opt/bbmap-37.90/current/cluster/ReclusterByKmer.java
opt/bbmap-37.90/current/var2/Realign$ProcessThread.class
opt/bbmap-37.90/current/sort/ReadComparatorPosition.class
opt/bbmap-37.90/current/var/StackVariations.java
opt/bbmap-37.90/current/driver/ProcessSpeed.class
opt/bbmap-37.90/current/kmer/TableReader.java
bin/filtersam.sh
opt/bbmap-37.90/current/jgi/CalcTrueQuality.class
opt/bbmap-37.90/current/bloom/KmerCount7MT$CountThread.class
opt/bbmap-37.90/current/var2/VcfWriter.class
opt/bbmap-37.90/current/bloom/KmerCountAbstract.class
opt/bbmap-37.90/docs/Legal_Illumina.txt
opt/bbmap-37.90/current/driver/SelectReads.class
opt/bbmap-37.90/statswrapper.sh
opt/bbmap-37.90/removehuman.sh
opt/bbmap-37.90/current/driver/CompareReferenceGenomes.java
opt/bbmap-37.90/current/var2/VCFLine.java
bin/rqcfilter.sh
bin/kmercoverage.sh
bin/sketch.sh
opt/bbmap-37.90/current/stream/SamReadStreamer.java
opt/bbmap-37.90/current/align2/GapTools.java
opt/bbmap-37.90/current/tax/GiToNcbi.java
opt/bbmap-37.90/current/driver/ParseCrossblockResults.java
opt/bbmap-37.90/current/pacbio/ProcessStackedSitesNormalized$1.class
opt/bbmap-37.90/current/driver/PrintEnv.class
opt/bbmap-37.90/docs/guides/TaxonomyGuide.txt
opt/bbmap-37.90/current/bloom/KCountArray2.class
opt/bbmap-37.90/current/jgi/Dedupe2$ClusterThread.class
opt/bbmap-37.90/clumpify.sh
opt/bbmap-37.90/current/jgi/GradeMergedReads.java
opt/bbmap-37.90/current/kmer/AbstractKmerTable.java
opt/bbmap-37.90/current/structures/CoverageArray2.java
opt/bbmap-37.90/current/jgi/Dedupe$MstThread.class
opt/bbmap-37.90/current/fun/FindPath$Node.class
opt/bbmap-37.90/shred.sh
opt/bbmap-37.90/current/align2/BBMap.java
opt/bbmap-37.90/current/stream/Read.java
opt/bbmap-37.90/current/structures/IntLongHashMap.class
opt/bbmap-37.90/current/jgi/FilterBySequence.java
opt/bbmap-37.90/current/dna/GeneSet.java
opt/bbmap-37.90/current/stream/FastaReadInputStream.java
opt/bbmap-37.90/current/jgi/KmerNormalize$1.class
bin/gi2taxid.sh
opt/bbmap-37.90/current/bloom/KCountArray5MT.java
opt/bbmap-37.90/current/stream/CrisContainer.java
opt/bbmap-37.90/current/jgi/CutPrimers.class
bin/callpeaks.sh
bin/commonkmers.sh
opt/bbmap-37.90/current/jgi/DedupeProtein$ClusterThread.class
opt/bbmap-37.90/current/jgi/BBMergeOverlapper.class
opt/bbmap-37.90/current/shared/PreParser$NullOutputStream.class
opt/bbmap-37.90/current/stream/ArrayListSet$Pack.class
opt/bbmap-37.90/license.txt
opt/bbmap-37.90/current/jgi/DedupeProtein.class
bin/crosscontaminate.sh
opt/bbmap-37.90/current/jgi/KmerCoverage$1.class
opt/bbmap-37.90/current/sort/ReadLengthComparator.java
opt/bbmap-37.90/current/bloom/KCountArray4.class
opt/bbmap-37.90/current/driver/SummarizeSealStats.class
opt/bbmap-37.90/makecontaminatedgenomes.sh
opt/bbmap-37.90/current/jgi/Info.class
opt/bbmap-37.90/resources/pJET1.2.fa
opt/bbmap-37.90/current/jgi/Consect.java
bin/samtoroc.sh
opt/bbmap-37.90/current/kmer/HashForest.java
opt/bbmap-37.90/current/align2/IndexMaker5.class
opt/bbmap-37.90/current/cluster/ClusterTools.class
opt/bbmap-37.90/current/jgi/A_SampleMT.class
opt/bbmap-37.90/decontaminate.sh
opt/bbmap-37.90/current/jgi/Dedupe2.java
opt/bbmap-37.90/current/ukmer/HashBufferU.class
opt/bbmap-37.90/current/clump/KmerComparatorX.java
opt/bbmap-37.90/current/jgi/BBDuk2.java
opt/bbmap-37.90/current/stream/SamStreamer.class
opt/bbmap-37.90/loglog.sh
opt/bbmap-37.90/current/ukmer/KmerTableSetU$LoadThread.class
opt/bbmap-37.90/current/var2/SamFilter.java
opt/bbmap-37.90/current/pacbio/StackSites.class
opt/bbmap-37.90/current/stream/ConcurrentReadOutputStreamD.class
opt/bbmap-37.90/current/assemble/Shaver1$ShaveThread.class
opt/bbmap-37.90/current/jgi/DedupeByMapping.java
opt/bbmap-37.90/current/structures/JsonObject.java
opt/bbmap-37.90/current/assemble/ShaveObject.java
opt/bbmap-37.90/current/sketch/SummarizeSketchStats$SketchResultsLine.class
opt/bbmap-37.90/current/stream/FastaReadInputStream2.class
opt/bbmap-37.90/current/align2/MultiStateAligner9XFlat.class
opt/bbmap-37.90/current/align2/BBMap5.java
opt/bbmap-37.90/current/sort/ReadComparatorRandom.java
opt/bbmap-37.90/current/assemble/AbstractRemoveThread.java
opt/bbmap-37.90/current/fun/DiskBench.class
bin/matrixtocolumns.sh
opt/bbmap-37.90/replaceheaders.sh
opt/bbmap-37.90/current/fileIO/ByteFile2$BF1Thread.class
opt/bbmap-37.90/current/align2/Quad.class
opt/bbmap-37.90/current/sort/ReadComparatorTopological.class
bin/filterassemblysummary.sh
opt/bbmap-37.90/current/cluster/MergeReadHeaders.java
opt/bbmap-37.90/current/jgi/KmerCoverage$ProcessThread.class
opt/bbmap-37.90/current/cluster/ReclusterByKmer$ClusterThread.class
opt/bbmap-37.90/current/stream/CrisContainer.class
opt/bbmap-37.90/jni/jgi_BBMergeOverlapper.h
opt/bbmap-37.90/resources/truseq.fa.gz
bin/tadpipe.sh
opt/bbmap-37.90/current/jgi/TranslateSixFrames.java
opt/bbmap-37.90/current/var2/VCFFile.java
bin/stats.sh
opt/bbmap-37.90/current/tax/ImgRecord.class
opt/bbmap-37.90/current/bloom/KmerCount6MT$CountThread.class
opt/bbmap-37.90/current/driver/SummarizeCoverage.class
opt/bbmap-37.90/current/align2/GradeSamFile.java
opt/bbmap-37.90/current/sort/Shuffle.class
opt/bbmap-37.90/current/sort/SortReadsByID.java
bin/mergesam.sh
opt/bbmap-37.90/bbmerge.sh
opt/bbmap-37.90/current/jgi/Seal$ProcessThread.class
opt/bbmap-37.90/current/pacbio/ProcessStackedSitesNormalized$Ssra.class
opt/bbmap-37.90/current/jgi/SplitNexteraLMP.class
opt/bbmap-37.90/jni/MultiStateAligner11tsJNI.c
bin/summarizeseal.sh
opt/bbmap-37.90/current/align2/Solver.java
opt/bbmap-37.90/current/structures/AtomicBitSet.java
bin/addadapters.sh
opt/bbmap-37.90/current/driver/BBVersion.class
opt/bbmap-37.90/current/hiseq/FlowCell.class
opt/bbmap-37.90/addadapters.sh
opt/bbmap-37.90/current/jgi/UnicodeToAscii.java
opt/bbmap-37.90/current/jgi/GetReads.java
opt/bbmap-37.90/current/stream/ConcurrentGenericReadInputStream.class
opt/bbmap-37.90/current/var/ApplyVarsToReference.class
opt/bbmap-37.90/current/var2/VarFilter.class
opt/bbmap-37.90/current/sketch/BlacklistMaker.class
opt/bbmap-37.90/current/pacbio/MakePacBioScript.class
opt/bbmap-37.90/current/sort/ReadComparatorID.class
opt/bbmap-37.90/current/align2/QualityTools.java
opt/bbmap-37.90/current/jgi/MergeBarcodes.class
bin/statswrapper.sh
opt/bbmap-37.90/current/stream/SamReadInputStream.class
opt/bbmap-37.90/current/fileIO/TextFile.java
opt/bbmap-37.90/current/jgi/PhylipToFasta.java
opt/bbmap-37.90/current/fileIO/ChainLine.java
opt/bbmap-37.90/current/align2/BBMapPacBio.class
opt/bbmap-37.90/current/align2/IndexMaker5$BlockMaker$CountThread.class
opt/bbmap-37.90/current/sketch/SketchObject.class
opt/bbmap-37.90/current/structures/LongHeapSet.java
opt/bbmap-37.90/mapPacBio.sh
opt/bbmap-37.90/current/align2/BBMapThreadPacBioSkimmer.java
opt/bbmap-37.90/current/align2/BandedAlignerConcrete.class
opt/bbmap-37.90/current/jgi/BBMerge$MateThread.class
opt/bbmap-37.90/current/align2/BandedAlignerJNI.java
opt/bbmap-37.90/renameimg.sh
opt/bbmap-37.90/current/clump/KmerSplit$HashThread.class
opt/bbmap-37.90/current/structures/IntList2.java
bin/renameimg.sh
opt/bbmap-37.90/callpeaks.sh
opt/bbmap-37.90/current/clump/KmerReduce.java
opt/bbmap-37.90/current/stream/ReadStreamStringWriter.java
opt/bbmap-37.90/current/cluster/Cluster.class
opt/bbmap-37.90/current/align2/PrintTime.class
opt/bbmap-37.90/current/jgi/CountBarcodes.class
opt/bbmap-37.90/current/stream/FastaQualReadInputStream.class
opt/bbmap-37.90/current/align2/MakeRocCurve.class
opt/bbmap-37.90/current/fileIO/MatrixFile.java
opt/bbmap-37.90/current/tax/ImgRecord2.java
opt/bbmap-37.90/current/clump/KmerComparatorX.class
opt/bbmap-37.90/current/assemble/Tadpole$MakeKhistThread.class
opt/bbmap-37.90/current/driver/TestLockSpeed$1.class
opt/bbmap-37.90/current/jgi/SamToEst.class
opt/bbmap-37.90/current/jgi/BBMask.java
opt/bbmap-37.90/current/tax/TaxServer$IconHandler.class
opt/bbmap-37.90/current/jgi/DedupeProtein$HashThread.class
opt/bbmap-37.90/current/sketch/SketchTool.class
opt/bbmap-37.90/current/hiseq/FlowcellCoordinate.class
opt/bbmap-37.90/bbmapskimmer.sh
opt/bbmap-37.90/current/clump/KmerComparator2.class
opt/bbmap-37.90/current/tax/ExplodeTree.java
opt/bbmap-37.90/current/dna/FastaToChromArrays2$1.class
opt/bbmap-37.90/current/var2/VarMap.java
opt/bbmap-37.90/current/tax/IDNode.class
bin/reducesilva.sh
opt/bbmap-37.90/current/driver/Translator.java
opt/bbmap-37.90/current/align2/Block.java
opt/bbmap-37.90/current/var/VarLine.java
opt/bbmap-37.90/removebadbarcodes.sh
opt/bbmap-37.90/current/sketch/Comparison$Depth2Comparator.class
opt/bbmap-37.90/current/sort/SortReadsByMapping$RegenMatchThread.class
opt/bbmap-37.90/current/align2/MultiStateAligner9PacBioAdapter.java
opt/bbmap-37.90/crossblock.sh
bin/makechimeras.sh
opt/bbmap-37.90/current/jgi/IdentityMatrix.class
opt/bbmap-37.90/current/dna/Exon.java
opt/bbmap-37.90/current/driver/A_Sample_Textfile.class
opt/bbmap-37.90/current/driver/GetSequence.java
opt/bbmap-37.90/docs/guides/BBMap_old_readme.txt
opt/bbmap-37.90/postfilter.sh
opt/bbmap-37.90/current/jgi/RepresentativeSet.class
opt/bbmap-37.90/current/structures/LongLongHashMap.class
opt/bbmap-37.90/current/jgi/SamToEst$1.class
opt/bbmap-37.90/current/ukmer/HashForestU.java
opt/bbmap-37.90/current/bloom/KCountArray4MT$WriteThread.class
opt/bbmap-37.90/current/pacbio/MergeFastaContigs.java
opt/bbmap-37.90/current/jgi/GreedyBarCodeFinder.java
bin/bbqc.sh
opt/bbmap-37.90/current/align2/Blacklist.java
opt/bbmap-37.90/current/var/GenerateVarlets3$1.class
opt/bbmap-37.90/current/fileIO/LoadThread.class
opt/bbmap-37.90/current/jgi/KmerCoverage.java
opt/bbmap-37.90/current/jgi/A_Sample_Unpaired.java
opt/bbmap-37.90/current/jgi/CallPeaks$Peak.class
opt/bbmap-37.90/current/fileIO/MatrixFile.class
opt/bbmap-37.90/current/structures/IntList2.class
opt/bbmap-37.90/current/dna/Data.java
opt/bbmap-37.90/current/shared/TrimRead.class
opt/bbmap-37.90/current/driver/ProcessSpeed2.java
opt/bbmap-37.90/current/jgi/CovStatsLine.class
opt/bbmap-37.90/removehuman2.sh
opt/bbmap-37.90/current/driver/ClearRam.java
opt/bbmap-37.90/shrinkaccession.sh
opt/bbmap-37.90/current/driver/Concatenator.class
bin/randomreads.sh
opt/bbmap-37.90/current/align2/TranslateColorspaceRead.class
opt/bbmap-37.90/filterassemblysummary.sh
opt/bbmap-37.90/current/fun/FindPath.class
opt/bbmap-37.90/current/bloom/KCountArray.java
opt/bbmap-37.90/current/hiseq/Lane.class
opt/bbmap-37.90/current/fun/ProbShared.java
opt/bbmap-37.90/current/dna/Scaffold.class
opt/bbmap-37.90/current/fun/Genetic$Bug.class
opt/bbmap-37.90/current/stream/ByteBuilder.java
opt/bbmap-37.90/current/assemble/TadpoleWrapper.class
opt/bbmap-37.90/current/driver/ConvertSamToAln.class
opt/bbmap-37.90/current/fileIO/ChainBlock.java
opt/bbmap-37.90/current/stream/SiteScore.java
opt/bbmap-37.90/current/structures/LongHeapSet.class
bin/grademerge.sh
opt/bbmap-37.90/current/driver/TestLockSpeed$LockBox.class
opt/bbmap-37.90/removemicrobes.sh
opt/bbmap-37.90/tadpole.sh
opt/bbmap-37.90/current/align2/BBIndexPacBio.java
opt/bbmap-37.90/current/structures/JsonParser.java
opt/bbmap-37.90/current/shared/Tools.class
opt/bbmap-37.90/current/jgi/CalcUniqueness$Counter.class
opt/bbmap-37.90/current/jgi/SplitSam4Way.java
opt/bbmap-37.90/pileup.sh
opt/bbmap-37.90/current/sort/ReadLengthComparator.class
opt/bbmap-37.90/current/stream/RandomReadInputStream3.class
opt/bbmap-37.90/repair.sh
opt/bbmap-37.90/current/align2/SplitMappedReads.java
opt/bbmap-37.90/current/driver/Sample.java
opt/bbmap-37.90/current/driver/CountSharedLines.java
opt/bbmap-37.90/current/stream/ReadStreamWriter$Job.class
opt/bbmap-37.90/current/stream/ReadStreamByteWriter.java
opt/bbmap-37.90/current/sketch/Comparison.class
opt/bbmap-37.90/current/jgi/TestFilesystem.class
opt/bbmap-37.90/current/hiseq/MicroTile.class
opt/bbmap-37.90/current/driver/Translator2.java
opt/bbmap-37.90/current/align2/BBMapThread.class
opt/bbmap-37.90/current/align2/RandomReads3.java
opt/bbmap-37.90/current/jgi/BBDuk2.class
opt/bbmap-37.90/current/driver/CorrelateIdentity.class
opt/bbmap-37.90/current/driver/ConcatenateTextFiles.java
opt/bbmap-37.90/current/structures/StringPair.java
opt/bbmap-37.90/current/jgi/KmerNormalize.class
bin/callvariants.sh
opt/bbmap-37.90/current/fileIO/CompressFiles.class
opt/bbmap-37.90/jni/libbbtoolsjni.so
opt/bbmap-37.90/mergebarcodes.sh
opt/bbmap-37.90/current/structures/StringPair.class
opt/bbmap-37.90/current/align2/BandedAlignerJNI.class
opt/bbmap-37.90/current/fun/ProbShared.class
opt/bbmap-37.90/current/server/SimpleHttpServer.java
opt/bbmap-37.90/current/driver/TestLockSpeed.java
opt/bbmap-37.90/current/tax/TaxSize.class
opt/bbmap-37.90/current/ukmer/HashArrayU.java
opt/bbmap-37.90/current/clump/KmerSort2.java
opt/bbmap-37.90/current/ukmer/KmerBufferU.java
opt/bbmap-37.90/current/fun/ProbShared3.java
opt/bbmap-37.90/current/kmer/TableLoaderLockFree.java
opt/bbmap-37.90/current/jgi/RepresentativeSet.java
opt/bbmap-37.90/current/jgi/RepresentativeSet$Node.class
bin/testformat2.sh
opt/bbmap-37.90/gi2ancestors.sh
opt/bbmap-37.90/current/kmer/AtomicShortArray.java
bin/textfile.sh
opt/bbmap-37.90/current/stream/DualCris.java
bin/bbstats.sh
opt/bbmap-37.90/current/jgi/BBMergeOverlapper.java
opt/bbmap-37.90/current/sketch/CompareBuffer.class
opt/bbmap-37.90/countsharedlines.sh
opt/bbmap-37.90/resources/mtst.fa
opt/bbmap-37.90/current/dna/Matrix.java
opt/bbmap-37.90/jni/makefile.linux
opt/bbmap-37.90/current/sort/ReadComparatorPosition.java
opt/bbmap-37.90/docs/guides/DedupeGuide.txt
opt/bbmap-37.90/current/align2/IndexMaker4$BlockMaker$CountThread.class
opt/bbmap-37.90/current/jgi/LogLog$LogLogWrapper$LogLogThread.class
opt/bbmap-37.90/current/structures/Heap.class
opt/bbmap-37.90/current/jgi/CountGC.java
opt/bbmap-37.90/current/driver/GetUniquePrefixes.java
opt/bbmap-37.90/current/stream/ConcurrentReadStreamInterface.class
opt/bbmap-37.90/current/structures/CoverageArray.java
opt/bbmap-37.90/makepolymers.sh
opt/bbmap-37.90/current/fileIO/CopyFile$1.class
opt/bbmap-37.90/current/jgi/LogLog$LogLogWrapper.class
opt/bbmap-37.90/current/sketch/SketchSearcher.class
opt/bbmap-37.90/current/kmer/KmerTableSet.class
bin/summarizemerge.sh
opt/bbmap-37.90/current/align2/ChromLoadThread.class
opt/bbmap-37.90/current/sort/ReadComparator.java
opt/bbmap-37.90/current/kmer/TableLoaderLockFree$LoadThread.class
opt/bbmap-37.90/randomreads.sh
bin/pileup.sh
opt/bbmap-37.90/current/bloom/KmerCount7MT.class
opt/bbmap-37.90/current/var2/Realign.class
opt/bbmap-37.90/current/clump/KmerComparator.java
opt/bbmap-37.90/pipelines/fetchRefSeq.sh
opt/bbmap-37.90/current/jgi/RemapQuality.class
opt/bbmap-37.90/pipelines/startRefseqServer.sh
opt/bbmap-37.90/current/stream/OnelineReadInputStream.class
opt/bbmap-37.90/testformat2.sh
opt/bbmap-37.90/current/pacbio/SortSites.class
opt/bbmap-37.90/current/align2/BBMapThreadAcc.java
opt/bbmap-37.90/current/stream/SamHeader.java
opt/bbmap-37.90/resources/blacklist_refseq_species_300.sketch
opt/bbmap-37.90/current/kmer/AbstractKmerTable$AllocThread.class
opt/bbmap-37.90/current/sort/ReadQualityComparator.java
opt/bbmap-37.90/current/align2/MultiStateAligner9ts.class
opt/bbmap-37.90/current/ukmer/KmerTableSetU.java
bin/bbmerge-auto.sh
opt/bbmap-37.90/current/kmer/KmerNode.java
bin/processspeed.sh
opt/bbmap-37.90/current/jgi/MergeSam.java
opt/bbmap-37.90/current/stream/SiteScoreR$NormalizedComparator.class
opt/bbmap-37.90/bbfakereads.sh
opt/bbmap-37.90/current/driver/CompareSequences.java
opt/bbmap-37.90/current/driver/RenameRefseqFiles.java
opt/bbmap-37.90/current/shared/Shared.class
opt/bbmap-37.90/current/driver/SelectReads.java
opt/bbmap-37.90/current/align2/Solver.class
opt/bbmap-37.90/current/structures/IntHashMap.class
opt/bbmap-37.90/current/sketch/Blacklist.java
bin/shrinkaccession.sh
opt/bbmap-37.90/current/kmer/HashArrayHybrid.java
opt/bbmap-37.90/msa.sh
opt/bbmap-37.90/current/align2/GapTools$Range.class
opt/bbmap-37.90/current/jgi/SynthMDA.java
opt/bbmap-37.90/current/bloom/KmerCount6.java
opt/bbmap-37.90/bbcountunique.sh
opt/bbmap-37.90/current/jgi/BBDukF$LoadThread.class
opt/bbmap-37.90/current/pacbio/StackSites.java
opt/bbmap-37.90/current/fileIO/TextFile.class
bin/bbsketch.sh
opt/bbmap-37.90/current/sketch/SummarizeSketchStats.class
opt/bbmap-37.90/current/driver/FindMotifs.class
opt/bbmap-37.90/current/jgi/MakeLengthHistogram.class
opt/bbmap-37.90/current/dna/ChromosomeArray.class
opt/bbmap-37.90/current/ukmer/HashArrayU1D.class
opt/bbmap-37.90/current/var2/CompareVCF.java
opt/bbmap-37.90/config/trimadapters.txt
opt/bbmap-37.90/current/var/StackVariations.class
opt/bbmap-37.90/current/driver/CountRNAs.class
opt/bbmap-37.90/current/ukmer/HashBufferU.java
opt/bbmap-37.90/current/align2/Index.class
opt/bbmap-37.90/current/driver/FilterAssemblySummary.java
opt/bbmap-37.90/current/jgi/CoveragePileup.java
opt/bbmap-37.90/seal.sh
opt/bbmap-37.90/current/structures/EntropyTracker.java
opt/bbmap-37.90/current/stream/ArrayListSet.class
bin/loglog.sh
bin/shred.sh
opt/bbmap-37.90/current/ukmer/DumpThreadU.java
opt/bbmap-37.90/current/jgi/SplitPairsAndSingles.java
opt/bbmap-37.90/current/driver/TestLockSpeed$CountBox.class
opt/bbmap-37.90/bbmerge-auto.sh
opt/bbmap-37.90/current/assemble/ShaveObject.class
opt/bbmap-37.90/taxonomy.sh
opt/bbmap-37.90/current/structures/Range.class
opt/bbmap-37.90/current/fun/Life.java
opt/bbmap-37.90/current/ukmer/KmerNodeU1D.class
bin/summarizequast.sh
opt/bbmap-37.90/current/clump/Clumpify.java
opt/bbmap-37.90/current/jgi/A_Sample_Unpaired.class
opt/bbmap-37.90/current/var2/FilterSam.java
opt/bbmap-37.90/current/driver/SummarizeCrossblock.java
opt/bbmap-37.90/jni/BandedAlignerJNI.c
opt/bbmap-37.90/current/jgi/BBDukF.class
opt/bbmap-37.90/current/sketch/Comparison$DepthComparator.class
opt/bbmap-37.90/current/sort/ReadComparatorMapping.class
opt/bbmap-37.90/current/tax/TaxServer$KillHandler.class
opt/bbmap-37.90/current/jgi/CalcUniqueness.class
opt/bbmap-37.90/current/align2/RefToIndex.class
opt/bbmap-37.90/current/jgi/PhylipToFasta.class
bin/rename.sh
opt/bbmap-37.90/current/jgi/SplitNexteraLMP.java
opt/bbmap-37.90/current/ukmer/KmerTableSetU.class
opt/bbmap-37.90/current/dna/Coverage.class
opt/bbmap-37.90/bbwrap.sh
opt/bbmap-37.90/config/filter16s.txt
opt/bbmap-37.90/current/jgi/KmerCoverage.class
opt/bbmap-37.90/current/structures/LongHashMap.class
opt/bbmap-37.90/jni/README.txt
opt/bbmap-37.90/kmercoverage.sh
opt/bbmap-37.90/pipelines/startNtServer.sh
opt/bbmap-37.90/resources/remote_files.txt
opt/bbmap-37.90/current/stream/ScarfReadInputStream.class
bin/explodetree.sh
opt/bbmap-37.90/current/sketch/SketchMaker.java
opt/bbmap-37.90/docs/guides/BBMaskGuide.txt
opt/bbmap-37.90/dedupe2.sh
opt/bbmap-37.90/diskbench.sh
opt/bbmap-37.90/current/stream/SamLineStreamer.class
opt/bbmap-37.90/current/align2/BBWrap.class
opt/bbmap-37.90/a_sample_mt.sh
opt/bbmap-37.90/current/var/Varlet.class
opt/bbmap-37.90/current/ukmer/KmerNodeU.class
opt/bbmap-37.90/current/var2/Var.java
opt/bbmap-37.90/explodetree.sh
opt/bbmap-37.90/callvariants.sh
opt/bbmap-37.90/plotgc.sh
opt/bbmap-37.90/current/clump/StreamToOutput.java
bin/summarizescafstats.sh
opt/bbmap-37.90/current/jgi/Info.java
opt/bbmap-37.90/resources/blacklist_nt_species_1000.sketch
opt/bbmap-37.90/current/driver/SummarizeQuast$Entry.class
opt/bbmap-37.90/jni/BBMergeOverlapper.c
opt/bbmap-37.90/current/align2/QuadHeap.java
opt/bbmap-37.90/current/align2/AbstractIndex.class
opt/bbmap-37.90/current/stream/ConcurrentDepot.class
opt/bbmap-37.90/current/sort/ReadComparatorName.java
opt/bbmap-37.90/current/driver/Search.java
opt/bbmap-37.90/current/driver/SummarizeSealStats$SealSummary.class
opt/bbmap-37.90/current/jgi/A_SampleD.class
bin/filterbarcodes.sh
opt/bbmap-37.90/samtoroc.sh
opt/bbmap-37.90/current/tax/ExplodeTree.class
bin/idtree.sh
opt/bbmap-37.90/current/align2/AbstractMapThread.java
bin/summarizesketch.sh
opt/bbmap-37.90/kmercountmulti.sh
opt/bbmap-37.90/current/bloom/ErrorCorrect.java
opt/bbmap-37.90/current/fun/FindPath$Path.class
opt/bbmap-37.90/current/align2/BBMapThread5.class
opt/bbmap-37.90/current/fileIO/CopyFiles2.java
opt/bbmap-37.90/current/jgi/RandomGenome.java
opt/bbmap-37.90/current/jgi/MakeChimeras.class
opt/bbmap-37.90/current/jgi/TetramerFrequencies.java
opt/bbmap-37.90/current/jgi/Shred.java
opt/bbmap-37.90/current/clump/PivotSet.class
opt/bbmap-37.90/current/dna/ChromToFasta$1.class
opt/bbmap-37.90/current/align2/BBMap.class
bin/diskbench.sh
opt/bbmap-37.90/current/align2/Block.class
opt/bbmap-37.90/current/jgi/TestFilesystem$WriteThread.class
opt/bbmap-37.90/current/jgi/DedupeProtein$MstThread.class
opt/bbmap-37.90/current/bloom/ErrorCorrect.class
opt/bbmap-37.90/current/stream/CrisWrapper.class
opt/bbmap-37.90/callvariants2.sh
opt/bbmap-37.90/current/align2/CompareSamFiles$1.class
opt/bbmap-37.90/current/dna/ChromArrayMaker.class
opt/bbmap-37.90/current/jgi/BBMask$MaskLowEntropyThread.class
opt/bbmap-37.90/current/driver/MakeTestScript.java
opt/bbmap-37.90/current/dna/ChromToFasta.class
opt/bbmap-37.90/current/jgi/Dedupe2$ClusterLengthComparator.class
opt/bbmap-37.90/current/jgi/SmallKmerFrequency$Kmer.class
opt/bbmap-37.90/current/align2/BBMapPacBioSkimmer.java
opt/bbmap-37.90/current/driver/FilterReadsByName.class
opt/bbmap-37.90/current/fileIO/SummaryFile$1.class
opt/bbmap-37.90/current/tax/AccessionToTaxid$HashThread.class
opt/bbmap-37.90/current/var/GenerateVarlets3.class
opt/bbmap-37.90/current/pacbio/GenerateMultiChrom.class
opt/bbmap-37.90/current/structures/JsonParser.class
opt/bbmap-37.90/current/fileIO/ReadWrite.java
opt/bbmap-37.90/current/sketch/SketchTool$LoadThread2.class
opt/bbmap-37.90/current/stream/SiteScore.class
opt/bbmap-37.90/current/jgi/Dedupe$HashThread.class
opt/bbmap-37.90/current/ukmer/HashArrayUHybrid.java
opt/bbmap-37.90/current/server/ServerTools.class
opt/bbmap-37.90/current/jgi/CountUniqueness.class
opt/bbmap-37.90/resources/nextera.fa.gz
opt/bbmap-37.90/current/jgi/FakeReads.class
opt/bbmap-37.90/current/jgi/BBDukF.java
opt/bbmap-37.90/current/jgi/GradeMergedReads.class
opt/bbmap-37.90/current/fun/ProbShared3.class
opt/bbmap-37.90/current/structures/LongList.java
opt/bbmap-37.90/current/jgi/SplitSam4Way.class
opt/bbmap-37.90/current/jgi/FindString.class
opt/bbmap-37.90/current/fun/DiskBench$WriteThread.class
opt/bbmap-37.90/kmercountexact.sh
opt/bbmap-37.90/current/driver/TestLockSpeed$AtomBox.class
opt/bbmap-37.90/current/jgi/FungalRelease.class
opt/bbmap-37.90/current/sketch/SketchIndex$IndexThread.class
opt/bbmap-37.90/current/clump/KmerSort2$FetchThread.class
opt/bbmap-37.90/current/tax/TaxNode.java
opt/bbmap-37.90/current/stream/ConcurrentReadStreamInterface.java
opt/bbmap-37.90/current/align2/RefToIndex.java
bin/plotgc.sh
bin/bbnorm.sh
opt/bbmap-37.90/current/driver/FixDumbFile.java
opt/bbmap-37.90/current/stream/MultiCros.java
opt/bbmap-37.90/current/stream/SamLine.class
opt/bbmap-37.90/current/driver/CountSharedLines.class
opt/bbmap-37.90/current/dna/FastaToChromArrays2.class
opt/bbmap-37.90/current/driver/TestLockSpeed.class
opt/bbmap-37.90/current/jgi/Dedupe.java
opt/bbmap-37.90/taxtree.sh
opt/bbmap-37.90/current/pacbio/MergeFastaContigs.class
opt/bbmap-37.90/current/align2/BBIndexPacBioSkimmer.java
opt/bbmap-37.90/current/jgi/CountGC$1.class
opt/bbmap-37.90/current/var/ApplyVarsToReference.java
opt/bbmap-37.90/current/assemble/Postfilter.java
opt/bbmap-37.90/current/var/GenerateConsensusVariations.class
opt/bbmap-37.90/bbrealign.sh
bin/getreads.sh
bin/idmatrix.sh
opt/bbmap-37.90/current/bloom/KCountArray7MTA$CountUsedThread.class
opt/bbmap-37.90/current/jgi/BBDukF$ProcessThread.class
opt/bbmap-37.90/current/clump/KmerSplit.class
opt/bbmap-37.90/current/structures/MultiBitSet.java
opt/bbmap-37.90/current/bloom/KCountArray8MT.java
opt/bbmap-37.90/current/shared/Tools.java
opt/bbmap-37.90/jni/align2_MultiStateAligner11tsJNI.h
opt/bbmap-37.90/current/kmer/HashBuffer.java
opt/bbmap-37.90/current/align2/BBMapAcc.class
opt/bbmap-37.90/unicode2ascii.sh
opt/bbmap-37.90/current/bloom/KmerCount7MTA$CountThread.class
opt/bbmap-37.90/current/stream/ConcurrentCollectionReadInputStream.class
opt/bbmap-37.90/filterbycoverage.sh
opt/bbmap-37.90/current/pacbio/SiteR.java
opt/bbmap-37.90/bbest.sh
bin/filterbytile.sh
opt/bbmap-37.90/current/jgi/AddAdapters.class
opt/bbmap-37.90/current/var2/VCFFile.class
opt/bbmap-37.90/current/kmer/HashForest.class
bin/filterbytaxa.sh
opt/bbmap-37.90/current/kmer/TableLoaderLockFree.class
opt/bbmap-37.90/current/jgi/FuseSequence.class
opt/bbmap-37.90/current/clump/Splitter.java
opt/bbmap-37.90/current/align2/BBIndexPacBioSkimmer.class
opt/bbmap-37.90/current/kmer/TableReader.class
opt/bbmap-37.90/current/var/StackVariations2$1.class
opt/bbmap-37.90/jni/makefile.osx
bin/filtervcf.sh
opt/bbmap-37.90/current/jgi/MergeSam.class
opt/bbmap-37.90/current/sort/ReadComparatorName.class
opt/bbmap-37.90/current/align2/PackedHeap.java
bin/postfilter.sh
bin/filterbyname.sh
opt/bbmap-37.90/current/fileIO/FileFormat.class
opt/bbmap-37.90/current/kmer/KmerNode1D.java
opt/bbmap-37.90/current/tax/IDTree.java
opt/bbmap-37.90/current/jgi/DecontaminateByNormalization.java
opt/bbmap-37.90/current/clump/KmerSort.java
opt/bbmap-37.90/current/driver/ParseCrossblockResults.class
opt/bbmap-37.90/current/kmer/HashArray1D.class
opt/bbmap-37.90/current/jgi/TetramerFrequencies.class
opt/bbmap-37.90/current/sketch/SendSketch.class
opt/bbmap-37.90/current/align2/Blacklist.class
bin/bbmap.sh
opt/bbmap-37.90/resources/kapatags.L40.fa
opt/bbmap-37.90/current/align2/IndexMaker4.class
opt/bbmap-37.90/current/structures/IntLongHashMap.java
opt/bbmap-37.90/current/align2/Pointer.class
opt/bbmap-37.90/docs/guides/BBDukGuide.txt
opt/bbmap-37.90/current/align2/BBMapThread5.java
opt/bbmap-37.90/current/var/ApplyVarsToReference$1.class
bin/splitsam.sh
opt/bbmap-37.90/current/jgi/DedupeByMapping$Quad.class
opt/bbmap-37.90/current/align2/MultiStateAligner9PacBio.class
opt/bbmap-37.90/current/tax/SplitByTaxa.java
opt/bbmap-37.90/current/var/GenerateVarlets2.class
opt/bbmap-37.90/current/jgi/MakePolymers.java
opt/bbmap-37.90/current/tax/TaxTree.java
bin/muxbyname.sh
opt/bbmap-37.90/current/jgi/CrossContaminate.class
bin/shuffle.sh
bin/filtersubs.sh
opt/bbmap-37.90/current/shared/Colors.class
opt/bbmap-37.90/current/driver/CorrelateIdentity.java
opt/bbmap-37.90/current/hiseq/FlowCell.java
bin/taxtree.sh
opt/bbmap-37.90/current/sketch/SketchSearcher$CompareThread.class
opt/bbmap-37.90/current/var/GenerateConsensusVariations$1.class
opt/bbmap-37.90/bbqc.sh
opt/bbmap-37.90/config/cluster16s.txt
opt/bbmap-37.90/current/pacbio/ProcessStackedSitesNormalized.java
opt/bbmap-37.90/current/clump/Splitter.class
opt/bbmap-37.90/synthmda.sh
opt/bbmap-37.90/current/jgi/TestFilesystem.java
opt/bbmap-37.90/current/sketch/Sketch.java
opt/bbmap-37.90/docs/guides/A_SampleGuide.txt
opt/bbmap-37.90/docs/guides/TadpoleGuide.txt
opt/bbmap-37.90/current/driver/CollateSpikeIn.class
opt/bbmap-37.90/current/align2/IndexMaker4$BlockMaker.class
opt/bbmap-37.90/current/dna/Gene.class
opt/bbmap-37.90/current/driver/SummarizeMSDIN.java
opt/bbmap-37.90/current/jgi/BBDuk2$ProcessThread.class
opt/bbmap-37.90/current/stream/ArrayListSet.java
bin/bbrename.sh
opt/bbmap-37.90/current/kmer/KmerTableSet.java
opt/bbmap-37.90/bbsplitpairs.sh
opt/bbmap-37.90/filterbytaxa.sh
opt/bbmap-37.90/current/driver/Concatenator.java
opt/bbmap-37.90/current/jgi/IdentityMatrix.java
bin/countbarcodes.sh
bin/mapPacBio.sh
opt/bbmap-37.90/current/fun/DiskBench.java
bin/msa.sh
bin/mutate.sh
opt/bbmap-37.90/current/bloom/KmerCount7MTA.java
bin/bbest.sh
opt/bbmap-37.90/current/ukmer/Kmer.class
opt/bbmap-37.90/current/stream/SiteScoreR$PositionComparator.class
opt/bbmap-37.90/current/var2/VcfLoader.java
bin/countgc.sh
opt/bbmap-37.90/filtervcf.sh
opt/bbmap-37.90/current/assemble/Shaver1.java
opt/bbmap-37.90/current/driver/RenameAndMux.java
opt/bbmap-37.90/current/sketch/Comparison.java
opt/bbmap-37.90/current/align2/RandomReads3$1.class
opt/bbmap-37.90/current/var2/VCFLine.class
opt/bbmap-37.90/current/bloom/LargeKmerCount.class
opt/bbmap-37.90/current/pacbio/RemoveAdapters2.java
opt/bbmap-37.90/current/stream/ConcurrentCollectionReadInputStream.java
bin/bbmerge.sh
opt/bbmap-37.90/current/var2/VarFilter.java
opt/bbmap-37.90/current/bloom/KmerCount3.class
opt/bbmap-37.90/current/bloom/KmerCount7MTA.class
opt/bbmap-37.90/current/ml/ProcessBBMergeHeaders.java
opt/bbmap-37.90/current/sort/SortReadsByID$1.class
opt/bbmap-37.90/current/jgi/MakeLengthHistogram$1.class
opt/bbmap-37.90/current/stream/SamReadStreamer$ProcessThread.class
opt/bbmap-37.90/bbmap.sh
opt/bbmap-37.90/current/tax/FindAncestor.class
opt/bbmap-37.90/pipelines/assemblyPipeline.sh
opt/bbmap-37.90/current/clump/ReadKey.java
opt/bbmap-37.90/current/sketch/InvertKey.class
opt/bbmap-37.90/current/align2/AbstractIndex.java
opt/bbmap-37.90/current/bloom/KCountArray5MT$WriteThread.class
bin/makecontaminatedgenomes.sh
opt/bbmap-37.90/current/align2/ReformatBatchOutput.class
opt/bbmap-37.90/current/clump/KmerSort2.class
opt/bbmap-37.90/current/var2/Realigner.class
opt/bbmap-37.90/current/jgi/DemuxByName.java
opt/bbmap-37.90/current/jgi/DedupeProtein$ClusterLengthComparator.class
opt/bbmap-37.90/current/kmer/HashArray2D.class
opt/bbmap-37.90/current/bloom/KmerCount6MT.java
opt/bbmap-37.90/current/cluster/ClusterTools.java
opt/bbmap-37.90/current/fun/FindPath.java
opt/bbmap-37.90/current/stream/ConcurrentLegacyReadInputStream.java
opt/bbmap-37.90/current/tax/TaxApp$1.class
opt/bbmap-37.90/current/jgi/FakeReads.java
opt/bbmap-37.90/gitable.sh
opt/bbmap-37.90/current/driver/MeasureGene.class
opt/bbmap-37.90/current/jgi/CallPeaks.class
opt/bbmap-37.90/current/stream/CrisWrapper.java
opt/bbmap-37.90/current/stream/SamHeader.class
opt/bbmap-37.90/current/assemble/Tadpole.java
opt/bbmap-37.90/current/pacbio/StackSites$1.class
opt/bbmap-37.90/sendsketch.sh
opt/bbmap-37.90/current/tax/TaxServer$SketchHandler.class
opt/bbmap-37.90/current/stream/ConcurrentReadInputStreamD.java
opt/bbmap-37.90/current/var2/CallVariants.java
opt/bbmap-37.90/current/ukmer/HashArrayU2D.java
opt/bbmap-37.90/pipelines/fetchSilva.sh
opt/bbmap-37.90/current/driver/ReduceSilva.java
opt/bbmap-37.90/current/jgi/TestFormat.class
opt/bbmap-37.90/current/kmer/DumpThread.class
opt/bbmap-37.90/current/structures/LongHeapSetInterface.java
opt/bbmap-37.90/current/driver/MakeTestScript.class
opt/bbmap-37.90/current/jgi/DedupeProtein.java
opt/bbmap-37.90/khist.sh
opt/bbmap-37.90/current/jgi/MakeLengthHistogram.java
opt/bbmap-37.90/current/kmer/HashArray.java
opt/bbmap-37.90/current/driver/MoveFiles.java
opt/bbmap-37.90/current/fileIO/CopyFiles.class
opt/bbmap-37.90/current/jgi/KmerCountExact$MakeKhistThread.class
opt/bbmap-37.90/current/driver/MakeTestScriptScoreOnly.class
opt/bbmap-37.90/current/var2/MergeSamples$MergeThread.class
opt/bbmap-37.90/current/align2/MultiStateAligner9Flat.class
opt/bbmap-37.90/current/sort/ReadComparatorTopological.java
opt/bbmap-37.90/current/driver/SummarizeQuast$QuastSummary.class
opt/bbmap-37.90/current/fun/Palindrome.java
opt/bbmap-37.90/current/sort/SortByName.class
bin/khist.sh
opt/bbmap-37.90/current/fileIO/FindFiles.java
bin/removemicrobes.sh
opt/bbmap-37.90/current/sketch/InvertKey.java
opt/bbmap-37.90/current/hiseq/AnalyzeFlowCell.java
opt/bbmap-37.90/current/stream/SiteScoreR$IDComparator.class
opt/bbmap-37.90/current/fileIO/GenericTextFile.class
opt/bbmap-37.90/current/sketch/Whitelist.java
opt/bbmap-37.90/current/var2/VcfLoader$ProcessThread.class
opt/bbmap-37.90/current/driver/GetSequence.class
opt/bbmap-37.90/current/var2/CallVariants2.java
opt/bbmap-37.90/current/align2/BBIndexAcc.java
opt/bbmap-37.90/current/pacbio/RemoveAdapters3.java
opt/bbmap-37.90/current/jgi/FilterBySequence$ProcessThread.class
opt/bbmap-37.90/README.md
opt/bbmap-37.90/docs/changelog.txt
opt/bbmap-37.90/docs/compiling.txt
opt/bbmap-37.90/current/structures/RawBitSet.class
opt/bbmap-37.90/current/driver/TrimSamFile.class
opt/bbmap-37.90/current/jgi/A_Sample2.class
opt/bbmap-37.90/current/jgi/MultiLogLog.class
opt/bbmap-37.90/current/stream/FastaReadInputStream.class
bin/taxsize.sh
opt/bbmap-37.90/current/var2/CallVariants2$Sample$ProcessThread.class
opt/bbmap-37.90/current/align2/BBMap5.class
opt/bbmap-37.90/docs/guides/PreprocessingGuide.txt
opt/bbmap-37.90/splitsam.sh
opt/bbmap-37.90/current/structures/IntHashSetList.class
opt/bbmap-37.90/current/driver/RenameNcbiToTid.java
opt/bbmap-37.90/current/sketch/SketchTool.java
opt/bbmap-37.90/current/tax/TaxFilter.java
opt/bbmap-37.90/current/jgi/SmallKmerFrequency.java
opt/bbmap-37.90/current/align2/RandomReads3.class
opt/bbmap-37.90/current/assemble/TadpoleWrapper$Record.class
opt/bbmap-37.90/current/jgi/AssemblyStatsWrapper.java
opt/bbmap-37.90/current/jgi/SmallKmerFrequency.class
opt/bbmap-37.90/textfile.sh
opt/bbmap-37.90/current/bloom/ErrorCorrect$1.class
opt/bbmap-37.90/current/align2/BBIndex.class
opt/bbmap-37.90/current/tax/TaxNode$CountComparator.class
opt/bbmap-37.90/current/sketch/CompareSketch$CompareThread.class
opt/bbmap-37.90/current/tax/TaxFilter$1.class
opt/bbmap-37.90/current/driver/LookAtID.class
opt/bbmap-37.90/current/stream/ConcurrentReadOutputStream.class
opt/bbmap-37.90/current/sketch/DisplayParams.java
opt/bbmap-37.90/current/jgi/CorrelateBarcodes.class
opt/bbmap-37.90/current/align2/Index.java
opt/bbmap-37.90/current/driver/SummarizeMSDIN.class
opt/bbmap-37.90/reformat.sh
opt/bbmap-37.90/current/fileIO/FileFormat.java
opt/bbmap-37.90/current/clump/KmerReduce$HashThread.class
opt/bbmap-37.90/sortbyname.sh
opt/bbmap-37.90/bbsplit.sh
opt/bbmap-37.90/current/tax/TaxApp.java
opt/bbmap-37.90/current/align2/MultiStateAligner10ts.class
opt/bbmap-37.90/current/jgi/AddAdapters.java
opt/bbmap-37.90/current/jgi/Difference.class
opt/bbmap-37.90/current/jgi/TranslateSixFrames.class
bin/readlength.sh
opt/bbmap-37.90/current/jgi/A_SampleByteFile.java
opt/bbmap-37.90/current/fileIO/ReadWrite.class
opt/bbmap-37.90/current/driver/ClearRam.class
bin/printtime.sh
opt/bbmap-37.90/current/jgi/KmerSample.class
opt/bbmap-37.90/current/fileIO/ByteStreamWriter.java
opt/bbmap-37.90/resources/adapters.fa
opt/bbmap-37.90/current/clump/KmerComparator.class
opt/bbmap-37.90/current/stream/MDWalker.java
opt/bbmap-37.90/current/align2/Quad64Heap.class
opt/bbmap-37.90/current/sketch/Blacklist.class
opt/bbmap-37.90/mutate.sh
opt/bbmap-37.90/current/sketch/Comparison$ScoreComparator.class
bin/bbmergegapped.sh
opt/bbmap-37.90/current/align2/MultiStateAligner9PacBio.java
opt/bbmap-37.90/current/stream/SamStreamerWrapper.java
opt/bbmap-37.90/bbmask.sh
opt/bbmap-37.90/docs/Legal.txt
opt/bbmap-37.90/streamsam.sh
opt/bbmap-37.90/summarizescafstats.sh
opt/bbmap-37.90/current/jgi/CountBarcodes.java
opt/bbmap-37.90/summarizequast.sh
opt/bbmap-37.90/current/stream/OnelineReadInputStream.java
opt/bbmap-37.90/current/fileIO/CopyFile.class
opt/bbmap-37.90/current/pacbio/PartitionReads.class
opt/bbmap-37.90/current/align2/BBMapThreadAcc$1.class
opt/bbmap-37.90/current/clump/KmerSort2$HashSplitThread.class
opt/bbmap-37.90/current/clump/KmerSort3.java
opt/bbmap-37.90/current/var2/MergeSamples.java
opt/bbmap-37.90/current/driver/TrimSamFile.java
opt/bbmap-37.90/bbstats.sh
opt/bbmap-37.90/current/tax/GiToNcbi.class
opt/bbmap-37.90/current/sort/Shuffle$ShuffleThread.class
opt/bbmap-37.90/current/jgi/CrossContaminate.java
opt/bbmap-37.90/current/driver/PlotGC.class
opt/bbmap-37.90/current/var/Variation.class
opt/bbmap-37.90/current/fileIO/ChainLine.class
opt/bbmap-37.90/current/align2/AbstractMapper.class
opt/bbmap-37.90/current/fileIO/CopyFiles2.class
opt/bbmap-37.90/current/sketch/SketchMakerMini.class
opt/bbmap-37.90/current/assemble/Shaver1.class
opt/bbmap-37.90/current/shared/Primes.class
opt/bbmap-37.90/current/tax/RenameGiToNcbi.java
opt/bbmap-37.90/current/align2/BBSplitter$SetCount.class
opt/bbmap-37.90/current/var/GenerateVarlets3.java
opt/bbmap-37.90/current/align2/BBSplitter.class
opt/bbmap-37.90/current/tax/AccessionToTaxid.java
opt/bbmap-37.90/current/pacbio/StackSites2.class
opt/bbmap-37.90/current/var/GenerateVarlets.java
opt/bbmap-37.90/current/driver/Sample.class
opt/bbmap-37.90/current/ml/ProcessBBMergeHeaders.class
opt/bbmap-37.90/current/fileIO/ArrayFile.class
opt/bbmap-37.90/removesmartbell.sh
opt/bbmap-37.90/current/fun/Calc.java
opt/bbmap-37.90/current/jgi/Orf.java
opt/bbmap-37.90/current/tax/ShrinkAccession.class
opt/bbmap-37.90/current/ukmer/KmerBufferU.class
opt/bbmap-37.90/current/align2/KeyRing.java
opt/bbmap-37.90/current/jgi/MergeBarcodes.java
opt/bbmap-37.90/current/align2/BandedAligner.java
opt/bbmap-37.90/current/structures/LongM.java
opt/bbmap-37.90/current/pacbio/StackSites$Glob.class
opt/bbmap-37.90/current/align2/BandedAlignerConcrete.java
opt/bbmap-37.90/current/ukmer/AbstractKmerTableU.java
opt/bbmap-37.90/current/var2/Scaffold.class
opt/bbmap-37.90/current/dna/AminoAcid.class
opt/bbmap-37.90/docs/guides/ReformatGuide.txt
opt/bbmap-37.90/current/jgi/AssemblyStatsWrapper.class
opt/bbmap-37.90/current/stream/ConcurrentReadOutputStreamD.java
opt/bbmap-37.90/current/structures/ListNum.java
opt/bbmap-37.90/current/jgi/KmerCountExact$DumpKmersThread.class
bin/representative.sh
opt/bbmap-37.90/current/jgi/FilterReadsWithSubs.class
opt/bbmap-37.90/current/jgi/CalcTrueQuality.java
opt/bbmap-37.90/resources/truseq_rna.fa.gz
opt/bbmap-37.90/current/jgi/DemuxByName.class
bin/removehuman.sh
opt/bbmap-37.90/current/stream/RTextInputStream.java
opt/bbmap-37.90/current/bloom/KCountArray$AllocThread.class
opt/bbmap-37.90/tadpipe.sh
opt/bbmap-37.90/current/jgi/SynthMDA.class
opt/bbmap-37.90/current/structures/IntList.java
bin/sketchblacklist.sh
bin/streamsam.sh
opt/bbmap-37.90/current/structures/LongHeap.class
opt/bbmap-37.90/current/var2/CompareVCF.class
opt/bbmap-37.90/current/jgi/KmerCountMulti.java
opt/bbmap-37.90/current/driver/SummarizeSealStats.java
opt/bbmap-37.90/current/cluster/MergeReadHeaders.class
opt/bbmap-37.90/resources/sample1.fq.gz
opt/bbmap-37.90/current/driver/A_Sample_Textfile.java
opt/bbmap-37.90/current/jgi/CoveragePileup.class
opt/bbmap-37.90/docs/guides/SplitNexteraGuide.txt
opt/bbmap-37.90/current/var2/FilterSam$ProcessThread.class
opt/bbmap-37.90/gradesam.sh
opt/bbmap-37.90/current/align2/CompareSamFiles.java
bin/normandcorrectwrapper.sh
opt/bbmap-37.90/summarizeseal.sh
opt/bbmap-37.90/current/stream/FastqReadInputStream.class
opt/bbmap-37.90/current/sketch/SketchMaker$WriteThread.class
opt/bbmap-37.90/current/clump/ClumpTools.class
bin/bbmask.sh
opt/bbmap-37.90/current/bloom/KCountArray6MT.class
bin/splitbytaxa.sh
opt/bbmap-37.90/current/jgi/A_SampleD.java
opt/bbmap-37.90/current/driver/ConcatenateFiles.class
opt/bbmap-37.90/current/sketch/BlacklistMaker$ProcessThread.class
opt/bbmap-37.90/current/driver/PlotGC.java
opt/bbmap-37.90/current/clump/KmerSort3$FetchThread.class
opt/bbmap-37.90/current/jgi/ReplaceHeaders.class
opt/bbmap-37.90/current/structures/IntHashSet.class
opt/bbmap-37.90/current/driver/MakeTestScriptScoreOnly.java
bin/bbduk.sh
opt/bbmap-37.90/current/sketch/SketchIndex.java
opt/bbmap-37.90/stats.sh
opt/bbmap-37.90/current/jgi/MutateGenome.class
opt/bbmap-37.90/current/jgi/MakeContaminatedGenomes.class
opt/bbmap-37.90/current/jgi/ReformatReads.java
opt/bbmap-37.90/resources/favicon.ico
bin/conda_build.sh
opt/bbmap-37.90/current/fileIO/ByteStreamWriter.class
opt/bbmap-37.90/current/driver/RenameNcbiToTid.class
opt/bbmap-37.90/current/clump/KmerSplit.java
opt/bbmap-37.90/current/dna/Matrix.class
opt/bbmap-37.90/comparesketch.sh
opt/bbmap-37.90/summarizecrossblock.sh
opt/bbmap-37.90/current/shared/PreParser.class
opt/bbmap-37.90/current/align2/PackedHeap.class
opt/bbmap-37.90/docs/guides/FilterByTileGuide.txt
bin/a_sample_mt.sh
opt/bbmap-37.90/current/stream/ReadInputStream.java
opt/bbmap-37.90/matrixtocolumns.sh
opt/bbmap-37.90/current/kmer/KmerTableSet$LoadThread.class
bin/cutprimers.sh
opt/bbmap-37.90/current/fun/MakeAdjacencyList.class
opt/bbmap-37.90/current/sketch/CompareSketch.java
opt/bbmap-37.90/current/cluster/ReclusterByKmer.class
opt/bbmap-37.90/current/jgi/Orf.class
opt/bbmap-37.90/current/sketch/SketchMaker.class
opt/bbmap-37.90/filtersubs.sh
opt/bbmap-37.90/current/dna/MotifMulti.java
opt/bbmap-37.90/sketchblacklist.sh
opt/bbmap-37.90/current/bloom/KCountArray4MT.java
opt/bbmap-37.90/current/jgi/BBMerge.java
opt/bbmap-37.90/resources/blacklist_silva_species_500.sketch
opt/bbmap-37.90/current/ukmer/KmerNodeU.java
opt/bbmap-37.90/current/tax/PrintTaxonomy.java
opt/bbmap-37.90/current/var/StackVariations2.java
opt/bbmap-37.90/current/jgi/SamToEst$EST.class
opt/bbmap-37.90/pipelines/fetchTaxonomy.sh
opt/bbmap-37.90/current/jgi/LogLog.class
opt/bbmap-37.90/current/jgi/BBMask$MaskSamThread.class
opt/bbmap-37.90/current/assemble/TadpoleWrapper$1.class
opt/bbmap-37.90/current/driver/RenameByHeader.class
bin/filterbysequence.sh
opt/bbmap-37.90/current/stream/SiteScoreR.class
opt/bbmap-37.90/current/tax/RenameIMG.java
opt/bbmap-37.90/current/pacbio/ProcessStackedSitesNormalized$Buffer.class
opt/bbmap-37.90/current/clump/KmerComparatorY.class
opt/bbmap-37.90/current/pacbio/MakePacBioScript.java
opt/bbmap-37.90/current/bloom/LargeKmerCount.java
opt/bbmap-37.90/current/bloom/KCountArray4.java
opt/bbmap-37.90/current/tax/TaxServer$HelpHandler.class
opt/bbmap-37.90/resources/sequencing_artifacts.fa.gz
opt/bbmap-37.90/current/pacbio/PartitionReads$1.class
opt/bbmap-37.90/current/stream/ConcurrentGenericReadInputStream$1.class
opt/bbmap-37.90/current/hiseq/Tile.java
opt/bbmap-37.90/current/stream/ConcurrentReadInputStream.class
bin/phylip2fasta.sh
opt/bbmap-37.90/current/cluster/Cluster.java
opt/bbmap-37.90/current/jgi/FilterByCoverage.java
opt/bbmap-37.90/current/assemble/Tadpole.class
opt/bbmap-37.90/current/driver/MergeCoverageOTU.java
opt/bbmap-37.90/current/structures/AbstractIntHashMap.java
opt/bbmap-37.90/current/jgi/SplitSamFile.java
opt/bbmap-37.90/current/jgi/Dedupe2.class
bin/testformat.sh
opt/bbmap-37.90/current/driver/SummarizeQuast.java
opt/bbmap-37.90/current/pacbio/SortSites.java
opt/bbmap-37.90/current/assemble/Tadpole$DumpKmersThread.class
bin/kmercountexact.sh
opt/bbmap-37.90/current/stream/ConcurrentDepot.java
opt/bbmap-37.90/current/stream/SequentialReadInputStream.java
opt/bbmap-37.90/current/align2/GradeSamFile$1.class
opt/bbmap-37.90/current/clump/ClumpList.java
opt/bbmap-37.90/current/align2/Quad64.class
opt/bbmap-37.90/current/stream/ReadInputStream.class
opt/bbmap-37.90/current/structures/LongHashMap.java
opt/bbmap-37.90/current/assemble/TadpoleWrapper.java
opt/bbmap-37.90/current/tax/FindAncestor.java
bin/decontaminate.sh
opt/bbmap-37.90/filterbytile.sh
opt/bbmap-37.90/getreads.sh
opt/bbmap-37.90/current/driver/TestCompressionSpeed.java
opt/bbmap-37.90/current/stream/ConcurrentReadListDepot.class
opt/bbmap-37.90/current/align2/AbstractMapThread.class
opt/bbmap-37.90/current/stream/SamReadStreamer.class
opt/bbmap-37.90/current/clump/ClumpList$ProcessThread.class
opt/bbmap-37.90/mergeOTUs.sh
opt/bbmap-37.90/current/jgi/CutPrimers.java
opt/bbmap-37.90/current/structures/LongM.class
opt/bbmap-37.90/current/driver/ConvertSamToAln.java
opt/bbmap-37.90/current/align2/ReformatBatchOutput2.class
opt/bbmap-37.90/current/sketch/SummarizeSketchStats.java
opt/bbmap-37.90/current/align2/SplitMappedReads.class
bin/bbcountunique.sh
bin/bbsplitpairs.sh
opt/bbmap-37.90/current/dna/ChromosomeArray.java
opt/bbmap-37.90/current/var2/CallVariants$ProcessThread.class
bin/summarizecrossblock.sh
opt/bbmap-37.90/comparevcf.sh
opt/bbmap-37.90/current/kmer/KmerBuffer.class
opt/bbmap-37.90/current/structures/AtomicBitSet.class
opt/bbmap-37.90/current/sort/ReadComparatorID.java
opt/bbmap-37.90/current/tax/RenameGiToNcbi.class
opt/bbmap-37.90/current/sketch/SketchMaker$ProcessThread.class
bin/loadreads.sh
opt/bbmap-37.90/current/fun/ProbShared2.java
opt/bbmap-37.90/current/align2/PrintTime.java
opt/bbmap-37.90/phylip2fasta.sh
opt/bbmap-37.90/current/jgi/TestFormat$Barcode.class
opt/bbmap-37.90/current/clump/KmerSort.class
opt/bbmap-37.90/current/kmer/KmerLink.java
opt/bbmap-37.90/current/fileIO/CompressFiles.java
opt/bbmap-37.90/current/jgi/BBMask$MaskRepeatThread.class
opt/bbmap-37.90/current/align2/BBSplitter$1.class
opt/bbmap-37.90/current/jgi/BBQC.class
opt/bbmap-37.90/current/driver/MergeTextFiles.class
opt/bbmap-37.90/current/shared/Parser.java
opt/bbmap-37.90/resources/phix174_ill.ref.fa.gz
opt/bbmap-37.90/current/align2/ChromLoadThread.java
opt/bbmap-37.90/current/jgi/FilterBySequence$Code.class
opt/bbmap-37.90/current/sketch/SendSketch.java
bin/tadwrapper.sh
opt/bbmap-37.90/current/var2/Realign.java
opt/bbmap-37.90/current/bloom/KCountArray7MT$WriteThread.class
opt/bbmap-37.90/current/sort/SortReadsByMapping$Block.class
opt/bbmap-37.90/current/stream/ConcurrentReadInputStreamD.class
opt/bbmap-37.90/current/tax/ImgRecord2.class
opt/bbmap-37.90/current/stream/FastaQualReadInputStream.java
opt/bbmap-37.90/current/dna/ScafLoc.class
bin/processfrag.sh
opt/bbmap-37.90/docs/UsageGuide.txt
opt/bbmap-37.90/current/assemble/AbstractRemoveThread$RemoveThread2.class
opt/bbmap-37.90/current/jgi/TetramerFrequencies$Line.class
opt/bbmap-37.90/current/bloom/KmerCount3.java
opt/bbmap-37.90/current/stream/ConcurrentGenericReadInputStream$ReadThread.class
opt/bbmap-37.90/current/sketch/CompareBuffer.java
opt/bbmap-37.90/current/dna/MotifMulti.class
opt/bbmap-37.90/current/jgi/RQCFilter.java
opt/bbmap-37.90/current/var2/FilterSam.class
opt/bbmap-37.90/current/fileIO/ByteFile.java
opt/bbmap-37.90/current/structures/LongHeap.java
opt/bbmap-37.90/current/structures/AbstractIntHashMap.class
opt/bbmap-37.90/current/align2/MultiStateAligner9PacBioAdapter2.class
opt/bbmap-37.90/current/sort/ReadComparatorTaxa.class
opt/bbmap-37.90/current/var/VarLine.class
opt/bbmap-37.90/current/bloom/KCountArray4MT.class
opt/bbmap-37.90/current/align2/MultiStateAligner9ts.java
opt/bbmap-37.90/current/sketch/SketchTool$LoadThread.class
opt/bbmap-37.90/current/stream/Read.class
opt/bbmap-37.90/current/stream/ByteBuilder.class
opt/bbmap-37.90/current/structures/Quantizer.class
opt/bbmap-37.90/current/bloom/KmerCount5.java
opt/bbmap-37.90/current/kmer/AbstractKmerTableSet.class
opt/bbmap-37.90/current/driver/RenameAndMux$MuxThread.class
opt/bbmap-37.90/splitsam6way.sh
bin/bbversion.sh
opt/bbmap-37.90/current/driver/FilterLines.java
opt/bbmap-37.90/current/fileIO/ByteFile2.class
opt/bbmap-37.90/current/stream/FASTQ.class
opt/bbmap-37.90/current/var2/Var.class
opt/bbmap-37.90/readlength.sh
opt/bbmap-37.90/current/driver/ProcessSpeed2.class
opt/bbmap-37.90/current/tax/FilterByTaxa.class
opt/bbmap-37.90/current/stream/ConcurrentLegacyReadInputStream.class
opt/bbmap-37.90/current/jgi/ReadKmerDepthDistribution.class
opt/bbmap-37.90/current/pacbio/PartitionFastaFile.class
opt/bbmap-37.90/current/jgi/ReformatReads.class
opt/bbmap-37.90/current/driver/Translator.class
opt/bbmap-37.90/current/bloom/KmerCountAbstract.java
opt/bbmap-37.90/current/bloom/KCountArray3.class
opt/bbmap-37.90/current/assemble/AbstractBuildThread.class
opt/bbmap-37.90/current/sort/SortReadsByID.class
opt/bbmap-37.90/config/recalibrate.txt
opt/bbmap-37.90/current/kmer/KmerNode1D.class
opt/bbmap-37.90/current/structures/LongHeapSetInterface.class
opt/bbmap-37.90/current/jgi/A_Sample.java
opt/bbmap-37.90/current/assemble/Tadpole2.class
opt/bbmap-37.90/current/driver/MergeBigelow.class
opt/bbmap-37.90/current/assemble/Shaver.class
opt/bbmap-37.90/current/clump/Clump.java
opt/bbmap-37.90/current/align2/MultiStateAligner11tsJNI.java
opt/bbmap-37.90/current/jgi/BBTool_ST.class
opt/bbmap-37.90/resources/phix_adapters.fa.gz
opt/bbmap-37.90/resources/contents.txt
opt/bbmap-37.90/current/fun/Calc.class
opt/bbmap-37.90/current/stream/ConcurrentGenericReadOutputStream.class
opt/bbmap-37.90/current/assemble/ErrorTracker.class
opt/bbmap-37.90/current/driver/TransposeTextFile.class
opt/bbmap-37.90/current/shared/ReadStats.java
opt/bbmap-37.90/current/stream/FastaReadInputStream2.java
opt/bbmap-37.90/current/jgi/KmerCountMulti.class
opt/bbmap-37.90/current/tax/SplitByTaxa.class
opt/bbmap-37.90/current/jgi/Dedupe$UnitOffsetComparator.class
opt/bbmap-37.90/current/driver/ProcessWebcheck.class
opt/bbmap-37.90/current/var/StackVariations$1.class
opt/bbmap-37.90/current/stream/ScarfReadInputStream.java
opt/bbmap-37.90/current/align2/Evaluate.class
opt/bbmap-37.90/current/fun/DiskBench$ReadThread.class
opt/bbmap-37.90/current/align2/NeedlemanWunsch.java
opt/bbmap-37.90/current/pacbio/MergeReadsAndGenome.class
opt/bbmap-37.90/current/var2/MergeSamples.class
opt/bbmap-37.90/resources/nextera_LMP_adapter.fa.gz
opt/bbmap-37.90/cutprimers.sh
opt/bbmap-37.90/current/sort/ReadComparator.class
opt/bbmap-37.90/current/jgi/CalcUniqueness.java
opt/bbmap-37.90/current/server/ServerTools.java
opt/bbmap-37.90/current/driver/LoadReads.class
opt/bbmap-37.90/current/driver/CountRNAs.java
opt/bbmap-37.90/current/bloom/KmerCount4.java
opt/bbmap-37.90/current/var2/VcfWriter$ProcessThread.class
opt/bbmap-37.90/current/driver/EstherFilter.class
opt/bbmap-37.90/pipelines/assembleMito_Illumina.sh
opt/bbmap-37.90/current/clump/StreamToOutput.class
opt/bbmap-37.90/current/sketch/SketchMakerMini.java
opt/bbmap-37.90/fungalrelease.sh
opt/bbmap-37.90/current/align2/BBMapThreadPacBio.class
opt/bbmap-37.90/mergesam.sh
opt/bbmap-37.90/pipelines/assembleMito_PacBio.sh
opt/bbmap-37.90/current/sketch/Sketch.class
opt/bbmap-37.90/current/var2/Realigner.java
opt/bbmap-37.90/current/stream/SamLineStreamer.java
opt/bbmap-37.90/current/assemble/Tadpole2$BuildThread.class
opt/bbmap-37.90/current/dna/Motif.java
opt/bbmap-37.90/current/jgi/Dedupe2$UnitOffsetComparator.class
bin/gradesam.sh
opt/bbmap-37.90/current/pacbio/RemoveNFromChromosome.java
opt/bbmap-37.90/current/bloom/KCountArray.class
opt/bbmap-37.90/current/structures/IntMap.java
opt/bbmap-37.90/current/driver/RenameAndMux.class
opt/bbmap-37.90/current/pacbio/CalcCoverageFromSites.java
opt/bbmap-37.90/current/tax/AccessionToTaxid.class
opt/bbmap-37.90/current/jgi/Difference.java
opt/bbmap-37.90/current/jgi/RandomGenome.class
opt/bbmap-37.90/estherfilter.sh
opt/bbmap-37.90/current/assemble/AbstractBuildThread.java
opt/bbmap-37.90/current/structures/LongHeapMap.class
opt/bbmap-37.90/current/driver/FixDumbFile.class
opt/bbmap-37.90/current/driver/LineCount.class
opt/bbmap-37.90/current/align2/QuadHeap.class
opt/bbmap-37.90/current/var2/CallVariants2.class
opt/bbmap-37.90/current/var/GenerateVarlets2$ProcessThread.class
bin/consect.sh
opt/bbmap-37.90/current/jgi/RQCFilter.class
opt/bbmap-37.90/current/jgi/MakeContaminatedGenomes.java
opt/bbmap-37.90/current/jgi/DedupeProtein$UnitOffsetComparator.class
opt/bbmap-37.90/current/cluster/ReadTag.java
opt/bbmap-37.90/conda_build.sh
opt/bbmap-37.90/current/jgi/KmerCountExact.class
opt/bbmap-37.90/current/structures/IntList.class
opt/bbmap-37.90/current/align2/MultiStateAligner11ts.java
opt/bbmap-37.90/current/sort/ReadQualityComparator.class
bin/fungalrelease.sh
opt/bbmap-37.90/normandcorrectwrapper.sh
opt/bbmap-37.90/current/ukmer/Kmer.java
opt/bbmap-37.90/current/stream/HeaderInputStream.class
opt/bbmap-37.90/current/jgi/DecontaminateByNormalization.class
opt/bbmap-37.90/crosscontaminate.sh
bin/bbwrap.sh
opt/bbmap-37.90/current/tax/Query.java
opt/bbmap-37.90/commonkmers.sh
opt/bbmap-37.90/current/ukmer/HashArrayU1D.java
opt/bbmap-37.90/current/fileIO/TextStreamWriter.java
bin/sortbyname.sh
opt/bbmap-37.90/current/align2/BBMapThread.java
opt/bbmap-37.90/current/var/Varlet.java
opt/bbmap-37.90/current/driver/CompareReferenceGenomes.class
opt/bbmap-37.90/resources/nextera_LMP_linker.fa.gz
opt/bbmap-37.90/current/shared/Parser.class
opt/bbmap-37.90/current/clump/KmerComparatorY.java
opt/bbmap-37.90/current/stream/ReadStreamByteWriter.class
opt/bbmap-37.90/current/driver/ParseCrossblockResults$ResultsLine.class
opt/bbmap-37.90/current/bloom/KCountArray8MT.class
opt/bbmap-37.90/current/jgi/ReadKmerDepthDistribution$ProcessThread.class
opt/bbmap-37.90/current/jgi/Dedupe$Unit.class
opt/bbmap-37.90/current/tax/TaxSize.java
opt/bbmap-37.90/current/ukmer/HashForestU.class
opt/bbmap-37.90/current/sort/ReadComparatorList.java
opt/bbmap-37.90/current/align2/IndexMaker5.java
bin/comparesketch.sh
opt/bbmap-37.90/idtree.sh
bin/dedupe2.sh
bin/taxserver.sh
opt/bbmap-37.90/taxsize.sh
opt/bbmap-37.90/current/jgi/CalcTrueQuality$CountMatrixSet.class
opt/bbmap-37.90/current/sort/SortReadsByID$Block.class
opt/bbmap-37.90/current/align2/MultiStateAligner9Flat.java
bin/bbfakereads.sh
opt/bbmap-37.90/current/align2/Pointer.java
opt/bbmap-37.90/current/align2/Evaluate.java
opt/bbmap-37.90/current/jgi/A_Sample.class
opt/bbmap-37.90/current/jgi/DedupeProtein$Unit.class
opt/bbmap-37.90/current/driver/TransposeTextFile.java
opt/bbmap-37.90/current/jgi/Consect.class
opt/bbmap-37.90/current/align2/MultiStateAligner10ts.java
opt/bbmap-37.90/current/var2/FilterVCF.java
opt/bbmap-37.90/current/assemble/Tadpole1.java
opt/bbmap-37.90/reducesilva.sh
opt/bbmap-37.90/current/align2/QualityTools.class
opt/bbmap-37.90/current/bloom/KCountArray7MTA.java
opt/bbmap-37.90/current/bloom/LargeKmerCount2.java
opt/bbmap-37.90/current/ukmer/KmerNodeU1D.java
bin/mergeOTUs.sh
opt/bbmap-37.90/current/fun/Life.class
opt/bbmap-37.90/current/align2/ReformatBatchOutput.java
opt/bbmap-37.90/current/clump/KmerSort$FetchThread.class
opt/bbmap-37.90/docs/guides/BBMapGuide.txt
opt/bbmap-37.90/current/driver/ConcatenateTextFiles$1.class
opt/bbmap-37.90/current/jgi/Dedupe2$Overlap.class
opt/bbmap-37.90/current/tax/PrintTaxonomy.class
opt/bbmap-37.90/current/clump/ClumpList$ClumpThread.class
opt/bbmap-37.90/current/sort/ReadComparatorFlowcell.class
opt/bbmap-37.90/current/jgi/FungalRelease.java
opt/bbmap-37.90/current/var/GenerateVarlets2$1.class
opt/bbmap-37.90/current/var/GenerateVarlets3$ProcessThread.class
opt/bbmap-37.90/current/jgi/ReplaceHeaders.java
opt/bbmap-37.90/current/driver/CompareSequences.class
opt/bbmap-37.90/current/kmer/KmerBuffer.java
opt/bbmap-37.90/current/assemble/AbstractRemoveThread.class
opt/bbmap-37.90/docs/guides/StatsGuide.txt
opt/bbmap-37.90/current/align2/BBIndexPacBio.class
opt/bbmap-37.90/kcompress.sh
opt/bbmap-37.90/current/dna/Coverage.java
opt/bbmap-37.90/current/var2/VcfLoader.class
opt/bbmap-37.90/current/driver/RenameByHeader.java
bin/dedupe.sh
opt/bbmap-37.90/current/jgi/BBDuk2$LoadThread.class
opt/bbmap-37.90/current/assemble/KmerCompressor$BuildThread.class
opt/bbmap-37.90/current/jgi/UnicodeToAscii.class
opt/bbmap-37.90/current/align2/MSA.class
opt/bbmap-37.90/current/driver/MoveFiles.class
opt/bbmap-37.90/pipelines/startSilvaServer.sh
opt/bbmap-37.90/current/shared/KillSwitch.java
opt/bbmap-37.90/current/bloom/TestLargeKmer.class
opt/bbmap-37.90/current/driver/CollateSpikeIn.java
opt/bbmap-37.90/current/stream/SamReadInputStream.java
opt/bbmap-37.90/current/jgi/SplitSam6Way.class
bin/gitable.sh
opt/bbmap-37.90/shuffle.sh
opt/bbmap-37.90/current/ukmer/HashArrayU.class
opt/bbmap-37.90/current/jgi/Dedupe2$Unit.class
opt/bbmap-37.90/current/align2/BBIndex.java
opt/bbmap-37.90/current/jgi/MakeChimeras.java
opt/bbmap-37.90/current/jgi/FilterBySequence.class
opt/bbmap-37.90/current/align2/GradeSamFile.class
opt/bbmap-37.90/current/jgi/Dedupe$ClusterLengthComparator.class
opt/bbmap-37.90/current/jgi/FuseSequence.java
opt/bbmap-37.90/dedupe.sh
opt/bbmap-37.90/current/stream/ConcurrentReadListDepot.java
opt/bbmap-37.90/current/var2/VcfWriter.java
opt/bbmap-37.90/current/assemble/Shaver2.class
bin/removesmartbell.sh
opt/bbmap-37.90/pipelines/fetchNt.sh
opt/bbmap-37.90/pipelines/testPlatformQuality.sh
opt/bbmap-37.90/current/pacbio/RemoveAdapters2$1.class
opt/bbmap-37.90/current/jgi/Seal.java
opt/bbmap-37.90/current/sort/SortReadsByMapping.class
bin/unicode2ascii.sh
opt/bbmap-37.90/current/fileIO/CopyFiles.java
opt/bbmap-37.90/current/align2/MultiStateAligner11ts.class
opt/bbmap-37.90/current/stream/SiteScore$PositionComparator.class
opt/bbmap-37.90/current/tax/Query.class
opt/bbmap-37.90/current/jgi/AssemblyStats2.java
opt/bbmap-37.90/current/bloom/KCountArray7MT.java
opt/bbmap-37.90/current/stream/DualCris.class
opt/bbmap-37.90/current/fileIO/ByteFile2.java
bin/repair.sh
opt/bbmap-37.90/current/jgi/Dedupe2$HashThread.class
opt/bbmap-37.90/current/bloom/KmerCount6MT.class
opt/bbmap-37.90/rqcfilter.sh
opt/bbmap-37.90/current/sort/SortByName.java
opt/bbmap-37.90/pipelines/callInsertions.sh
opt/bbmap-37.90/current/driver/BBVersion.java
opt/bbmap-37.90/current/fileIO/SummaryFile.java
opt/bbmap-37.90/bbduk.sh
opt/bbmap-37.90/current/stream/FastqReadInputStream.java
opt/bbmap-37.90/current/jgi/A_SampleMT.java
opt/bbmap-37.90/current/ukmer/HashArrayU2D.class
opt/bbmap-37.90/current/pacbio/RemoveAdapters3.class
opt/bbmap-37.90/current/dna/ChromArrayMaker.java
bin/removecatdogmousehuman.sh
opt/bbmap-37.90/current/kmer/HashArray1D.java
opt/bbmap-37.90/jni/align2_BandedAlignerJNI.h
opt/bbmap-37.90/current/tax/ImgRecord.java
opt/bbmap-37.90/docs/guides/CalcUniquenessGuide.txt
opt/bbmap-37.90/current/shared/Shared.java
opt/bbmap-37.90/current/stream/ReadStreamWriter.java
opt/bbmap-37.90/current/ukmer/AbstractKmerTableU.class
opt/bbmap-37.90/current/align2/BBMapThread5$1.class
opt/bbmap-37.90/current/assemble/Tadpole1.class
opt/bbmap-37.90/current/cluster/ReadTag.class
opt/bbmap-37.90/current/sort/ReadErrorComparator.class
bin/bbmapskimmer.sh
opt/bbmap-37.90/consect.sh
opt/bbmap-37.90/current/jgi/GetReads.class
opt/bbmap-37.90/current/sort/ReadComparatorMapping.java
bin/bbsplit.sh
opt/bbmap-37.90/current/jgi/RemoveBadBarcodes.class
opt/bbmap-37.90/current/fun/FindPath$Edge.class
opt/bbmap-37.90/current/jgi/DedupeProtein$Overlap.class
opt/bbmap-37.90/current/sort/Shuffle.java
opt/bbmap-37.90/current/jgi/Dedupe.class
opt/bbmap-37.90/current/var/StackVariations2$SVThread.class
opt/bbmap-37.90/current/fun/Genetic.java
opt/bbmap-37.90/current/assemble/Shaver2.java
opt/bbmap-37.90/current/kmer/KmerNode.class
opt/bbmap-37.90/current/driver/GenerateNoCallsFromCoverage.class
opt/bbmap-37.90/docs/guides/ClumpifyGuide.txt
bin/calctruequality.sh
opt/bbmap-37.90/current/hiseq/AnalyzeFlowCell.class
opt/bbmap-37.90/bbrename.sh
opt/bbmap-37.90/current/structures/CoverageArray2.class
opt/bbmap-37.90/current/jgi/RepresentativeSet$Edge.class
opt/bbmap-37.90/current/sort/ReadComparatorList.class
opt/bbmap-37.90/current/jgi/BBMask.class
opt/bbmap-37.90/current/jgi/A_SampleMT$ProcessThread.class
opt/bbmap-37.90/current/bloom/KCountArray6MT$WriteThread.class
opt/bbmap-37.90/current/sketch/Comparison$VolumeComparator.class
opt/bbmap-37.90/current/var2/VarMap$ProcessThread.class
opt/bbmap-37.90/docs/guides/SealGuide.txt
opt/bbmap-37.90/current/var2/Scaffold.java
opt/bbmap-37.90/current/jgi/FindPrimers.class
opt/bbmap-37.90/current/stream/SiteScoreR.java
opt/bbmap-37.90/current/tax/RenameIMG.class
bin/clumpify.sh
opt/bbmap-37.90/current/bloom/KmerCount7MT.java
opt/bbmap-37.90/current/jgi/CalcTrueQuality$Worker.class
opt/bbmap-37.90/resources/short.fa
opt/bbmap-37.90/current/sketch/SketchTool$SketchThread.class
bin/callvariants2.sh
opt/bbmap-37.90/current/dna/ChromToFasta.java
opt/bbmap-37.90/current/driver/LoadReads.java
opt/bbmap-37.90/current/var2/VarMap.class
opt/bbmap-37.90/current/sketch/BlacklistMaker$ListHolder.class
bin/demuxbyname.sh
opt/bbmap-37.90/current/fileIO/ReadWrite$WriteStringThread.class
opt/bbmap-37.90/current/jgi/RemapQuality.java
opt/bbmap-37.90/current/assemble/AbstractExploreThread.java
opt/bbmap-37.90/current/align2/Quad.java
opt/bbmap-37.90/current/jgi/PartitionReads.class
opt/bbmap-37.90/current/jgi/Dedupe$Overlap.class
opt/bbmap-37.90/current/kmer/HashBuffer.class
bin/filterlines.sh
opt/bbmap-37.90/current/driver/FilterLines.class
opt/bbmap-37.90/current/sort/ReadComparatorFlowcell.java
opt/bbmap-37.90/current/ukmer/KmerNodeU2D.class
opt/bbmap-37.90/current/bloom/KmerCount4.class
opt/bbmap-37.90/current/stream/SamStreamerWrapper.class
opt/bbmap-37.90/current/clump/Clumpify.class
opt/bbmap-37.90/current/tax/TaxServer.java
opt/bbmap-37.90/resources/lambda.fa.gz
opt/bbmap-37.90/current/structures/IntHashSet.java
opt/bbmap-37.90/current/ukmer/DumpThreadU.class
opt/bbmap-37.90/current/assemble/KmerCompressor.class
opt/bbmap-37.90/current/jgi/Shred.class
opt/bbmap-37.90/current/driver/LookAtID.java
opt/bbmap-37.90/current/structures/EntropyTracker.class
opt/bbmap-37.90/current/align2/Quad64Heap.java
bin/gi2ancestors.sh
opt/bbmap-37.90/current/clump/KmerSort3$FetchThread$FetchSubThread.class
opt/bbmap-37.90/current/align2/BBMapPacBio.java
opt/bbmap-37.90/current/var/GenerateVarlets$ProcessThread.class
opt/bbmap-37.90/current/driver/ConcatenateTextFiles$WriteThread.class
opt/bbmap-37.90/current/fileIO/ByteFile1.java
opt/bbmap-37.90/current/pacbio/SplitOffPerfectContigs$1.class
opt/bbmap-37.90/jni/CMakeLists.txt
opt/bbmap-37.90/current/tax/IDNode.java
opt/bbmap-37.90/current/structures/AbstractBitSet.java
opt/bbmap-37.90/current/kmer/KmerTable.java
opt/bbmap-37.90/current/driver/Search.class
opt/bbmap-37.90/current/jgi/KmerNormalize.java
opt/bbmap-37.90/current/var/GenerateVarlets2.java
opt/bbmap-37.90/current/var2/FilterVCF.class
opt/bbmap-37.90/tetramerfreq.sh
bin/invertkey.sh
bin/removehuman2.sh
opt/bbmap-37.90/testfilesystem.sh
opt/bbmap-37.90/current/structures/LongLongHashMap.java
opt/bbmap-37.90/taxserver.sh
opt/bbmap-37.90/current/stream/ScaffoldCoordinates.java
opt/bbmap-37.90/current/stream/MDWalker.class
opt/bbmap-37.90/current/jgi/RedirectTest.java
opt/bbmap-37.90/current/driver/TestLockSpeed$CountThread.class
opt/bbmap-37.90/printtime.sh
opt/bbmap-37.90/current/tax/FilterByTaxa.java
opt/bbmap-37.90/current/assemble/AbstractExploreThread.class
opt/bbmap-37.90/current/kmer/HashArrayHybrid.class
opt/bbmap-37.90/current/pacbio/MergeReadsAndGenome.java
opt/bbmap-37.90/current/stream/FASTQ.java
opt/bbmap-37.90/current/clump/PivotSet.java
opt/bbmap-37.90/current/dna/Gene.java
bin/calcmem.sh
opt/bbmap-37.90/current/align2/BBMapThreadPacBio.java
opt/bbmap-37.90/current/assemble/TadPipe.class
opt/bbmap-37.90/current/fileIO/ChainBlock.class
opt/bbmap-37.90/current/structures/LongHashSet.java
opt/bbmap-37.90/current/jgi/SplitPairsAndSingles.class
opt/bbmap-37.90/current/align2/MakeRocCurve$1.class
opt/bbmap-37.90/current/fun/Palindrome.class
opt/bbmap-37.90/current/dna/Exon.class
opt/bbmap-37.90/current/assemble/Tadpole1$BuildThread.class
opt/bbmap-37.90/current/align2/MakeQualityHistogram.class
opt/bbmap-37.90/current/jgi/CountUniqueness.java
opt/bbmap-37.90/current/kmer/DumpThread.java
opt/bbmap-37.90/current/jgi/Dedupe$ClusterThread.class
opt/bbmap-37.90/current/fileIO/CopyFile.java
opt/bbmap-37.90/current/driver/TestLockSpeed$VolatileBox.class
opt/bbmap-37.90/current/jgi/TestFormat$TestThread.class
opt/bbmap-37.90/current/bloom/KmerCount6.class
opt/bbmap-37.90/current/var/Variation.java
opt/bbmap-37.90/current/shared/TrimRead.java
opt/bbmap-37.90/current/shared/Timer.class
opt/bbmap-37.90/docs/guides/BBSketchGuide.txt
opt/bbmap-37.90/current/jgi/CountBarcodes$StringNum.class
opt/bbmap-37.90/current/jgi/KmerCountMulti$ProcessThread.class
opt/bbmap-37.90/current/align2/MSA.java
opt/bbmap-37.90/current/clump/KmerComparator$HashThread.class
opt/bbmap-37.90/current/hiseq/MicroTile.java
opt/bbmap-37.90/current/sketch/SketchResults.java
bin/fuse.sh
opt/bbmap-37.90/current/tax/ShrinkAccession.java
opt/bbmap-37.90/gi2taxid.sh
bin/sendsketch.sh
opt/bbmap-37.90/current/stream/ConcurrentReadInputStream.java
opt/bbmap-37.90/current/tax/IDTree.class
opt/bbmap-37.90/current/bloom/KmerCount5.class
opt/bbmap-37.90/current/jgi/Seal.class
opt/bbmap-37.90/current/jgi/FilterBySequence$LoadThread.class
opt/bbmap-37.90/current/bloom/LargeKmerCount2.class
opt/bbmap-37.90/current/hiseq/FlowcellCoordinate.java
opt/bbmap-37.90/current/align2/BBMapThread$1.class
opt/bbmap-37.90/current/jgi/SmallKmerFrequency$NumComparator.class
opt/bbmap-37.90/bbmergegapped.sh
bin/dedupebymapping.sh
opt/bbmap-37.90/current/jgi/SplitSamFile.class
opt/bbmap-37.90/muxbyname.sh
opt/bbmap-37.90/countgc.sh
opt/bbmap-37.90/current/align2/MultiStateAligner11tsJNI.class
opt/bbmap-37.90/current/driver/Grep.class
opt/bbmap-37.90/resources/sample2.fq.gz
opt/bbmap-37.90/current/fileIO/TextStreamWriter.class
opt/bbmap-37.90/testformat.sh
opt/bbmap-37.90/current/clump/ClumpTools.java
opt/bbmap-37.90/current/assemble/Shaver2$ShaveThread.class
opt/bbmap-37.90/current/bloom/KCountArray7MTA.class
opt/bbmap-37.90/filtersam.sh
bin/crossblock.sh
opt/bbmap-37.90/filterbarcodes.sh
bin/reformat.sh
opt/bbmap-37.90/current/structures/LongList.class
opt/bbmap-37.90/current/stream/ScaffoldCoordinates.class
opt/bbmap-37.90/current/align2/MultiStateAligner9PacBioAdapter.class
opt/bbmap-37.90/filterbyname.sh
opt/bbmap-37.90/current/server/SimpleHttpServer.class
opt/bbmap-37.90/current/stream/RandomReadInputStream3.java
bin/splitnextera.sh
opt/bbmap-37.90/current/driver/GenerateNoCallsFromCoverage.java
opt/bbmap-37.90/current/jgi/SmallKmerFrequency$CountComparator.class
opt/bbmap-37.90/current/var/StackVariations2.class
opt/bbmap-37.90/current/bloom/KmerCount7MTA$1.class
opt/bbmap-37.90/current/bloom/KCountArray2.java
opt/bbmap-37.90/current/driver/ProcessFragMerging.class
opt/bbmap-37.90/current/shared/KillSwitch.class
opt/bbmap-37.90/current/stream/SamStreamer.java
bin/taxonomy.sh
opt/bbmap-37.90/current/align2/NeedlemanWunsch.class
bin/replaceheaders.sh
opt/bbmap-37.90/current/dna/MotifSimple.java
opt/bbmap-37.90/current/sort/SortByName$WriteThread.class
opt/bbmap-37.90/current/var2/ScafMap.java
opt/bbmap-37.90/current/fileIO/ReadWrite$WriteObjectThread.class
opt/bbmap-37.90/current/kmer/AtomicShortArray.class
opt/bbmap-37.90/docs/readme_config.txt
opt/bbmap-37.90/current/pacbio/CalcCoverageFromSites.class
opt/bbmap-37.90/current/align2/IndexMaker4.java
opt/bbmap-37.90/current/hiseq/Lane.java
opt/bbmap-37.90/current/jgi/StringCount.class
opt/bbmap-37.90/current/kmer/KmerTable.class
opt/bbmap-37.90/current/fileIO/ByteFile1.class
opt/bbmap-37.90/removecatdogmousehuman.sh
opt/bbmap-37.90/current/assemble/AbstractShaveThread.class
opt/bbmap-37.90/current/sketch/SketchHeap.class
opt/bbmap-37.90/current/structures/CoverageArray3.java
opt/bbmap-37.90/current/jgi/CrossContaminate$Vessel.class
opt/bbmap-37.90/calctruequality.sh
opt/bbmap-37.90/current/align2/CompressString.class
opt/bbmap-37.90/current/assemble/Tadpole2.java
opt/bbmap-37.90/current/jgi/IdentityMatrix$ProcessThread.class
opt/bbmap-37.90/current/structures/IntHashSetList.java
opt/bbmap-37.90/current/jgi/ReadKmerDepthDistribution.java
bin/bbrealign.sh
opt/bbmap-37.90/current/align2/BBIndexAcc.class
opt/bbmap-37.90/current/driver/Grep.java
bin/synthmda.sh
opt/bbmap-37.90/current/shared/Colors.java
opt/bbmap-37.90/bbversion.sh
opt/bbmap-37.90/grademerge.sh
opt/bbmap-37.90/tadwrapper.sh
opt/bbmap-37.90/current/align2/MultiStateAligner9XFlat.java
opt/bbmap-37.90/current/driver/LineCount.java
opt/bbmap-37.90/current/align2/BBMapPacBioSkimmer.class
opt/bbmap-37.90/current/fun/MakeAdjacencyList.java
opt/bbmap-37.90/current/var2/SamFilter.class
opt/bbmap-37.90/current/tax/TaxNode.class
opt/bbmap-37.90/current/jgi/CalcTrueQuality$GBMatrixSet.class
opt/bbmap-37.90/current/driver/SniffSplices.class
opt/bbmap-37.90/current/sketch/SketchHeap.java
opt/bbmap-37.90/current/structures/CoverageArray3.class
opt/bbmap-37.90/current/sort/ReadComparatorRandom.class
opt/bbmap-37.90/makechimeras.sh
opt/bbmap-37.90/current/fun/ProbShared2.class
opt/bbmap-37.90/current/sketch/CompareSketch.class
opt/bbmap-37.90/current/stream/SamLine.java
opt/bbmap-37.90/current/bloom/KCountArray3.java
opt/bbmap-37.90/current/clump/KmerComparator2.java
opt/bbmap-37.90/current/assemble/KmerCompressor.java
opt/bbmap-37.90/current/dna/MotifProbsN.java
opt/bbmap-37.90/current/ukmer/AbstractKmerTableU$AllocThread.class
opt/bbmap-37.90/current/sketch/DisplayParams.class
bin/kmercountmulti.sh
opt/bbmap-37.90/current/kmer/KmerLink.class
opt/bbmap-37.90/current/var/GenerateConsensusVariations.java
opt/bbmap-37.90/current/fileIO/ReadWrite$1.class
opt/bbmap-37.90/processfrag.sh
opt/bbmap-37.90/current/assemble/Shaver2$ExploreThread.class
opt/bbmap-37.90/docs/guides/RepairGuide.txt
opt/bbmap-37.90/current/align2/AbstractMapper.java
opt/bbmap-37.90/current/driver/EstherFilter.java
opt/bbmap-37.90/docs/readme_filetypes.txt
opt/bbmap-37.90/current/align2/MakeRocCurve.java
opt/bbmap-37.90/current/structures/AbstractBitSet.class
opt/bbmap-37.90/current/jgi/ReadKmerDepthDistribution$1.class
opt/bbmap-37.90/current/align2/GapTools.class
opt/bbmap-37.90/current/var2/ScafMap.class
opt/bbmap-37.90/current/pacbio/StackSites2$1.class
opt/bbmap-37.90/current/align2/MakeQualityHistogram.java
opt/bbmap-37.90/current/clump/ClumpList.class
opt/bbmap-37.90/current/structures/LongHeapMap.java
opt/bbmap-37.90/current/clump/KmerReduce.class
opt/bbmap-37.90/current/tax/TaxFilter.class
opt/bbmap-37.90/current/stream/ConcurrentGenericReadInputStream.java
opt/bbmap-37.90/current/dna/Scaffold.java
opt/bbmap-37.90/current/align2/ReformatBatchOutput2.java
opt/bbmap-37.90/current/fileIO/ArrayFile.java
opt/bbmap-37.90/filterbysequence.sh
opt/bbmap-37.90/current/ukmer/KmerNodeU2D.java
opt/bbmap-37.90/current/align2/MultiStateAligner9PacBioAdapter_WithBarriers.java
opt/bbmap-37.90/current/sketch/SketchSearcher.java
opt/bbmap-37.90/current/bloom/KCountArray8MT$WriteThread.class
opt/bbmap-37.90/current/align2/BBIndex5.class
opt/bbmap-37.90/current/dna/ScafLoc.java
opt/bbmap-37.90/current/assemble/TadPipe.java
opt/bbmap-37.90/current/align2/IndexMaker5$BlockMaker.class
opt/bbmap-37.90/current/sketch/SketchIndex.class
opt/bbmap-37.90/current/driver/ReduceSilva.class
opt/bbmap-37.90/current/clump/Clump.class
opt/bbmap-37.90/current/assemble/ErrorTracker.java
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bin/splitsam4way.sh
opt/bbmap-37.90/current/sketch/SketchObject.java
opt/bbmap-37.90/summarizemerge.sh
opt/bbmap-37.90/current/jgi/FilterByCoverage.class
opt/bbmap-37.90/current/jgi/RenameReads.java
opt/bbmap-37.90/current/var/GenerateVarlets.class
opt/bbmap-37.90/current/assemble/Shaver1$ExploreThread.class
opt/bbmap-37.90/pipelines/variantPipeline.sh
opt/bbmap-37.90/current/align2/BBMapThreadPacBio$1.class
bin/estherfilter.sh
opt/bbmap-37.90/config/histograms.txt
bin/comparevcf.sh
opt/bbmap-37.90/current/driver/ProcessSpeed.java
opt/bbmap-37.90/current/sketch/BlacklistMaker.java
opt/bbmap-37.90/current/structures/IntMap.class
opt/bbmap-37.90/current/server/SimpleHttpServer$GetHandler.class
opt/bbmap-37.90/resources/blacklist_img_species_300.sketch
bin/removebadbarcodes.sh
opt/bbmap-37.90/current/dna/MotifSimple.class
opt/bbmap-37.90/current/fileIO/ByteFile.class
opt/bbmap-37.90/current/structures/IntHashMap.java
opt/bbmap-37.90/representative.sh
opt/bbmap-37.90/countbarcodes.sh
opt/bbmap-37.90/current/bloom/KCountArray5MT.class
opt/bbmap-37.90/current/jgi/RenameReads.class
opt/bbmap-37.90/current/pacbio/SplitOffPerfectContigs.java
opt/bbmap-37.90/current/structures/CoverageArray.class
opt/bbmap-37.90/current/stream/ConcurrentGenericReadOutputStream.java
opt/bbmap-37.90/current/align2/BBWrap.java
opt/bbmap-37.90/current/clump/KmerSort3$HashSplitThread.class
opt/bbmap-37.90/current/var2/VCFFile$1.class
opt/bbmap-37.90/pipelines/processIMG.sh
bin/testfilesystem.sh
opt/bbmap-37.90/current/pacbio/RemoveNFromChromosome.class
opt/bbmap-37.90/current/tax/TaxServer.class
opt/bbmap-37.90/current/jgi/A_Sample2.java
opt/bbmap-37.90/current/kmer/AbstractKmerTableSet.java
opt/bbmap-37.90/current/structures/MultiBitSet.class
opt/bbmap-37.90/resources/primes.txt.gz
opt/bbmap-37.90/config/rnaseq.txt
opt/bbmap-37.90/current/assemble/AbstractShaveThread.java
opt/bbmap-37.90/webcheck.sh
opt/bbmap-37.90/current/jgi/TestFormat.java
opt/bbmap-37.90/current/pacbio/PartitionReads.java
opt/bbmap-37.90/current/structures/IntHashMapBinary.class
opt/bbmap-37.90/current/jgi/KmerSample.java
opt/bbmap-37.90/current/jgi/FindString.java
opt/bbmap-37.90/current/jgi/MutateGenome.java
opt/bbmap-37.90/current/jgi/RemoveBadBarcodes.java
opt/bbmap-37.90/current/jgi/KmerNormalize$ProcessThread.class
opt/bbmap-37.90/current/jgi/FilterReadsWithSubs.java
opt/bbmap-37.90/current/var/StackVariations$SVThread.class
bin/countsharedlines.sh
opt/bbmap-37.90/calcmem.sh
opt/bbmap-37.90/current/fileIO/GenericTextFile.java
bin/partition.sh
opt/bbmap-37.90/loadreads.sh
opt/bbmap-37.90/current/structures/Quantizer.java
opt/bbmap-37.90/current/structures/RawBitSet.java
opt/bbmap-37.90/current/bloom/TestLargeKmer.java
opt/bbmap-37.90/current/pacbio/GenerateMultiChrom.java
opt/bbmap-37.90/current/align2/MultiStateAligner9PacBioAdapter_WithBarriers.class
opt/bbmap-37.90/current/fileIO/FindFiles.class
bin/mergebarcodes.sh
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opt/bbmap-37.90/current/stream/ConcurrentReadOutputStream.java
opt/bbmap-37.90/current/driver/FindMotifs.java
opt/bbmap-37.90/current/driver/RenameRefseqFiles.class
opt/bbmap-37.90/current/structures/Heap.java
opt/bbmap-37.90/current/pacbio/ProcessStackedSitesNormalized.class
opt/bbmap-37.90/current/jgi/LogLog.java
opt/bbmap-37.90/splitbytaxa.sh
opt/bbmap-37.90/current/kmer/AbstractKmerTable.class
opt/bbmap-37.90/current/driver/PrintEnv.java
opt/bbmap-37.90/current/jgi/CountGC.class
opt/bbmap-37.90/docs/guides/AddAdaptersGuide.txt
opt/bbmap-37.90/current/driver/FilterReadsByName.java
opt/bbmap-37.90/current/dna/Data.class
opt/bbmap-37.90/current/align2/CompareSamFiles.class
opt/bbmap-37.90/current/jgi/KmerCountExact.java
opt/bbmap-37.90/docs/guides/CallVariantsGuide.txt
opt/bbmap-37.90/dedupebymapping.sh
opt/bbmap-37.90/current/stream/RTextInputStream.class
opt/bbmap-37.90/current/jgi/TetramerFrequencies$PrintThread.class
opt/bbmap-37.90/partition.sh
opt/bbmap-37.90/current/dna/MotifProbsN.class
opt/bbmap-37.90/current/ukmer/HashArrayUHybrid.class
opt/bbmap-37.90/current/shared/Timer.java
opt/bbmap-37.90/current/driver/MergeTextFiles2.class
opt/bbmap-37.90/current/sort/SortReadsByMapping.java
opt/bbmap-37.90/current/driver/SummarizeCoverage.java
bin/seal.sh
opt/bbmap-37.90/invertkey.sh
opt/bbmap-37.90/current/pacbio/RemoveAdapters2.class
opt/bbmap-37.90/current/align2/BBSplitter.java
opt/bbmap-37.90/current/assemble/Tadpole$ExtendThread.class
opt/bbmap-37.90/current/jgi/MultiLogLog.java
opt/bbmap-37.90/current/jgi/AssemblyStats2$Triple.class
opt/bbmap-37.90/idmatrix.sh
opt/bbmap-37.90/resources/adapters_no_transposase.fa.gz
opt/bbmap-37.90/docs/guides/BBMergeGuide.txt
opt/bbmap-37.90/current/kmer/HashArray2D.java
opt/bbmap-37.90/current/driver/ProcessFragMerging.java
opt/bbmap-37.90/current/dna/AminoAcid.java
opt/bbmap-37.90/current/jgi/A_SampleByteFile.class
opt/bbmap-37.90/current/stream/ReadStreamWriter.class
opt/bbmap-37.90/current/bloom/KCountArray7MT.class
opt/bbmap-37.90/current/pacbio/MergeReadsAndGenome$1.class
opt/bbmap-37.90/current/driver/MergeTextFiles.java
opt/bbmap-37.90/current/align2/Quad64.java
opt/bbmap-37.90/current/stream/ReadStreamStringWriter.class
opt/bbmap-37.90/current/jgi/PartitionReads.java
opt/bbmap-37.90/summarizesketch.sh
opt/bbmap-37.90/current/align2/BandedAligner.class
opt/bbmap-37.90/current/jgi/GreedyBarCodeFinder.class
opt/bbmap-37.90/current/kmer/KmerNode2D.class
opt/bbmap-37.90/current/pacbio/SplitOffPerfectContigs.class
opt/bbmap-37.90/current/var2/CallVariants.class
opt/bbmap-37.90/current/sketch/SummarizeSketchStats$SketchResultsSummary.class
opt/bbmap-37.90/current/stream/MultiCros.class
opt/bbmap-37.90/current/jgi/BBQC.java
opt/bbmap-37.90/current/fileIO/LoadThread.java
opt/bbmap-37.90/current/driver/ProcessWebcheck.java
opt/bbmap-37.90/current/structures/ListNum.class
opt/bbmap-37.90/current/tax/TaxApp.class
bin/kcompress.sh
bin/webcheck.sh
opt/bbmap-37.90/current/driver/TestCompressionSpeed.class
opt/bbmap-37.90/current/stream/SequentialReadInputStream.class
opt/bbmap-37.90/current/assemble/Shaver.java
opt/bbmap-37.90/current/fileIO/PipeThread.java
opt/bbmap-37.90/current/fileIO/SummaryFile.class
opt/bbmap-37.90/current/kmer/HashArray.class
opt/bbmap-37.90/current/jgi/CallPeaks.java
opt/bbmap-37.90/current/structures/JsonObject.class
opt/bbmap-37.90/current/driver/SniffSplices.java
opt/bbmap-37.90/current/driver/SummarizeCrossblock.class
opt/bbmap-37.90/current/clump/KmerSort3.class
bin/tetramerfreq.sh
bin/translate6frames.sh
opt/bbmap-37.90/current/driver/ConcatenateTextFiles.class
opt/bbmap-37.90/current/jgi/CorrelateBarcodes.java
opt/bbmap-37.90/current/jgi/Dedupe2$MstThread.class
opt/bbmap-37.90/current/fileIO/PipeThread.class
opt/bbmap-37.90/current/tax/TaxTree.class
opt/bbmap-37.90/current/assemble/Postfilter.class
opt/bbmap-37.90/docs/readme.txt
opt/bbmap-37.90/current/driver/MergeBigelow.java
opt/bbmap-37.90/current/structures/IntHashMapBinary.java
opt/bbmap-37.90/current/dna/Motif.class
opt/bbmap-37.90/current/driver/GetUniquePrefixes.class
opt/bbmap-37.90/current/align2/BBMapThreadAcc.class
opt/bbmap-37.90/current/jgi/SplitSam6Way.java
opt/bbmap-37.90/bbnorm.sh
opt/bbmap-37.90/current/dna/GeneSet.class
opt/bbmap-37.90/sketch.sh
opt/bbmap-37.90/bbsketch.sh
opt/bbmap-37.90/rename.sh
opt/bbmap-37.90/current/driver/Translator2.class
bin/filterbycoverage.sh
opt/bbmap-37.90/current/pacbio/RemoveAdapters3$ProcessThread.class
opt/bbmap-37.90/current/stream/SamLineStreamer$ProcessThread.class
opt/bbmap-37.90/current/var2/CallVariants2$Sample.class
opt/bbmap-37.90/current/sort/ReadComparatorTaxa.java
opt/bbmap-37.90/current/align2/BBMapAcc.java
opt/bbmap-37.90/current/align2/BBMapThreadPacBioSkimmer.class
opt/bbmap-37.90/filterlines.sh
opt/bbmap-37.90/splitnextera.sh
opt/bbmap-37.90/current/structures/LongHashSet.class
bin/splitsam6way.sh
opt/bbmap-37.90/current/align2/CompressString.java
opt/bbmap-37.90/current/jgi/BBMerge.class
opt/bbmap-37.90/current/tax/TaxServer$TaxHandler.class
opt/bbmap-37.90/current/driver/ConcatenateFiles.java
opt/bbmap-37.90/current/jgi/Seal$LoadThread.class
opt/bbmap-37.90/current/pacbio/StackSites2.java
opt/bbmap-37.90/current/assemble/AbstractRemoveThread$RemoveThread1.class
opt/bbmap-37.90/current/hiseq/Tile.class
opt/bbmap-37.90/docs/guides/BBNormGuide.txt
opt/bbmap-37.90/current/ml/ProcessBBMergeHeaders$Header.class
opt/bbmap-37.90/current/pacbio/StackSites2$Glob.class
opt/bbmap-37.90/current/pacbio/CalcCoverageFromSites$1.class
opt/bbmap-37.90/current/clump/ReadKey.class
opt/bbmap-37.90/current/align2/MultiStateAligner9PacBioAdapter2.java
opt/bbmap-37.90/current/clump/PivotSet$HashThread.class
opt/bbmap-37.90/current/shared/PreParser.java
opt/bbmap-37.90/current/driver/MergeTextFiles2.java
opt/bbmap-37.90/current/jgi/MakePolymers.class
opt/bbmap-37.90/processspeed.sh
opt/bbmap-37.90/current/shared/ReadStats.class
opt/bbmap-37.90/current/jgi/FindPrimers.java
opt/bbmap-37.90/current/sketch/Whitelist.class
opt/bbmap-37.90/current/sort/ReadErrorComparator.java
opt/bbmap-37.90/splitsam4way.sh
opt/bbmap-37.90/current/shared/Primes.java
opt/bbmap-37.90/current/driver/MergeCoverageOTU.class
opt/bbmap-37.90/current/kmer/KmerNode2D.java
opt/bbmap-37.90/current/pacbio/RemoveAdapters2$ProcessThread.class
opt/bbmap-37.90/current/jgi/RedirectTest.class
opt/bbmap-37.90/docs/ToolDescriptions.txt
opt/bbmap-37.90/current/align2/KeyRing.class
opt/bbmap-37.90/current/jgi/BBTool_ST.java
opt/bbmap-37.90/fuse.sh
opt/bbmap-37.90/current/driver/MeasureGene.java
opt/bbmap-37.90/current/jgi/CovStatsLine.java
opt/bbmap-37.90/current/pacbio/MergeFastaContigs$1.class
opt/bbmap-37.90/current/structures/Range.java
opt/bbmap-37.90/current/align2/BBIndex5.java
opt/bbmap-37.90/current/stream/HeaderInputStream.java
opt/bbmap-37.90/current/sketch/SketchResults.class
bin/tadpole.sh
opt/bbmap-37.90/translate6frames.sh
opt/bbmap-37.90/current/jgi/DedupeByMapping.class
opt/bbmap-37.90/current/dna/FastaToChromArrays2.java
opt/bbmap-37.90/current/driver/FilterAssemblySummary.class
opt/bbmap-37.90/current/align2/TranslateColorspaceRead.java
opt/bbmap-37.90/pipelines/startTaxServer.sh
opt/bbmap-37.90/current/pacbio/SortSites$1.class
opt/bbmap-37.90/current/pacbio/SiteR.class
opt/bbmap-37.90/current/jgi/StringCount.java
opt/bbmap-37.90/current/jgi/SamToEst.java
opt/bbmap-37.90/current/fun/Genetic.class
opt/bbmap-37.90/current/bloom/KCountArray6MT.java
opt/bbmap-37.90/current/pacbio/PartitionFastaFile.java
opt/bbmap-37.90/current/fun/MakeAdjacencyList$1.class
opt/bbmap-37.90/current/jgi/AssemblyStats2.class
opt/bbmap-37.90/current/stream/ConcurrentReadOutputStreamD$ListenThread.class
opt/bbmap-37.90/demuxbyname.sh
