt/bbmap-39.08-0/current/sketch/Comparison$WKIDComparator.class
opt/bbmap-39.08-0/current/sketch/Comparison.class
opt/bbmap-39.08-0/current/sketch/Comparison.java
opt/bbmap-39.08-0/current/sketch/DisplayParams.class
opt/bbmap-39.08-0/current/sketch/DisplayParams.java
opt/bbmap-39.08-0/current/sketch/GlocalAligner.class
opt/bbmap-39.08-0/current/sketch/GlocalAligner.java
opt/bbmap-39.08-0/current/sketch/InvertKey.class
opt/bbmap-39.08-0/current/sketch/InvertKey.java
opt/bbmap-39.08-0/current/sketch/KmerLimit$ProcessThread.class
opt/bbmap-39.08-0/current/sketch/KmerLimit.class
opt/bbmap-39.08-0/current/sketch/KmerLimit.java
opt/bbmap-39.08-0/current/sketch/KmerLimit2$ProcessThread.class
opt/bbmap-39.08-0/current/sketch/KmerLimit2.class
opt/bbmap-39.08-0/current/sketch/KmerLimit2.java
opt/bbmap-39.08-0/current/sketch/MergeSketch.class
opt/bbmap-39.08-0/current/sketch/MergeSketch.java
opt/bbmap-39.08-0/current/sketch/Record.class
opt/bbmap-39.08-0/current/sketch/Record.java
opt/bbmap-39.08-0/current/sketch/RecordSet.class
opt/bbmap-39.08-0/current/sketch/RecordSet.java
opt/bbmap-39.08-0/current/sketch/ResultLineParser.class
opt/bbmap-39.08-0/current/sketch/ResultLineParser.java
opt/bbmap-39.08-0/current/sketch/SSUMap.class
opt/bbmap-39.08-0/current/sketch/SSUMap.java
opt/bbmap-39.08-0/current/sketch/SendSketch.class
opt/bbmap-39.08-0/current/sketch/SendSketch.java
opt/bbmap-39.08-0/current/sketch/Sketch.class
opt/bbmap-39.08-0/current/sketch/Sketch.java
opt/bbmap-39.08-0/current/sketch/SketchHeap.class
opt/bbmap-39.08-0/current/sketch/SketchHeap.java
opt/bbmap-39.08-0/current/sketch/SketchIdComparator.class
opt/bbmap-39.08-0/current/sketch/SketchIdComparator.java
opt/bbmap-39.08-0/current/sketch/SketchIndex$IndexThread.class
opt/bbmap-39.08-0/current/sketch/SketchIndex.class
opt/bbmap-39.08-0/current/sketch/SketchIndex.java
opt/bbmap-39.08-0/current/sketch/SketchMaker$ProcessThread.class
opt/bbmap-39.08-0/current/sketch/SketchMaker$WriteThread.class
opt/bbmap-39.08-0/current/sketch/SketchMaker.class
opt/bbmap-39.08-0/current/sketch/SketchMaker.java
opt/bbmap-39.08-0/current/sketch/SketchMakerMini.class
opt/bbmap-39.08-0/current/sketch/SketchMakerMini.java
opt/bbmap-39.08-0/current/sketch/SketchObject.class
opt/bbmap-39.08-0/current/sketch/SketchObject.java
opt/bbmap-39.08-0/current/sketch/SketchResults.class
opt/bbmap-39.08-0/current/sketch/SketchResults.java
opt/bbmap-39.08-0/current/sketch/SketchSearcher$CompareThread.class
opt/bbmap-39.08-0/current/sketch/SketchSearcher.class
opt/bbmap-39.08-0/current/sketch/SketchSearcher.java
opt/bbmap-39.08-0/current/sketch/SketchTool$LoadThread.class
opt/bbmap-39.08-0/current/sketch/SketchTool$LoadThread2.class
opt/bbmap-39.08-0/current/sketch/SketchTool$SketchThread.class
opt/bbmap-39.08-0/current/sketch/SketchTool.class
opt/bbmap-39.08-0/current/sketch/SketchTool.java
opt/bbmap-39.08-0/current/sketch/SubSketch.class
opt/bbmap-39.08-0/current/sketch/SubSketch.java
opt/bbmap-39.08-0/current/sketch/SummarizeSketchStats$SketchResultsLine.class
opt/bbmap-39.08-0/current/sketch/SummarizeSketchStats$SketchResultsSummary.class
opt/bbmap-39.08-0/current/sketch/SummarizeSketchStats.class
opt/bbmap-39.08-0/current/sketch/SummarizeSketchStats.java
opt/bbmap-39.08-0/current/sketch/Whitelist.class
opt/bbmap-39.08-0/current/sketch/Whitelist.java
opt/bbmap-39.08-0/current/sort/ContigLengthComparator.class
opt/bbmap-39.08-0/current/sort/ContigLengthComparator.java
opt/bbmap-39.08-0/current/sort/MergeSorted.class
opt/bbmap-39.08-0/current/sort/MergeSorted.java
opt/bbmap-39.08-0/current/sort/ReadComparator.class
opt/bbmap-39.08-0/current/sort/ReadComparator.java
opt/bbmap-39.08-0/current/sort/ReadComparatorClump.class
opt/bbmap-39.08-0/current/sort/ReadComparatorClump.java
opt/bbmap-39.08-0/current/sort/ReadComparatorCrispr.class
opt/bbmap-39.08-0/current/sort/ReadComparatorCrispr.java
opt/bbmap-39.08-0/current/sort/ReadComparatorFlowcell.class
opt/bbmap-39.08-0/current/sort/ReadComparatorFlowcell.java
opt/bbmap-39.08-0/current/sort/ReadComparatorID.class
opt/bbmap-39.08-0/current/sort/ReadComparatorID.java
opt/bbmap-39.08-0/current/sort/ReadComparatorList.class
opt/bbmap-39.08-0/current/sort/ReadComparatorList.java
opt/bbmap-39.08-0/current/sort/ReadComparatorMapping.class
opt/bbmap-39.08-0/current/sort/ReadComparatorMapping.java
opt/bbmap-39.08-0/current/sort/ReadComparatorName.class
opt/bbmap-39.08-0/current/sort/ReadComparatorName.java
opt/bbmap-39.08-0/current/sort/ReadComparatorPosition.class
opt/bbmap-39.08-0/current/sort/ReadComparatorPosition.java
opt/bbmap-39.08-0/current/sort/ReadComparatorRandom.class
opt/bbmap-39.08-0/current/sort/ReadComparatorRandom.java
opt/bbmap-39.08-0/current/sort/ReadComparatorTaxa.class
opt/bbmap-39.08-0/current/sort/ReadComparatorTaxa.java
opt/bbmap-39.08-0/current/sort/ReadComparatorTopological.class
opt/bbmap-39.08-0/current/sort/ReadComparatorTopological.java
opt/bbmap-39.08-0/current/sort/ReadComparatorTopological5Bit.class
opt/bbmap-39.08-0/current/sort/ReadComparatorTopological5Bit.java
opt/bbmap-39.08-0/current/sort/ReadErrorComparator.class
opt/bbmap-39.08-0/current/sort/ReadErrorComparator.java
opt/bbmap-39.08-0/current/sort/ReadLengthComparator.class
opt/bbmap-39.08-0/current/sort/ReadLengthComparator.java
opt/bbmap-39.08-0/current/sort/ReadQualityComparator.class
opt/bbmap-39.08-0/current/sort/ReadQualityComparator.java
opt/bbmap-39.08-0/current/sort/Shuffle$ShuffleThread.class
opt/bbmap-39.08-0/current/sort/Shuffle.class
opt/bbmap-39.08-0/current/sort/Shuffle.java
opt/bbmap-39.08-0/current/sort/Shuffle2$WriteThread.class
opt/bbmap-39.08-0/current/sort/Shuffle2.class
opt/bbmap-39.08-0/current/sort/Shuffle2.java
opt/bbmap-39.08-0/current/sort/SortByName$WriteThread.class
opt/bbmap-39.08-0/current/sort/SortByName.class
opt/bbmap-39.08-0/current/sort/SortByName.java
opt/bbmap-39.08-0/current/sort/SortReadsByID$1.class
opt/bbmap-39.08-0/current/sort/SortReadsByID$Block.class
opt/bbmap-39.08-0/current/sort/SortReadsByID.class
opt/bbmap-39.08-0/current/sort/SortReadsByID.java
opt/bbmap-39.08-0/current/stream/ArrayListSet$Pack.class
opt/bbmap-39.08-0/current/stream/ArrayListSet.class
opt/bbmap-39.08-0/current/stream/ArrayListSet.java
opt/bbmap-39.08-0/current/stream/BufferedMultiCros.class
opt/bbmap-39.08-0/current/stream/BufferedMultiCros.java
opt/bbmap-39.08-0/current/stream/ConcurrentCollectionReadInputStream.class
opt/bbmap-39.08-0/current/stream/ConcurrentCollectionReadInputStream.java
opt/bbmap-39.08-0/current/stream/ConcurrentDepot.class
opt/bbmap-39.08-0/current/stream/ConcurrentDepot.java
opt/bbmap-39.08-0/current/stream/ConcurrentGenericReadInputStream$1.class
opt/bbmap-39.08-0/current/stream/ConcurrentGenericReadInputStream$ReadThread.class
opt/bbmap-39.08-0/current/stream/ConcurrentGenericReadInputStream.class
opt/bbmap-39.08-0/current/stream/ConcurrentGenericReadInputStream.java
opt/bbmap-39.08-0/current/stream/ConcurrentGenericReadOutputStream.class
opt/bbmap-39.08-0/current/stream/ConcurrentGenericReadOutputStream.java
opt/bbmap-39.08-0/current/stream/ConcurrentLegacyReadInputStream.class
opt/bbmap-39.08-0/current/stream/ConcurrentLegacyReadInputStream.java
opt/bbmap-39.08-0/current/stream/ConcurrentReadInputStream.class
opt/bbmap-39.08-0/current/stream/ConcurrentReadInputStream.java
opt/bbmap-39.08-0/current/stream/ConcurrentReadInputStreamD.class
opt/bbmap-39.08-0/current/stream/ConcurrentReadInputStreamD.java
opt/bbmap-39.08-0/current/stream/ConcurrentReadListDepot.class
opt/bbmap-39.08-0/current/stream/ConcurrentReadListDepot.java
opt/bbmap-39.08-0/current/stream/ConcurrentReadOutputStream.class
opt/bbmap-39.08-0/current/stream/ConcurrentReadOutputStream.java
opt/bbmap-39.08-0/current/stream/ConcurrentReadOutputStreamD$ListenThread.class
opt/bbmap-39.08-0/current/stream/ConcurrentReadOutputStreamD.class
opt/bbmap-39.08-0/current/stream/ConcurrentReadOutputStreamD.java
opt/bbmap-39.08-0/current/stream/ConcurrentReadStreamInterface.class
opt/bbmap-39.08-0/current/stream/ConcurrentReadStreamInterface.java
opt/bbmap-39.08-0/current/stream/CrisContainer.class
opt/bbmap-39.08-0/current/stream/CrisContainer.java
opt/bbmap-39.08-0/current/stream/CrisWrapper.class
opt/bbmap-39.08-0/current/stream/CrisWrapper.java
opt/bbmap-39.08-0/current/stream/CustomHeader.class
opt/bbmap-39.08-0/current/stream/CustomHeader.java
opt/bbmap-39.08-0/current/stream/DualCris.class
opt/bbmap-39.08-0/current/stream/DualCris.java
opt/bbmap-39.08-0/current/stream/EmblReadInputStream.class
opt/bbmap-39.08-0/current/stream/EmblReadInputStream.java
opt/bbmap-39.08-0/current/stream/FASTQ.class
opt/bbmap-39.08-0/current/stream/FASTQ.java
opt/bbmap-39.08-0/current/stream/FastaQualReadInputStream.class
opt/bbmap-39.08-0/current/stream/FastaQualReadInputStream.java
opt/bbmap-39.08-0/current/stream/FastaReadInputStream.class
opt/bbmap-39.08-0/current/stream/FastaReadInputStream.java
opt/bbmap-39.08-0/current/stream/FastaShredInputStream.class
opt/bbmap-39.08-0/current/stream/FastaShredInputStream.java
opt/bbmap-39.08-0/current/stream/FastqReadInputStream.class
opt/bbmap-39.08-0/current/stream/FastqReadInputStream.java
opt/bbmap-39.08-0/current/stream/GbkReadInputStream.class
opt/bbmap-39.08-0/current/stream/GbkReadInputStream.java
opt/bbmap-39.08-0/current/stream/HeaderInputStream.class
opt/bbmap-39.08-0/current/stream/HeaderInputStream.java
opt/bbmap-39.08-0/current/stream/MDWalker.class
opt/bbmap-39.08-0/current/stream/MDWalker.java
opt/bbmap-39.08-0/current/stream/MultiCros.class
opt/bbmap-39.08-0/current/stream/MultiCros.java
opt/bbmap-39.08-0/current/stream/MultiCros2$Buffer.class
opt/bbmap-39.08-0/current/stream/MultiCros2.class
opt/bbmap-39.08-0/current/stream/MultiCros2.java
opt/bbmap-39.08-0/current/stream/MultiCros3$Buffer.class
opt/bbmap-39.08-0/current/stream/MultiCros3.class
opt/bbmap-39.08-0/current/stream/MultiCros3.java
opt/bbmap-39.08-0/current/stream/MultiCros4$Buffer.class
opt/bbmap-39.08-0/current/stream/MultiCros4$RetireThread.class
opt/bbmap-39.08-0/current/stream/MultiCros4$Token.class
opt/bbmap-39.08-0/current/stream/MultiCros4.class
opt/bbmap-39.08-0/current/stream/MultiCros4.java
opt/bbmap-39.08-0/current/stream/MultiCros5$Buffer.class
opt/bbmap-39.08-0/current/stream/MultiCros5.class
opt/bbmap-39.08-0/current/stream/MultiCros5.java
opt/bbmap-39.08-0/current/stream/MultiCros6$Buffer.class
opt/bbmap-39.08-0/current/stream/MultiCros6$TimestampComparator.class
opt/bbmap-39.08-0/current/stream/MultiCros6.class
opt/bbmap-39.08-0/current/stream/MultiCros6.java
opt/bbmap-39.08-0/current/stream/NullOutputStream.class
opt/bbmap-39.08-0/current/stream/NullOutputStream.java
opt/bbmap-39.08-0/current/stream/OnelineReadInputStream.class
opt/bbmap-39.08-0/current/stream/OnelineReadInputStream.java
opt/bbmap-39.08-0/current/stream/RTextInputStream.class
opt/bbmap-39.08-0/current/stream/RTextInputStream.java
opt/bbmap-39.08-0/current/stream/RandomReadInputStream3.class
opt/bbmap-39.08-0/current/stream/RandomReadInputStream3.java
opt/bbmap-39.08-0/current/stream/Read.class
opt/bbmap-39.08-0/current/stream/Read.java
opt/bbmap-39.08-0/current/stream/ReadInputStream.class
opt/bbmap-39.08-0/current/stream/ReadInputStream.java
opt/bbmap-39.08-0/current/stream/ReadStreamByteWriter.class
opt/bbmap-39.08-0/current/stream/ReadStreamByteWriter.java
opt/bbmap-39.08-0/current/stream/ReadStreamWriter$Job.class
opt/bbmap-39.08-0/current/stream/ReadStreamWriter.class
opt/bbmap-39.08-0/current/stream/ReadStreamWriter.java
opt/bbmap-39.08-0/current/stream/SamHeader.class
opt/bbmap-39.08-0/current/stream/SamHeader.java
opt/bbmap-39.08-0/current/stream/SamLine.class
opt/bbmap-39.08-0/current/stream/SamLine.java
opt/bbmap-39.08-0/current/stream/SamLineStreamer$ProcessThread.class
opt/bbmap-39.08-0/current/stream/SamLineStreamer.class
opt/bbmap-39.08-0/current/stream/SamLineStreamer.java
opt/bbmap-39.08-0/current/stream/SamReadInputStream.class
opt/bbmap-39.08-0/current/stream/SamReadInputStream.java
opt/bbmap-39.08-0/current/stream/SamReadStreamer$ProcessThread.class
opt/bbmap-39.08-0/current/stream/SamReadStreamer.class
opt/bbmap-39.08-0/current/stream/SamReadStreamer.java
opt/bbmap-39.08-0/current/stream/SamStreamer.class
opt/bbmap-39.08-0/current/stream/SamStreamer.java
opt/bbmap-39.08-0/current/stream/SamStreamerMF.class
opt/bbmap-39.08-0/current/stream/SamStreamerMF.java
opt/bbmap-39.08-0/current/stream/SamStreamerWrapper.class
opt/bbmap-39.08-0/current/stream/SamStreamerWrapper.java
opt/bbmap-39.08-0/current/stream/ScaffoldCoordinates.class
opt/bbmap-39.08-0/current/stream/ScaffoldCoordinates.java
opt/bbmap-39.08-0/current/stream/ScarfReadInputStream.class
opt/bbmap-39.08-0/current/stream/ScarfReadInputStream.java
opt/bbmap-39.08-0/current/stream/SequentialReadInputStream.class
opt/bbmap-39.08-0/current/stream/SequentialReadInputStream.java
opt/bbmap-39.08-0/current/stream/SiteScore$PositionComparator.class
opt/bbmap-39.08-0/current/stream/SiteScore.class
opt/bbmap-39.08-0/current/stream/SiteScore.java
opt/bbmap-39.08-0/current/stream/SiteScoreR$IDComparator.class
opt/bbmap-39.08-0/current/stream/SiteScoreR$NormalizedComparator.class
opt/bbmap-39.08-0/current/stream/SiteScoreR$PositionComparator.class
opt/bbmap-39.08-0/current/stream/SiteScoreR.class
opt/bbmap-39.08-0/current/stream/SiteScoreR.java
opt/bbmap-39.08-0/current/structures/AbstractBitSet.class
opt/bbmap-39.08-0/current/structures/AbstractBitSet.java
opt/bbmap-39.08-0/current/structures/AbstractIntHashMap.class
opt/bbmap-39.08-0/current/structures/AbstractIntHashMap.java
opt/bbmap-39.08-0/current/structures/AtomicBitSet.class
opt/bbmap-39.08-0/current/structures/AtomicBitSet.java
opt/bbmap-39.08-0/current/structures/ByteBuilder.class
opt/bbmap-39.08-0/current/structures/ByteBuilder.java
opt/bbmap-39.08-0/current/structures/CRange.class
opt/bbmap-39.08-0/current/structures/CRange.java
opt/bbmap-39.08-0/current/structures/CoverageArray.class
opt/bbmap-39.08-0/current/structures/CoverageArray.java
opt/bbmap-39.08-0/current/structures/CoverageArray2.class
opt/bbmap-39.08-0/current/structures/CoverageArray2.java
opt/bbmap-39.08-0/current/structures/CoverageArray2A.class
opt/bbmap-39.08-0/current/structures/CoverageArray2A.java
opt/bbmap-39.08-0/current/structures/CoverageArray3.class
opt/bbmap-39.08-0/current/structures/CoverageArray3.java
opt/bbmap-39.08-0/current/structures/CoverageArray3A.class
opt/bbmap-39.08-0/current/structures/CoverageArray3A.java
opt/bbmap-39.08-0/current/structures/Crispr.class
opt/bbmap-39.08-0/current/structures/Crispr.java
opt/bbmap-39.08-0/current/structures/DoubleList.class
opt/bbmap-39.08-0/current/structures/DoubleList.java
opt/bbmap-39.08-0/current/structures/Feature.class
opt/bbmap-39.08-0/current/structures/Feature.java
opt/bbmap-39.08-0/current/structures/FloatList.class
opt/bbmap-39.08-0/current/structures/FloatList.java
opt/bbmap-39.08-0/current/structures/Heap$HeapIterator.class
opt/bbmap-39.08-0/current/structures/Heap.class
opt/bbmap-39.08-0/current/structures/Heap.java
opt/bbmap-39.08-0/current/structures/HeapLoc$HeapIterator.class
opt/bbmap-39.08-0/current/structures/HeapLoc.class
opt/bbmap-39.08-0/current/structures/HeapLoc.java
opt/bbmap-39.08-0/current/structures/IntHashMap.class
opt/bbmap-39.08-0/current/structures/IntHashMap.java
opt/bbmap-39.08-0/current/structures/IntHashMapBinary.class
opt/bbmap-39.08-0/current/structures/IntHashMapBinary.java
opt/bbmap-39.08-0/current/structures/IntHashSet.class
opt/bbmap-39.08-0/current/structures/IntHashSet.java
opt/bbmap-39.08-0/current/structures/IntHashSetList.class
opt/bbmap-39.08-0/current/structures/IntHashSetList.java
opt/bbmap-39.08-0/current/structures/IntList.class
opt/bbmap-39.08-0/current/structures/IntList.java
opt/bbmap-39.08-0/current/structures/IntList2.class
opt/bbmap-39.08-0/current/structures/IntList2.java
opt/bbmap-39.08-0/current/structures/IntList3.class
opt/bbmap-39.08-0/current/structures/IntList3.java
opt/bbmap-39.08-0/current/structures/IntListCompressor.class
opt/bbmap-39.08-0/current/structures/IntListCompressor.java
opt/bbmap-39.08-0/current/structures/IntLongHashMap.class
opt/bbmap-39.08-0/current/structures/IntLongHashMap.java
opt/bbmap-39.08-0/current/structures/IntMap.class
opt/bbmap-39.08-0/current/structures/IntMap.java
opt/bbmap-39.08-0/current/structures/ListNum.class
opt/bbmap-39.08-0/current/structures/ListNum.java
opt/bbmap-39.08-0/current/structures/LongArrayListHashMap.class
opt/bbmap-39.08-0/current/structures/LongArrayListHashMap.java
opt/bbmap-39.08-0/current/structures/LongHashMap.class
opt/bbmap-39.08-0/current/structures/LongHashMap.java
opt/bbmap-39.08-0/current/structures/LongHashSet.class
opt/bbmap-39.08-0/current/structures/LongHashSet.java
opt/bbmap-39.08-0/current/structures/LongHeap.class
opt/bbmap-39.08-0/current/structures/LongHeap.java
opt/bbmap-39.08-0/current/structures/LongHeapMap.class
opt/bbmap-39.08-0/current/structures/LongHeapMap.java
opt/bbmap-39.08-0/current/structures/LongHeapSet.class
opt/bbmap-39.08-0/current/structures/LongHeapSet.java
opt/bbmap-39.08-0/current/structures/LongHeapSetInterface.class
opt/bbmap-39.08-0/current/structures/LongHeapSetInterface.java
opt/bbmap-39.08-0/current/structures/LongList.class
opt/bbmap-39.08-0/current/structures/LongList.java
opt/bbmap-39.08-0/current/structures/LongList2.class
opt/bbmap-39.08-0/current/structures/LongList2.java
opt/bbmap-39.08-0/current/structures/LongList3.class
opt/bbmap-39.08-0/current/structures/LongList3.java
opt/bbmap-39.08-0/current/structures/LongListSet$LongListSetIterator.class
opt/bbmap-39.08-0/current/structures/LongListSet.class
opt/bbmap-39.08-0/current/structures/LongListSet.java
opt/bbmap-39.08-0/current/structures/LongLongHashMap.class
opt/bbmap-39.08-0/current/structures/LongLongHashMap.java
opt/bbmap-39.08-0/current/structures/LongLongListHashMap.class
opt/bbmap-39.08-0/current/structures/LongLongListHashMap.java
opt/bbmap-39.08-0/current/structures/LongM.class
opt/bbmap-39.08-0/current/structures/LongM.java
opt/bbmap-39.08-0/current/structures/LongPair.class
opt/bbmap-39.08-0/current/structures/LongPair.java
opt/bbmap-39.08-0/current/structures/MultiBitSet.class
opt/bbmap-39.08-0/current/structures/MultiBitSet.java
opt/bbmap-39.08-0/current/structures/Quantizer.class
opt/bbmap-39.08-0/current/structures/Quantizer.java
opt/bbmap-39.08-0/current/structures/Range.class
opt/bbmap-39.08-0/current/structures/Range.java
opt/bbmap-39.08-0/current/structures/RawBitSet.class
opt/bbmap-39.08-0/current/structures/RawBitSet.java
opt/bbmap-39.08-0/current/structures/SeqCount.class
opt/bbmap-39.08-0/current/structures/SeqCount.java
opt/bbmap-39.08-0/current/structures/SeqCountM.class
opt/bbmap-39.08-0/current/structures/SeqCountM.java
opt/bbmap-39.08-0/current/structures/SeqMap$1.class
opt/bbmap-39.08-0/current/structures/SeqMap$2.class
opt/bbmap-39.08-0/current/structures/SeqMap$3.class
opt/bbmap-39.08-0/current/structures/SeqMap.class
opt/bbmap-39.08-0/current/structures/SeqMap.java
opt/bbmap-39.08-0/current/structures/SeqPos.class
opt/bbmap-39.08-0/current/structures/SeqPos.java
opt/bbmap-39.08-0/current/structures/SeqPosM.class
opt/bbmap-39.08-0/current/structures/SeqPosM.java
opt/bbmap-39.08-0/current/structures/SetLoc.class
opt/bbmap-39.08-0/current/structures/SetLoc.java
opt/bbmap-39.08-0/current/structures/StandardDeviator$ProcessThread.class
opt/bbmap-39.08-0/current/structures/StandardDeviator.class
opt/bbmap-39.08-0/current/structures/StandardDeviator.java
opt/bbmap-39.08-0/current/structures/StringNum.class
opt/bbmap-39.08-0/current/structures/StringNum.java
opt/bbmap-39.08-0/current/structures/StringPair.class
opt/bbmap-39.08-0/current/structures/StringPair.java
opt/bbmap-39.08-0/current/structures/SuperLongList.class
opt/bbmap-39.08-0/current/structures/SuperLongList.java
opt/bbmap-39.08-0/current/tax/AccessionToTaxid$HashThread.class
opt/bbmap-39.08-0/current/tax/AccessionToTaxid.class
opt/bbmap-39.08-0/current/tax/AccessionToTaxid.java
opt/bbmap-39.08-0/current/tax/AccessionToTaxid_old$HashThread.class
opt/bbmap-39.08-0/current/tax/AccessionToTaxid_old.class
opt/bbmap-39.08-0/current/tax/AccessionToTaxid_old.java
opt/bbmap-39.08-0/current/tax/AnalyzeAccession$ProcessThread.class
opt/bbmap-39.08-0/current/tax/AnalyzeAccession.class
opt/bbmap-39.08-0/current/tax/AnalyzeAccession.java
opt/bbmap-39.08-0/current/tax/AnalyzeAccession_ST.class
opt/bbmap-39.08-0/current/tax/AnalyzeAccession_ST.java
opt/bbmap-39.08-0/current/tax/ExplodeTree.class
opt/bbmap-39.08-0/current/tax/ExplodeTree.java
opt/bbmap-39.08-0/current/tax/FilterByTaxa.class
opt/bbmap-39.08-0/current/tax/FilterByTaxa.java
opt/bbmap-39.08-0/current/tax/FindAncestor.class
opt/bbmap-39.08-0/current/tax/FindAncestor.java
opt/bbmap-39.08-0/current/tax/GiToTaxid.class
opt/bbmap-39.08-0/current/tax/GiToTaxid.java
opt/bbmap-39.08-0/current/tax/GiToTaxidInt.class
opt/bbmap-39.08-0/current/tax/GiToTaxidInt.java
opt/bbmap-39.08-0/current/tax/IDNode.class
opt/bbmap-39.08-0/current/tax/IDNode.java
opt/bbmap-39.08-0/current/tax/IDTree.class
opt/bbmap-39.08-0/current/tax/IDTree.java
opt/bbmap-39.08-0/current/tax/ImgRecord.class
opt/bbmap-39.08-0/current/tax/ImgRecord.java
opt/bbmap-39.08-0/current/tax/ImgRecord2.class
opt/bbmap-39.08-0/current/tax/ImgRecord2.java
opt/bbmap-39.08-0/current/tax/PrintTaxonomy.class
opt/bbmap-39.08-0/current/tax/PrintTaxonomy.java
opt/bbmap-39.08-0/current/tax/Query.class
opt/bbmap-39.08-0/current/tax/Query.java
opt/bbmap-39.08-0/current/tax/RenameGiToTaxid.class
opt/bbmap-39.08-0/current/tax/RenameGiToTaxid.java
opt/bbmap-39.08-0/current/tax/RenameIMG.class
opt/bbmap-39.08-0/current/tax/RenameIMG.java
opt/bbmap-39.08-0/current/tax/ShrinkAccession.class
opt/bbmap-39.08-0/current/tax/ShrinkAccession.java
opt/bbmap-39.08-0/current/tax/SplitByTaxa.class
opt/bbmap-39.08-0/current/tax/SplitByTaxa.java
opt/bbmap-39.08-0/current/tax/TaxApp$1.class
opt/bbmap-39.08-0/current/tax/TaxApp.class
opt/bbmap-39.08-0/current/tax/TaxApp.java
opt/bbmap-39.08-0/current/tax/TaxClient.class
opt/bbmap-39.08-0/current/tax/TaxClient.java
opt/bbmap-39.08-0/current/tax/TaxFilter$1.class
opt/bbmap-39.08-0/current/tax/TaxFilter.class
opt/bbmap-39.08-0/current/tax/TaxFilter.java
opt/bbmap-39.08-0/current/tax/TaxNode$CountComparator.class
opt/bbmap-39.08-0/current/tax/TaxNode.class
opt/bbmap-39.08-0/current/tax/TaxNode.java
opt/bbmap-39.08-0/current/tax/TaxServer$CompareThread.class
opt/bbmap-39.08-0/current/tax/TaxServer$HelpHandler.class
opt/bbmap-39.08-0/current/tax/TaxServer$IconHandler.class
opt/bbmap-39.08-0/current/tax/TaxServer$KillHandler.class
opt/bbmap-39.08-0/current/tax/TaxServer$SketchHandler$SketchInstance.class
opt/bbmap-39.08-0/current/tax/TaxServer$SketchHandler.class
opt/bbmap-39.08-0/current/tax/TaxServer$StatsHandler.class
opt/bbmap-39.08-0/current/tax/TaxServer$TaxHandler.class
opt/bbmap-39.08-0/current/tax/TaxServer.class
opt/bbmap-39.08-0/current/tax/TaxServer.java
opt/bbmap-39.08-0/current/tax/TaxSize.class
opt/bbmap-39.08-0/current/tax/TaxSize.java
opt/bbmap-39.08-0/current/tax/TaxTree.class
opt/bbmap-39.08-0/current/tax/TaxTree.java
opt/bbmap-39.08-0/current/template/A_Sample.class
opt/bbmap-39.08-0/current/template/A_Sample.java
opt/bbmap-39.08-0/current/template/A_Sample2.class
opt/bbmap-39.08-0/current/template/A_Sample2.java
opt/bbmap-39.08-0/current/template/A_SampleBasic.class
opt/bbmap-39.08-0/current/template/A_SampleBasic.java
opt/bbmap-39.08-0/current/template/A_SampleBasic2.class
opt/bbmap-39.08-0/current/template/A_SampleBasic2.java
opt/bbmap-39.08-0/current/template/A_SampleByteFile.class
opt/bbmap-39.08-0/current/template/A_SampleByteFile.java
opt/bbmap-39.08-0/current/template/A_SampleByteFileMT$ProcessThread.class
opt/bbmap-39.08-0/current/template/A_SampleByteFileMT.class
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opt/bbmap-39.08-0/pytools/filter_desc/fungal.txt
opt/bbmap-39.08-0/pytools/filter_desc/iso.txt
opt/bbmap-39.08-0/pytools/filter_desc/itag.txt
opt/bbmap-39.08-0/pytools/filter_desc/lfpe.txt
opt/bbmap-39.08-0/pytools/filter_desc/metagenome.txt
opt/bbmap-39.08-0/pytools/filter_desc/microtrans.txt
opt/bbmap-39.08-0/pytools/filter_desc/mtaa.txt
opt/bbmap-39.08-0/pytools/filter_desc/nextera-lmp.txt
opt/bbmap-39.08-0/pytools/filter_desc/plant-2x150.txt
opt/bbmap-39.08-0/pytools/filter_desc/plant-2x250.txt
opt/bbmap-39.08-0/pytools/filter_desc/rna.txt
opt/bbmap-39.08-0/pytools/filter_desc/rnawohuman.txt
opt/bbmap-39.08-0/pytools/filter_desc/sag.txt
opt/bbmap-39.08-0/pytools/filter_desc/smrna.txt
opt/bbmap-39.08-0/pytools/filter_desc/sop_list.txt
opt/bbmap-39.08-0/pytools/filter_desc/viral-metagenome.txt
opt/bbmap-39.08-0/pytools/filter_param/3primerna.config
opt/bbmap-39.08-0/pytools/filter_param/bisulphite.config
opt/bbmap-39.08-0/pytools/filter_param/cell-enrichment.config
opt/bbmap-39.08-0/pytools/filter_param/chip-seq.config
opt/bbmap-39.08-0/pytools/filter_param/clip-pe.config
opt/bbmap-39.08-0/pytools/filter_param/clrs.config
opt/bbmap-39.08-0/pytools/filter_param/dna.config
opt/bbmap-39.08-0/pytools/filter_param/fungal.config
opt/bbmap-39.08-0/pytools/filter_param/iso.config
opt/bbmap-39.08-0/pytools/filter_param/itag.config
opt/bbmap-39.08-0/pytools/filter_param/lfpe.config
opt/bbmap-39.08-0/pytools/filter_param/metagenome.config
opt/bbmap-39.08-0/pytools/filter_param/microtrans.config
opt/bbmap-39.08-0/pytools/filter_param/mtaa.config
opt/bbmap-39.08-0/pytools/filter_param/nextera-lmp.config
opt/bbmap-39.08-0/pytools/filter_param/nextseq.config
opt/bbmap-39.08-0/pytools/filter_param/plant-2x150.config
opt/bbmap-39.08-0/pytools/filter_param/plant-2x250.config
opt/bbmap-39.08-0/pytools/filter_param/rna.config
opt/bbmap-39.08-0/pytools/filter_param/rnawohuman.config
opt/bbmap-39.08-0/pytools/filter_param/sag.config
opt/bbmap-39.08-0/pytools/filter_param/smrna.config
opt/bbmap-39.08-0/pytools/filter_param/viral-metagenome.config
opt/bbmap-39.08-0/pytools/images/JGI_logo.jpg
opt/bbmap-39.08-0/pytools/images/favicon.ico
opt/bbmap-39.08-0/pytools/images/jgi_log_transparent.png
opt/bbmap-39.08-0/pytools/lib/common.py
opt/bbmap-39.08-0/pytools/lib/html_utility.py
opt/bbmap-39.08-0/pytools/lib/kmercount_pos.py
opt/bbmap-39.08-0/pytools/lib/os_utility.py
opt/bbmap-39.08-0/pytools/lib/readSeq.py
opt/bbmap-39.08-0/pytools/lib/readqc_constants.py
opt/bbmap-39.08-0/pytools/lib/readqc_report.py
opt/bbmap-39.08-0/pytools/lib/readqc_utils.py
opt/bbmap-39.08-0/pytools/lib/rqc_constants.py
opt/bbmap-39.08-0/pytools/lib/rqc_fastq.py
opt/bbmap-39.08-0/pytools/lib/rqc_utility.py
opt/bbmap-39.08-0/pytools/readqc.py
opt/bbmap-39.08-0/pytools/template/filter_body_template.html
opt/bbmap-39.08-0/pytools/template/readqc_artifacts.html
opt/bbmap-39.08-0/pytools/template/readqc_body_template.html
opt/bbmap-39.08-0/pytools/template/template.html
opt/bbmap-39.08-0/pytools/tools/patterN_fastq.pl
opt/bbmap-39.08-0/randomgenome.sh
opt/bbmap-39.08-0/randomreads.sh
opt/bbmap-39.08-0/readlength.sh
opt/bbmap-39.08-0/readqc.sh
opt/bbmap-39.08-0/reducesilva.sh
opt/bbmap-39.08-0/reformat.sh
opt/bbmap-39.08-0/reformatpb.sh
opt/bbmap-39.08-0/removebadbarcodes.sh
opt/bbmap-39.08-0/removecatdogmousehuman.sh
opt/bbmap-39.08-0/removehuman.sh
opt/bbmap-39.08-0/removehuman2.sh
opt/bbmap-39.08-0/removemicrobes.sh
opt/bbmap-39.08-0/removesmartbell.sh
opt/bbmap-39.08-0/rename.sh
opt/bbmap-39.08-0/renameimg.sh
opt/bbmap-39.08-0/repair.sh
opt/bbmap-39.08-0/replaceheaders.sh
opt/bbmap-39.08-0/representative.sh
opt/bbmap-39.08-0/resources/16S_15mers.fa
opt/bbmap-39.08-0/resources/16S_consensus_sequence.fa
opt/bbmap-39.08-0/resources/18S_15mers.fa
opt/bbmap-39.08-0/resources/18S_consensus_sequence.fa
opt/bbmap-39.08-0/resources/23S_15mers.fa
opt/bbmap-39.08-0/resources/23S_consensus_sequence.fa
opt/bbmap-39.08-0/resources/5S_10mers.fa
opt/bbmap-39.08-0/resources/5S_11mers.fa
opt/bbmap-39.08-0/resources/5S_12mers.fa
opt/bbmap-39.08-0/resources/5S_15mers.fa
opt/bbmap-39.08-0/resources/5S_9mers.fa
opt/bbmap-39.08-0/resources/5S_consensus_sequence.fa
opt/bbmap-39.08-0/resources/Covid19_ref.fa
opt/bbmap-39.08-0/resources/ITS_animal_consensus_sequence.fq
opt/bbmap-39.08-0/resources/ITS_consensus_sequence.fq
opt/bbmap-39.08-0/resources/ITS_fungi_consensus_sequence.fq
opt/bbmap-39.08-0/resources/ITS_nonfungi_consensus_sequence.fq
opt/bbmap-39.08-0/resources/ITS_other_consensus_sequence.fq
opt/bbmap-39.08-0/resources/ITS_plant_consensus_sequence.fq
opt/bbmap-39.08-0/resources/ITS_universal_consensus_sequence.fq
opt/bbmap-39.08-0/resources/PacBioAdapter.fa
opt/bbmap-39.08-0/resources/SIP_spikeins.fa.gz
opt/bbmap-39.08-0/resources/adapters.fa
opt/bbmap-39.08-0/resources/adapters_no_transposase.fa.gz
opt/bbmap-39.08-0/resources/artic3.fasta
opt/bbmap-39.08-0/resources/bbmerge.bbnet
opt/bbmap-39.08-0/resources/blacklist_nt_merged.sketch
opt/bbmap-39.08-0/resources/blacklist_prokprot_merged.sketch
opt/bbmap-39.08-0/resources/blacklist_refseq_merged.sketch
opt/bbmap-39.08-0/resources/blacklist_silva_merged.sketch
opt/bbmap-39.08-0/resources/contents.txt
opt/bbmap-39.08-0/resources/crelox.fa.gz
opt/bbmap-39.08-0/resources/crispr.bbnet.gz
opt/bbmap-39.08-0/resources/crisprs.fa.gz
opt/bbmap-39.08-0/resources/favicon.ico
opt/bbmap-39.08-0/resources/kapatags.L40.fa
opt/bbmap-39.08-0/resources/lambda.fa.gz
opt/bbmap-39.08-0/resources/lfpe.linker.fa.gz
opt/bbmap-39.08-0/resources/lsu_15mers.fa
opt/bbmap-39.08-0/resources/m16S_consensus_sequence.fa
opt/bbmap-39.08-0/resources/m18S_consensus_sequence.fa
opt/bbmap-39.08-0/resources/minorAlleleCount.txt
opt/bbmap-39.08-0/resources/model.pgm
opt/bbmap-39.08-0/resources/mtst.fa
opt/bbmap-39.08-0/resources/nextera.fa.gz
opt/bbmap-39.08-0/resources/nextera_LMP_adapter.fa.gz
opt/bbmap-39.08-0/resources/nextera_LMP_linker.fa.gz
opt/bbmap-39.08-0/resources/p16S_consensus_sequence.fa
opt/bbmap-39.08-0/resources/pJET1.2.fa
opt/bbmap-39.08-0/resources/phix174_ill.ref.fa.gz
opt/bbmap-39.08-0/resources/phix_adapters.fa.gz
opt/bbmap-39.08-0/resources/polyA.fa.gz
opt/bbmap-39.08-0/resources/primes.txt.gz
opt/bbmap-39.08-0/resources/remote_files.txt
opt/bbmap-39.08-0/resources/remote_files_old.txt
opt/bbmap-39.08-0/resources/sample1.fq.gz
opt/bbmap-39.08-0/resources/sample2.fq.gz
opt/bbmap-39.08-0/resources/sequencing_artifacts.fa.gz
opt/bbmap-39.08-0/resources/short.fa
opt/bbmap-39.08-0/resources/ssu_15mers.fa
opt/bbmap-39.08-0/resources/tRNA_10mers.fa
opt/bbmap-39.08-0/resources/tRNA_11mers.fa
opt/bbmap-39.08-0/resources/tRNA_15mers.fa
opt/bbmap-39.08-0/resources/tRNA_16mers.fa
opt/bbmap-39.08-0/resources/tRNA_consensus_sequence.fa
opt/bbmap-39.08-0/resources/tax_server.html
opt/bbmap-39.08-0/resources/truseq.fa.gz
opt/bbmap-39.08-0/resources/truseq_rna.fa.gz
opt/bbmap-39.08-0/rqcfilter.sh
opt/bbmap-39.08-0/rqcfilter2.sh
opt/bbmap-39.08-0/runhmm.sh
opt/bbmap-39.08-0/samtoroc.sh
opt/bbmap-39.08-0/scoresequence.sh
opt/bbmap-39.08-0/seal.sh
opt/bbmap-39.08-0/sendsketch.sh
opt/bbmap-39.08-0/seqtovec.sh
opt/bbmap-39.08-0/shred.sh
opt/bbmap-39.08-0/shrinkaccession.sh
opt/bbmap-39.08-0/shuffle.sh
opt/bbmap-39.08-0/shuffle2.sh
opt/bbmap-39.08-0/sketch.sh
opt/bbmap-39.08-0/sketchblacklist.sh
opt/bbmap-39.08-0/sketchblacklist2.sh
opt/bbmap-39.08-0/sortbyname.sh
opt/bbmap-39.08-0/splitbytaxa.sh
opt/bbmap-39.08-0/splitnextera.sh
opt/bbmap-39.08-0/splitribo.sh
opt/bbmap-39.08-0/splitsam.sh
opt/bbmap-39.08-0/splitsam4way.sh
opt/bbmap-39.08-0/splitsam6way.sh
opt/bbmap-39.08-0/stats.sh
opt/bbmap-39.08-0/statswrapper.sh
opt/bbmap-39.08-0/streamsam.sh
opt/bbmap-39.08-0/subsketch.sh
opt/bbmap-39.08-0/summarizecontam.sh
opt/bbmap-39.08-0/summarizecoverage.sh
opt/bbmap-39.08-0/summarizecrossblock.sh
opt/bbmap-39.08-0/summarizemerge.sh
opt/bbmap-39.08-0/summarizequast.sh
opt/bbmap-39.08-0/summarizescafstats.sh
opt/bbmap-39.08-0/summarizeseal.sh
opt/bbmap-39.08-0/summarizesketch.sh
opt/bbmap-39.08-0/synthmda.sh
opt/bbmap-39.08-0/tadpipe.sh
opt/bbmap-39.08-0/tadpole.sh
opt/bbmap-39.08-0/tadwrapper.sh
opt/bbmap-39.08-0/tagandmerge.sh
opt/bbmap-39.08-0/taxonomy.sh
opt/bbmap-39.08-0/taxserver.sh
opt/bbmap-39.08-0/taxsize.sh
opt/bbmap-39.08-0/taxtree.sh
opt/bbmap-39.08-0/testfilesystem.sh
opt/bbmap-39.08-0/testformat.sh
opt/bbmap-39.08-0/testformat2.sh
opt/bbmap-39.08-0/tetramerfreq.sh
opt/bbmap-39.08-0/textfile.sh
opt/bbmap-39.08-0/train.sh
opt/bbmap-39.08-0/translate6frames.sh
opt/bbmap-39.08-0/unicode2ascii.sh
opt/bbmap-39.08-0/unzip.sh
opt/bbmap-39.08-0/vcf2gff.sh
opt/bbmap-39.08-0/webcheck.sh
share/bbmap/resources/16S_15mers.fa
share/bbmap/resources/16S_consensus_sequence.fa
share/bbmap/resources/18S_15mers.fa
share/bbmap/resources/18S_consensus_sequence.fa
share/bbmap/resources/23S_15mers.fa
share/bbmap/resources/23S_consensus_sequence.fa
share/bbmap/resources/5S_10mers.fa
share/bbmap/resources/5S_11mers.fa
share/bbmap/resources/5S_12mers.fa
share/bbmap/resources/5S_15mers.fa
share/bbmap/resources/5S_9mers.fa
share/bbmap/resources/5S_consensus_sequence.fa
share/bbmap/resources/Covid19_ref.fa
share/bbmap/resources/ITS_animal_consensus_sequence.fq
share/bbmap/resources/ITS_consensus_sequence.fq
share/bbmap/resources/ITS_fungi_consensus_sequence.fq
share/bbmap/resources/ITS_nonfungi_consensus_sequence.fq
share/bbmap/resources/ITS_other_consensus_sequence.fq
share/bbmap/resources/ITS_plant_consensus_sequence.fq
share/bbmap/resources/ITS_universal_consensus_sequence.fq
share/bbmap/resources/PacBioAdapter.fa
share/bbmap/resources/SIP_spikeins.fa.gz
share/bbmap/resources/adapters.fa
share/bbmap/resources/adapters_no_transposase.fa.gz
share/bbmap/resources/artic3.fasta
share/bbmap/resources/bbmerge.bbnet
share/bbmap/resources/blacklist_nt_merged.sketch
share/bbmap/resources/blacklist_prokprot_merged.sketch
share/bbmap/resources/blacklist_refseq_merged.sketch
share/bbmap/resources/blacklist_silva_merged.sketch
share/bbmap/resources/contents.txt
share/bbmap/resources/crelox.fa.gz
share/bbmap/resources/crispr.bbnet.gz
share/bbmap/resources/crisprs.fa.gz
share/bbmap/resources/favicon.ico
share/bbmap/resources/kapatags.L40.fa
share/bbmap/resources/lambda.fa.gz
share/bbmap/resources/lfpe.linker.fa.gz
share/bbmap/resources/lsu_15mers.fa
share/bbmap/resources/m16S_consensus_sequence.fa
share/bbmap/resources/m18S_consensus_sequence.fa
share/bbmap/resources/minorAlleleCount.txt
share/bbmap/resources/model.pgm
share/bbmap/resources/mtst.fa
share/bbmap/resources/nextera.fa.gz
share/bbmap/resources/nextera_LMP_adapter.fa.gz
share/bbmap/resources/nextera_LMP_linker.fa.gz
share/bbmap/resources/p16S_consensus_sequence.fa
share/bbmap/resources/pJET1.2.fa
share/bbmap/resources/phix174_ill.ref.fa.gz
share/bbmap/resources/phix_adapters.fa.gz
share/bbmap/resources/polyA.fa.gz
share/bbmap/resources/primes.txt.gz
share/bbmap/resources/remote_files.txt
share/bbmap/resources/remote_files_old.txt
share/bbmap/resources/sample1.fq.gz
share/bbmap/resources/sample2.fq.gz
share/bbmap/resources/sequencing_artifacts.fa.gz
share/bbmap/resources/short.fa
share/bbmap/resources/ssu_15mers.fa
share/bbmap/resources/tRNA_10mers.fa
share/bbmap/resources/tRNA_11mers.fa
share/bbmap/resources/tRNA_15mers.fa
share/bbmap/resources/tRNA_16mers.fa
share/bbmap/resources/tRNA_consensus_sequence.fa
share/bbmap/resources/tax_server.html
share/bbmap/resources/truseq.fa.gz
share/bbmap/resources/truseq_rna.fa.gz
