.gitignore
LICENSE
README.md
pyproject.toml
.github/workflows/python-publish.yml
bbmapy/__init__.py
bbmapy/_version.py
bbmapy/base.py
bbmapy/commands.py
bbmapy/ex.py
bbmapy/scanner.py
bbmapy.egg-info/PKG-INFO
bbmapy.egg-info/SOURCES.txt
bbmapy.egg-info/dependency_links.txt
bbmapy.egg-info/entry_points.txt
bbmapy.egg-info/requires.txt
bbmapy.egg-info/top_level.txt
vendor/bbtools.tar.gz
vendor/bbmap/.gitignore
vendor/bbmap/README.md
vendor/bbmap/a_sample_mt.sh
vendor/bbmap/addadapters.sh
vendor/bbmap/addssu.sh
vendor/bbmap/adjusthomopolymers.sh
vendor/bbmap/alltoall.sh
vendor/bbmap/analyzeaccession.sh
vendor/bbmap/analyzegenes.sh
vendor/bbmap/analyzesketchresults.sh
vendor/bbmap/applyvariants.sh
vendor/bbmap/bbcms.sh
vendor/bbmap/bbcountunique.sh
vendor/bbmap/bbcrisprfinder.sh
vendor/bbmap/bbduk.sh
vendor/bbmap/bbest.sh
vendor/bbmap/bbfakereads.sh
vendor/bbmap/bbmap.sh
vendor/bbmap/bbmapskimmer.sh
vendor/bbmap/bbmask.sh
vendor/bbmap/bbmerge-auto.sh
vendor/bbmap/bbmerge.sh
vendor/bbmap/bbnorm.sh
vendor/bbmap/bbrealign.sh
vendor/bbmap/bbrename.sh
vendor/bbmap/bbsketch.sh
vendor/bbmap/bbsort.sh
vendor/bbmap/bbsplit.sh
vendor/bbmap/bbsplitpairs.sh
vendor/bbmap/bbstats.sh
vendor/bbmap/bbversion.sh
vendor/bbmap/bbwrap.sh
vendor/bbmap/bitbucket-pipelines.yml
vendor/bbmap/bloomfilter.sh
vendor/bbmap/bloomfilterparser.sh
vendor/bbmap/calcmem.sh
vendor/bbmap/calctruequality.sh
vendor/bbmap/callgenes.sh
vendor/bbmap/callpeaks.sh
vendor/bbmap/callvariants.sh
vendor/bbmap/callvariants2.sh
vendor/bbmap/cg2illumina.sh
vendor/bbmap/checkstrand.sh
vendor/bbmap/clumpify.sh
vendor/bbmap/commonkmers.sh
vendor/bbmap/comparegff.sh
vendor/bbmap/comparelabels.sh
vendor/bbmap/comparesketch.sh
vendor/bbmap/comparessu.sh
vendor/bbmap/comparevcf.sh
vendor/bbmap/consect.sh
vendor/bbmap/consensus.sh
vendor/bbmap/copyfile.sh
vendor/bbmap/countbarcodes.sh
vendor/bbmap/countbarcodes2.sh
vendor/bbmap/countduplicates.sh
vendor/bbmap/countgc.sh
vendor/bbmap/countsharedlines.sh
vendor/bbmap/crossblock.sh
vendor/bbmap/crosscontaminate.sh
vendor/bbmap/cutgff.sh
vendor/bbmap/cutprimers.sh
vendor/bbmap/decontaminate.sh
vendor/bbmap/dedupe.sh
vendor/bbmap/dedupe2.sh
vendor/bbmap/dedupebymapping.sh
vendor/bbmap/demuxbyname.sh
vendor/bbmap/demuxserver.sh
vendor/bbmap/diskbench.sh
vendor/bbmap/estherfilter.sh
vendor/bbmap/explodetree.sh
vendor/bbmap/fetchproks.sh
vendor/bbmap/filterassemblysummary.sh
vendor/bbmap/filterbarcodes.sh
vendor/bbmap/filterbycoverage.sh
vendor/bbmap/filterbyname.sh
vendor/bbmap/filterbysequence.sh
vendor/bbmap/filterbytaxa.sh
vendor/bbmap/filterbytile.sh
vendor/bbmap/filterlines.sh
vendor/bbmap/filterqc.sh
vendor/bbmap/filtersam.sh
vendor/bbmap/filtersilva.sh
vendor/bbmap/filtersubs.sh
vendor/bbmap/filtervcf.sh
vendor/bbmap/findrepeats.sh
vendor/bbmap/fixgaps.sh
vendor/bbmap/fungalrelease.sh
vendor/bbmap/fuse.sh
vendor/bbmap/gbff2gff.sh
vendor/bbmap/getreads.sh
vendor/bbmap/gi2ancestors.sh
vendor/bbmap/gi2taxid.sh
vendor/bbmap/gitable.sh
vendor/bbmap/grademerge.sh
vendor/bbmap/gradesam.sh
vendor/bbmap/icecreamfinder.sh
vendor/bbmap/icecreamgrader.sh
vendor/bbmap/icecreammaker.sh
vendor/bbmap/idmatrix.sh
vendor/bbmap/idtree.sh
vendor/bbmap/invertkey.sh
vendor/bbmap/kapastats.sh
vendor/bbmap/kcompress.sh
vendor/bbmap/keepbestcopy.sh
vendor/bbmap/khist.sh
vendor/bbmap/kmercountexact.sh
vendor/bbmap/kmercountmulti.sh
vendor/bbmap/kmercoverage.sh
vendor/bbmap/kmerfilterset.sh
vendor/bbmap/kmerlimit.sh
vendor/bbmap/kmerlimit2.sh
vendor/bbmap/kmerposition.sh
vendor/bbmap/kmutate.sh
vendor/bbmap/license.txt
vendor/bbmap/lilypad.sh
vendor/bbmap/loadreads.sh
vendor/bbmap/loglog.sh
vendor/bbmap/makechimeras.sh
vendor/bbmap/makecontaminatedgenomes.sh
vendor/bbmap/makepolymers.sh
vendor/bbmap/mapPacBio.sh
vendor/bbmap/matrixtocolumns.sh
vendor/bbmap/mergeOTUs.sh
vendor/bbmap/mergebarcodes.sh
vendor/bbmap/mergepgm.sh
vendor/bbmap/mergeribo.sh
vendor/bbmap/mergesam.sh
vendor/bbmap/mergesketch.sh
vendor/bbmap/mergesorted.sh
vendor/bbmap/msa.sh
vendor/bbmap/mutate.sh
vendor/bbmap/muxbyname.sh
vendor/bbmap/netfilter.sh
vendor/bbmap/novademux.sh
vendor/bbmap/partition.sh
vendor/bbmap/phylip2fasta.sh
vendor/bbmap/pileup.sh
vendor/bbmap/pileup2.sh
vendor/bbmap/plotflowcell.sh
vendor/bbmap/plotgc.sh
vendor/bbmap/plotreadposition.sh
vendor/bbmap/postfilter.sh
vendor/bbmap/printtime.sh
vendor/bbmap/processfrag.sh
vendor/bbmap/processhi-c.sh
vendor/bbmap/processspeed.sh
vendor/bbmap/randomgenome.sh
vendor/bbmap/randomreads.sh
vendor/bbmap/readlength.sh
vendor/bbmap/readqc.sh
vendor/bbmap/reducesilva.sh
vendor/bbmap/reformat.sh
vendor/bbmap/reformatpb.sh
vendor/bbmap/removebadbarcodes.sh
vendor/bbmap/removecatdogmousehuman.sh
vendor/bbmap/removehuman.sh
vendor/bbmap/removehuman2.sh
vendor/bbmap/removemicrobes.sh
vendor/bbmap/removesmartbell.sh
vendor/bbmap/rename.sh
vendor/bbmap/renameimg.sh
vendor/bbmap/repair.sh
vendor/bbmap/replaceheaders.sh
vendor/bbmap/representative.sh
vendor/bbmap/rqcfilter.sh
vendor/bbmap/rqcfilter2.sh
vendor/bbmap/runhmm.sh
vendor/bbmap/samtoroc.sh
vendor/bbmap/scoresequence.sh
vendor/bbmap/seal.sh
vendor/bbmap/sendsketch.sh
vendor/bbmap/seqtovec.sh
vendor/bbmap/shred.sh
vendor/bbmap/shrinkaccession.sh
vendor/bbmap/shuffle.sh
vendor/bbmap/shuffle2.sh
vendor/bbmap/sketch.sh
vendor/bbmap/sketchblacklist.sh
vendor/bbmap/sketchblacklist2.sh
vendor/bbmap/sortbyname.sh
vendor/bbmap/splitbytaxa.sh
vendor/bbmap/splitnextera.sh
vendor/bbmap/splitribo.sh
vendor/bbmap/splitsam.sh
vendor/bbmap/splitsam4way.sh
vendor/bbmap/splitsam6way.sh
vendor/bbmap/stats.sh
vendor/bbmap/statswrapper.sh
vendor/bbmap/streamsam.sh
vendor/bbmap/subsketch.sh
vendor/bbmap/summarizecontam.sh
vendor/bbmap/summarizecoverage.sh
vendor/bbmap/summarizecrossblock.sh
vendor/bbmap/summarizemerge.sh
vendor/bbmap/summarizequast.sh
vendor/bbmap/summarizescafstats.sh
vendor/bbmap/summarizeseal.sh
vendor/bbmap/summarizesketch.sh
vendor/bbmap/synthmda.sh
vendor/bbmap/tadpipe.sh
vendor/bbmap/tadpole.sh
vendor/bbmap/tadwrapper.sh
vendor/bbmap/tagandmerge.sh
vendor/bbmap/taxonomy.sh
vendor/bbmap/taxserver.sh
vendor/bbmap/taxsize.sh
vendor/bbmap/taxtree.sh
vendor/bbmap/testfilesystem.sh
vendor/bbmap/testformat.sh
vendor/bbmap/testformat2.sh
vendor/bbmap/tetramerfreq.sh
vendor/bbmap/textfile.sh
vendor/bbmap/train.sh
vendor/bbmap/translate6frames.sh
vendor/bbmap/unicode2ascii.sh
vendor/bbmap/unzip.sh
vendor/bbmap/vcf2gff.sh
vendor/bbmap/webcheck.sh
vendor/bbmap/config/cluster16s.txt
vendor/bbmap/config/filter16s.txt
vendor/bbmap/config/histograms.txt
vendor/bbmap/config/recalibrate.txt
vendor/bbmap/config/rnaseq.txt
vendor/bbmap/config/trimadapters.txt
vendor/bbmap/current/align2/AbstractIndex.java
vendor/bbmap/current/align2/AbstractMapThread.java
vendor/bbmap/current/align2/AbstractMapper.java
vendor/bbmap/current/align2/BBIndex.java
vendor/bbmap/current/align2/BBIndex5.java
vendor/bbmap/current/align2/BBIndexAcc.java
vendor/bbmap/current/align2/BBIndexPacBio.java
vendor/bbmap/current/align2/BBIndexPacBioSkimmer.java
vendor/bbmap/current/align2/BBMap.java
vendor/bbmap/current/align2/BBMap5.java
vendor/bbmap/current/align2/BBMapAcc.java
vendor/bbmap/current/align2/BBMapPacBio.java
vendor/bbmap/current/align2/BBMapPacBioSkimmer.java
vendor/bbmap/current/align2/BBMapThread.java
vendor/bbmap/current/align2/BBMapThread5.java
vendor/bbmap/current/align2/BBMapThreadAcc.java
vendor/bbmap/current/align2/BBMapThreadPacBio.java
vendor/bbmap/current/align2/BBMapThreadPacBioSkimmer.java
vendor/bbmap/current/align2/BBSplitter.java
vendor/bbmap/current/align2/BBWrap.java
vendor/bbmap/current/align2/BandedAligner.java
vendor/bbmap/current/align2/BandedAlignerConcrete.java
vendor/bbmap/current/align2/BandedAlignerJNI.java
vendor/bbmap/current/align2/Blacklist.java
vendor/bbmap/current/align2/Block.java
vendor/bbmap/current/align2/ChromLoadThread.java
vendor/bbmap/current/align2/CompareSamFiles.java
vendor/bbmap/current/align2/CompressString.java
vendor/bbmap/current/align2/GapTools.java
vendor/bbmap/current/align2/GradeSamFile.java
vendor/bbmap/current/align2/Index.java
vendor/bbmap/current/align2/IndexMaker4.java
vendor/bbmap/current/align2/IndexMaker5.java
vendor/bbmap/current/align2/KeyRing.java
vendor/bbmap/current/align2/MSA.java
vendor/bbmap/current/align2/MakeQualityHistogram.java
vendor/bbmap/current/align2/MakeRocCurve.java
vendor/bbmap/current/align2/MultiStateAligner10ts.java
vendor/bbmap/current/align2/MultiStateAligner11ts.java
vendor/bbmap/current/align2/MultiStateAligner11tsJNI.java
vendor/bbmap/current/align2/MultiStateAligner9Flat.java
vendor/bbmap/current/align2/MultiStateAligner9PacBio.java
vendor/bbmap/current/align2/MultiStateAligner9XFlat.java
vendor/bbmap/current/align2/MultiStateAligner9ts.java
vendor/bbmap/current/align2/NeedlemanWunsch.java
vendor/bbmap/current/align2/PackedHeap.java
vendor/bbmap/current/align2/Pointer.java
vendor/bbmap/current/align2/PrintTime.java
vendor/bbmap/current/align2/Quad.java
vendor/bbmap/current/align2/Quad64.java
vendor/bbmap/current/align2/Quad64Heap.java
vendor/bbmap/current/align2/QuadHeap.java
vendor/bbmap/current/align2/QualityTools.java
vendor/bbmap/current/align2/RandomReads3.java
vendor/bbmap/current/align2/RefToIndex.java
vendor/bbmap/current/align2/ReformatBatchOutput.java
vendor/bbmap/current/align2/ReformatBatchOutput2.java
vendor/bbmap/current/align2/Solver.java
vendor/bbmap/current/align2/SplitMappedReads.java
vendor/bbmap/current/align2/TranslateColorspaceRead.java
vendor/bbmap/current/aligner/Aligner.java
vendor/bbmap/current/aligner/Alignment.java
vendor/bbmap/current/aligner/AlignmentResult.java
vendor/bbmap/current/aligner/AllToAll.java
vendor/bbmap/current/aligner/FlatAligner.java
vendor/bbmap/current/aligner/FlatAligner2.java
vendor/bbmap/current/aligner/MicroAligner.java
vendor/bbmap/current/aligner/MicroAligner2.java
vendor/bbmap/current/aligner/MultiStateAligner9PacBioAdapter.java
vendor/bbmap/current/aligner/MultiStateAligner9PacBioAdapter2.java
vendor/bbmap/current/aligner/MultiStateAligner9PacBioAdapter3.java
vendor/bbmap/current/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.java
vendor/bbmap/current/aligner/SingleStateAlignerFlat.java
vendor/bbmap/current/aligner/SingleStateAlignerFlat2.java
vendor/bbmap/current/aligner/SingleStateAlignerFlat2Amino.java
vendor/bbmap/current/aligner/SingleStateAlignerFlat2_1D.java
vendor/bbmap/current/aligner/SingleStateAlignerFlat3.java
vendor/bbmap/current/aligner/SingleStateAlignerFlatFloat.java
vendor/bbmap/current/aligner/SingleStateAlignerPacBioAdapter.java
vendor/bbmap/current/assemble/AbstractBuildThread.java
vendor/bbmap/current/assemble/AbstractExploreThread.java
vendor/bbmap/current/assemble/AbstractProcessContigThread.java
vendor/bbmap/current/assemble/AbstractRemoveThread.java
vendor/bbmap/current/assemble/AbstractShaveThread.java
vendor/bbmap/current/assemble/BubblePopper.java
vendor/bbmap/current/assemble/Contig.java
vendor/bbmap/current/assemble/Edge.java
vendor/bbmap/current/assemble/ErrorTracker.java
vendor/bbmap/current/assemble/KmerCompressor.java
vendor/bbmap/current/assemble/Postfilter.java
vendor/bbmap/current/assemble/Rollback.java
vendor/bbmap/current/assemble/ShaveObject.java
vendor/bbmap/current/assemble/Shaver.java
vendor/bbmap/current/assemble/Shaver1.java
vendor/bbmap/current/assemble/Shaver2.java
vendor/bbmap/current/assemble/TadPipe.java
vendor/bbmap/current/assemble/Tadpole.java
vendor/bbmap/current/assemble/Tadpole1.java
vendor/bbmap/current/assemble/Tadpole2.java
vendor/bbmap/current/assemble/TadpoleWrapper.java
vendor/bbmap/current/barcode/AnalyzeBarcodes.java
vendor/bbmap/current/barcode/Barcode.java
vendor/bbmap/current/barcode/BarcodeCounter.java
vendor/bbmap/current/barcode/BarcodeMappingStats.java
vendor/bbmap/current/barcode/BarcodeStats.java
vendor/bbmap/current/barcode/CompareLabels.java
vendor/bbmap/current/barcode/CorrelateBarcodes.java
vendor/bbmap/current/barcode/CountBarcodes.java
vendor/bbmap/current/barcode/CountBarcodes2.java
vendor/bbmap/current/barcode/DemuxClient.java
vendor/bbmap/current/barcode/DemuxData.java
vendor/bbmap/current/barcode/DemuxServer.java
vendor/bbmap/current/barcode/LegacyFileWriter.java
vendor/bbmap/current/barcode/NovaDemux.java
vendor/bbmap/current/barcode/PCRMatrix.java
vendor/bbmap/current/barcode/PCRMatrixHDist.java
vendor/bbmap/current/barcode/PCRMatrixHDist_old.java
vendor/bbmap/current/barcode/TagAndMerge.java
vendor/bbmap/current/barcode/Transition.java
vendor/bbmap/current/barcode/prob/PCRMatrixProb.java
vendor/bbmap/current/barcode/prob/PCRMatrixProbAbstract.java
vendor/bbmap/current/barcode/prob/PCRMatrixTile.java
vendor/bbmap/current/bbmin/LongHashSet.java
vendor/bbmap/current/bbmin/LongList.java
vendor/bbmap/current/bbmin/Minimizer.java
vendor/bbmap/current/bloom/BloomFilter.java
vendor/bbmap/current/bloom/BloomFilterCorrector.java
vendor/bbmap/current/bloom/BloomFilterCorrectorWrapper.java
vendor/bbmap/current/bloom/BloomFilterWrapper.java
vendor/bbmap/current/bloom/ErrorCorrect.java
vendor/bbmap/current/bloom/IndexCounter.java
vendor/bbmap/current/bloom/KCountArray.java
vendor/bbmap/current/bloom/KCountArray2.java
vendor/bbmap/current/bloom/KCountArray3.java
vendor/bbmap/current/bloom/KCountArray4.java
vendor/bbmap/current/bloom/KCountArray4MT.java
vendor/bbmap/current/bloom/KCountArray5MT.java
vendor/bbmap/current/bloom/KCountArray6MT.java
vendor/bbmap/current/bloom/KCountArray7MT.java
vendor/bbmap/current/bloom/KCountArray7MTA.java
vendor/bbmap/current/bloom/KCountArray8MT.java
vendor/bbmap/current/bloom/KmerCount3.java
vendor/bbmap/current/bloom/KmerCount4.java
vendor/bbmap/current/bloom/KmerCount5.java
vendor/bbmap/current/bloom/KmerCount6.java
vendor/bbmap/current/bloom/KmerCountAbstract.java
vendor/bbmap/current/bloom/LargeKmerCount.java
vendor/bbmap/current/bloom/LargeKmerCount2.java
vendor/bbmap/current/bloom/ParseBloomFilter.java
vendor/bbmap/current/bloom/ReadCounter.java
vendor/bbmap/current/bloom/ReadCounter_old.java
vendor/bbmap/current/bloom/TestLargeKmer.java
vendor/bbmap/current/cardinality/BBLog.java
vendor/bbmap/current/cardinality/BBLog_simple.java
vendor/bbmap/current/cardinality/CardinalityTracker.java
vendor/bbmap/current/cardinality/LogLog.java
vendor/bbmap/current/cardinality/LogLog16.java
vendor/bbmap/current/cardinality/LogLog2.java
vendor/bbmap/current/cardinality/LogLog8.java
vendor/bbmap/current/cardinality/LogLog8_simple.java
vendor/bbmap/current/cardinality/LogLogWrapper.java
vendor/bbmap/current/cardinality/LogLog_old.java
vendor/bbmap/current/cardinality/MultiLogLog.java
vendor/bbmap/current/clump/Clump.java
vendor/bbmap/current/clump/ClumpList.java
vendor/bbmap/current/clump/ClumpTools.java
vendor/bbmap/current/clump/Clumpify.java
vendor/bbmap/current/clump/Hasher.java
vendor/bbmap/current/clump/KmerComparator.java
vendor/bbmap/current/clump/KmerComparator2.java
vendor/bbmap/current/clump/KmerComparatorX.java
vendor/bbmap/current/clump/KmerComparatorY.java
vendor/bbmap/current/clump/KmerReduce.java
vendor/bbmap/current/clump/KmerSort.java
vendor/bbmap/current/clump/KmerSort1.java
vendor/bbmap/current/clump/KmerSort2.java
vendor/bbmap/current/clump/KmerSort3.java
vendor/bbmap/current/clump/KmerSplit.java
vendor/bbmap/current/clump/PivotSet.java
vendor/bbmap/current/clump/ReadKey.java
vendor/bbmap/current/clump/Splitter.java
vendor/bbmap/current/clump/StreamToOutput.java
vendor/bbmap/current/cluster/Cluster.java
vendor/bbmap/current/cluster/ClusterTools.java
vendor/bbmap/current/cluster/MergeReadHeaders.java
vendor/bbmap/current/cluster/ReadTag.java
vendor/bbmap/current/cluster/ReclusterByKmer.java
vendor/bbmap/current/consensus/BaseGraph.java
vendor/bbmap/current/consensus/BaseGraphPart.java
vendor/bbmap/current/consensus/BaseNode.java
vendor/bbmap/current/consensus/ConsensusMaker.java
vendor/bbmap/current/consensus/ConsensusObject.java
vendor/bbmap/current/consensus/FixScaffoldGaps.java
vendor/bbmap/current/consensus/Lilypad.java
vendor/bbmap/current/covid/SummarizeCoverage.java
vendor/bbmap/current/dna/AminoAcid.java
vendor/bbmap/current/dna/ChromArrayMaker.java
vendor/bbmap/current/dna/ChromToFasta.java
vendor/bbmap/current/dna/ChromosomeArray.java
vendor/bbmap/current/dna/Data.java
vendor/bbmap/current/dna/Exon.java
vendor/bbmap/current/dna/FastaToChromArrays2.java
vendor/bbmap/current/dna/Gene.java
vendor/bbmap/current/dna/GeneSet.java
vendor/bbmap/current/dna/Matrix.java
vendor/bbmap/current/dna/Motif.java
vendor/bbmap/current/dna/MotifMulti.java
vendor/bbmap/current/dna/MotifProbsN.java
vendor/bbmap/current/dna/MotifSimple.java
vendor/bbmap/current/dna/ScafLoc.java
vendor/bbmap/current/dna/Scaffold.java
vendor/bbmap/current/driver/BBVersion.java
vendor/bbmap/current/driver/ClearRam.java
vendor/bbmap/current/driver/CollateSpikeIn.java
vendor/bbmap/current/driver/CompareReferenceGenomes.java
vendor/bbmap/current/driver/CompareSequences.java
vendor/bbmap/current/driver/ConcatenateFiles.java
vendor/bbmap/current/driver/ConcatenateTextFiles.java
vendor/bbmap/current/driver/Concatenator.java
vendor/bbmap/current/driver/ConvertSamToAln.java
vendor/bbmap/current/driver/CorrelateIdentity.java
vendor/bbmap/current/driver/CountRNAs.java
vendor/bbmap/current/driver/CountSharedLines.java
vendor/bbmap/current/driver/EstherFilter.java
vendor/bbmap/current/driver/FilterAssemblySummary.java
vendor/bbmap/current/driver/FilterLines.java
vendor/bbmap/current/driver/FilterReadsByName.java
vendor/bbmap/current/driver/FindMotifs.java
vendor/bbmap/current/driver/FixChr.java
vendor/bbmap/current/driver/FixDumbFile.java
vendor/bbmap/current/driver/GenerateNoCallsFromCoverage.java
vendor/bbmap/current/driver/GetSequence.java
vendor/bbmap/current/driver/GetUniquePrefixes.java
vendor/bbmap/current/driver/Grep.java
vendor/bbmap/current/driver/Life.java
vendor/bbmap/current/driver/LineCount.java
vendor/bbmap/current/driver/LoadReads.java
vendor/bbmap/current/driver/LookAtID.java
vendor/bbmap/current/driver/MakeTestScript.java
vendor/bbmap/current/driver/MakeTestScriptScoreOnly.java
vendor/bbmap/current/driver/MeasureGene.java
vendor/bbmap/current/driver/MergeBigelow.java
vendor/bbmap/current/driver/MergeCoverageOTU.java
vendor/bbmap/current/driver/MergeTextFiles.java
vendor/bbmap/current/driver/MergeTextFiles2.java
vendor/bbmap/current/driver/MoveFiles.java
vendor/bbmap/current/driver/ParseCrossblockResults.java
vendor/bbmap/current/driver/PlotGC.java
vendor/bbmap/current/driver/PrintEnv.java
vendor/bbmap/current/driver/ProcessFragMerging.java
vendor/bbmap/current/driver/ProcessSpeed.java
vendor/bbmap/current/driver/ProcessSpeed2.java
vendor/bbmap/current/driver/ProcessWebcheck.java
vendor/bbmap/current/driver/ReduceSilva.java
vendor/bbmap/current/driver/RenameAndMux.java
vendor/bbmap/current/driver/RenameByHeader.java
vendor/bbmap/current/driver/RenameNcbiToTid.java
vendor/bbmap/current/driver/RenameRefseqFiles.java
vendor/bbmap/current/driver/Sample.java
vendor/bbmap/current/driver/Search.java
vendor/bbmap/current/driver/SelectReads.java
vendor/bbmap/current/driver/SniffSplices.java
vendor/bbmap/current/driver/SummarizeContamReport.java
vendor/bbmap/current/driver/SummarizeCoverage.java
vendor/bbmap/current/driver/SummarizeCrossblock.java
vendor/bbmap/current/driver/SummarizeMSDIN.java
vendor/bbmap/current/driver/SummarizeQuast.java
vendor/bbmap/current/driver/SummarizeSealCrosstalk.java
vendor/bbmap/current/driver/SummarizeSealStats.java
vendor/bbmap/current/driver/TestCompressionSpeed.java
vendor/bbmap/current/driver/TestLockSpeed.java
vendor/bbmap/current/driver/Translator.java
vendor/bbmap/current/driver/Translator2.java
vendor/bbmap/current/driver/TransposeTextFile.java
vendor/bbmap/current/driver/TrimSamFile.java
vendor/bbmap/current/fileIO/ArrayFile.java
vendor/bbmap/current/fileIO/ByteFile.java
vendor/bbmap/current/fileIO/ByteFile1.java
vendor/bbmap/current/fileIO/ByteFile2.java
vendor/bbmap/current/fileIO/ByteStreamWriter.java
vendor/bbmap/current/fileIO/ChainBlock.java
vendor/bbmap/current/fileIO/ChainLine.java
vendor/bbmap/current/fileIO/CompressFiles.java
vendor/bbmap/current/fileIO/CopyFile.java
vendor/bbmap/current/fileIO/CopyFiles.java
vendor/bbmap/current/fileIO/CopyFiles2.java
vendor/bbmap/current/fileIO/FileFormat.java
vendor/bbmap/current/fileIO/FindFiles.java
vendor/bbmap/current/fileIO/GenericTextFile.java
vendor/bbmap/current/fileIO/LoadThread.java
vendor/bbmap/current/fileIO/MatrixFile.java
vendor/bbmap/current/fileIO/OpenFile.java
vendor/bbmap/current/fileIO/PipeThread.java
vendor/bbmap/current/fileIO/QuickFile.java
vendor/bbmap/current/fileIO/ReadWrite.java
vendor/bbmap/current/fileIO/SummaryFile.java
vendor/bbmap/current/fileIO/TextFile.java
vendor/bbmap/current/fileIO/TextStreamWriter.java
vendor/bbmap/current/fun/Calc.java
vendor/bbmap/current/fun/Chance.java
vendor/bbmap/current/fun/Crunch.java
vendor/bbmap/current/fun/DiskBench.java
vendor/bbmap/current/fun/Dongle.java
vendor/bbmap/current/fun/FindPath.java
vendor/bbmap/current/fun/Foo.java
vendor/bbmap/current/fun/Foo2.java
vendor/bbmap/current/fun/Foo3.java
vendor/bbmap/current/fun/Foo4.java
vendor/bbmap/current/fun/Foo5.java
vendor/bbmap/current/fun/Foo6.java
vendor/bbmap/current/fun/Foo7.java
vendor/bbmap/current/fun/Genetic.java
vendor/bbmap/current/fun/Life.java
vendor/bbmap/current/fun/MakeAdjacencyList.java
vendor/bbmap/current/fun/Merced.java
vendor/bbmap/current/fun/PalSim.java
vendor/bbmap/current/fun/Palindrome.java
vendor/bbmap/current/fun/Palindrome2.java
vendor/bbmap/current/fun/ProbShared.java
vendor/bbmap/current/fun/ProbShared2.java
vendor/bbmap/current/fun/ProbShared3.java
vendor/bbmap/current/gff/CompareGff.java
vendor/bbmap/current/gff/CompareGff_old.java
vendor/bbmap/current/gff/CutGff.java
vendor/bbmap/current/gff/CutGff_ST.java
vendor/bbmap/current/gff/GbffFeature.java
vendor/bbmap/current/gff/GbffFile.java
vendor/bbmap/current/gff/GbffLocus.java
vendor/bbmap/current/gff/GffLine.java
vendor/bbmap/current/gff/ParseCrispr.java
vendor/bbmap/current/gff/VcfToGff.java
vendor/bbmap/current/hiseq/AnalyzeFlowCell.java
vendor/bbmap/current/hiseq/BGI2Illumina.java
vendor/bbmap/current/hiseq/BGIHeaderParser.java
vendor/bbmap/current/hiseq/BGIHeaderParser2.java
vendor/bbmap/current/hiseq/CycleTracker.java
vendor/bbmap/current/hiseq/FlowCell.java
vendor/bbmap/current/hiseq/FlowcellCoordinate.java
vendor/bbmap/current/hiseq/IlluminaHeaderParser1.java
vendor/bbmap/current/hiseq/IlluminaHeaderParser2.java
vendor/bbmap/current/hiseq/Lane.java
vendor/bbmap/current/hiseq/MicroTile.java
vendor/bbmap/current/hiseq/PlotFlowCell.java
vendor/bbmap/current/hiseq/PlotReadPosition.java
vendor/bbmap/current/hiseq/ReadHeaderParser.java
vendor/bbmap/current/hiseq/Tile.java
vendor/bbmap/current/hmm/HMMSearchLine.java
vendor/bbmap/current/hmm/HMMSearchReport.java
vendor/bbmap/current/hmm/ProteinSummary.java
vendor/bbmap/current/icecream/IceCreamAligner.java
vendor/bbmap/current/icecream/IceCreamAlignerJNI.java
vendor/bbmap/current/icecream/IceCreamAlignerJava.java
vendor/bbmap/current/icecream/IceCreamFinder.java
vendor/bbmap/current/icecream/IceCreamGrader.java
vendor/bbmap/current/icecream/IceCreamMaker.java
vendor/bbmap/current/icecream/PBHeader.java
vendor/bbmap/current/icecream/PolymerTrimmer.java
vendor/bbmap/current/icecream/ReadBuilder.java
vendor/bbmap/current/icecream/ReformatPacBio.java
vendor/bbmap/current/icecream/ZMW.java
vendor/bbmap/current/icecream/ZMWStreamer.java
vendor/bbmap/current/jasper/Comparison.java
vendor/bbmap/current/jasper/DenseSimilarityMatrix.java
vendor/bbmap/current/jasper/DenseTree.java
vendor/bbmap/current/jasper/DenseTreeValidate.java
vendor/bbmap/current/jasper/KmerPosition.java
vendor/bbmap/current/jasper/KmerPosition3.java
vendor/bbmap/current/jasper/NCBIComparison.java
vendor/bbmap/current/jasper/NCBISparseSimilarityMatrix.java
vendor/bbmap/current/jasper/NCBISparseTree.java
vendor/bbmap/current/jasper/NCBISparseTreeValidate.java
vendor/bbmap/current/jasper/NCBITreeNode.java
vendor/bbmap/current/jasper/Organism.java
vendor/bbmap/current/jasper/SimilarityMatrix.java
vendor/bbmap/current/jasper/SparseSimilarityMatrix.java
vendor/bbmap/current/jasper/SparseTree.java
vendor/bbmap/current/jasper/SparseTreeValidate.java
vendor/bbmap/current/jasper/TaxCompare.java
vendor/bbmap/current/jasper/TreeNode.java
vendor/bbmap/current/jgi/AddAdapters.java
vendor/bbmap/current/jgi/AdjustHomopolymers.java
vendor/bbmap/current/jgi/AssemblyStats2.java
vendor/bbmap/current/jgi/AssemblyStatsWrapper.java
vendor/bbmap/current/jgi/BBDuk.java
vendor/bbmap/current/jgi/BBDuk2.java
vendor/bbmap/current/jgi/BBMask.java
vendor/bbmap/current/jgi/BBMerge.java
vendor/bbmap/current/jgi/BBMergeOverlapper.java
vendor/bbmap/current/jgi/BBQC.java
vendor/bbmap/current/jgi/CalcTrueQuality.java
vendor/bbmap/current/jgi/CalcUniqueness.java
vendor/bbmap/current/jgi/CallPeaks.java
vendor/bbmap/current/jgi/CheckStrand.java
vendor/bbmap/current/jgi/CheckStrand2.java
vendor/bbmap/current/jgi/Consect.java
vendor/bbmap/current/jgi/CountDuplicates.java
vendor/bbmap/current/jgi/CountDuplicatesBuffered.java
vendor/bbmap/current/jgi/CountGC.java
vendor/bbmap/current/jgi/CountUniqueness.java
vendor/bbmap/current/jgi/CovStatsLine.java
vendor/bbmap/current/jgi/CoveragePileup.java
vendor/bbmap/current/jgi/CoveragePileupMT.java
vendor/bbmap/current/jgi/CrisprFinder.java
vendor/bbmap/current/jgi/CrossContaminate.java
vendor/bbmap/current/jgi/CutPrimers.java
vendor/bbmap/current/jgi/DecontaminateByNormalization.java
vendor/bbmap/current/jgi/Dedupe.java
vendor/bbmap/current/jgi/Dedupe2.java
vendor/bbmap/current/jgi/DedupeByMapping.java
vendor/bbmap/current/jgi/DedupeProtein.java
vendor/bbmap/current/jgi/DemuxByName.java
vendor/bbmap/current/jgi/DemuxByName2.java
vendor/bbmap/current/jgi/Difference.java
vendor/bbmap/current/jgi/FakeReads.java
vendor/bbmap/current/jgi/FilterByCoverage.java
vendor/bbmap/current/jgi/FilterBySequence.java
vendor/bbmap/current/jgi/FilterReadsWithSubs.java
vendor/bbmap/current/jgi/FindHiCJunctions.java
vendor/bbmap/current/jgi/FindPrimers.java
vendor/bbmap/current/jgi/FindPrimers_old.java
vendor/bbmap/current/jgi/FindString.java
vendor/bbmap/current/jgi/FungalRelease.java
vendor/bbmap/current/jgi/FuseSequence.java
vendor/bbmap/current/jgi/GatherKapaStats.java
vendor/bbmap/current/jgi/GetReads.java
vendor/bbmap/current/jgi/GradeMergedReads.java
vendor/bbmap/current/jgi/GreedyBarCodeFinder.java
vendor/bbmap/current/jgi/IdentityMatrix.java
vendor/bbmap/current/jgi/Info.java
vendor/bbmap/current/jgi/KExpand.java
vendor/bbmap/current/jgi/KeepBestCopy.java
vendor/bbmap/current/jgi/KmerCountExact.java
vendor/bbmap/current/jgi/KmerCountMulti.java
vendor/bbmap/current/jgi/KmerCoverage.java
vendor/bbmap/current/jgi/KmerFilterSetMaker.java
vendor/bbmap/current/jgi/KmerNormalize.java
vendor/bbmap/current/jgi/KmerSample.java
vendor/bbmap/current/jgi/MakeChimeras.java
vendor/bbmap/current/jgi/MakeContaminatedGenomes.java
vendor/bbmap/current/jgi/MakeLengthHistogram.java
vendor/bbmap/current/jgi/MakePolymers.java
vendor/bbmap/current/jgi/MergeBarcodes.java
vendor/bbmap/current/jgi/MergeSam.java
vendor/bbmap/current/jgi/MutateGenome.java
vendor/bbmap/current/jgi/MutateGenome2.java
vendor/bbmap/current/jgi/Orf.java
vendor/bbmap/current/jgi/PartitionReads.java
vendor/bbmap/current/jgi/PhylipToFasta.java
vendor/bbmap/current/jgi/RQCFilter2.java
vendor/bbmap/current/jgi/RQCFilterStats.java
vendor/bbmap/current/jgi/RandomGenome.java
vendor/bbmap/current/jgi/ReadKmerDepthDistribution.java
vendor/bbmap/current/jgi/RedirectTest.java
vendor/bbmap/current/jgi/ReformatReads.java
vendor/bbmap/current/jgi/RemapQuality.java
vendor/bbmap/current/jgi/RemoveBadBarcodes.java
vendor/bbmap/current/jgi/RenameReads.java
vendor/bbmap/current/jgi/ReplaceHeaders.java
vendor/bbmap/current/jgi/RepresentativeSet.java
vendor/bbmap/current/jgi/SamToEst.java
vendor/bbmap/current/jgi/Seal.java
vendor/bbmap/current/jgi/SealRefInfo.java
vendor/bbmap/current/jgi/Shred.java
vendor/bbmap/current/jgi/SmallKmerFrequency.java
vendor/bbmap/current/jgi/SplitNexteraLMP.java
vendor/bbmap/current/jgi/SplitPairsAndSingles.java
vendor/bbmap/current/jgi/SplitSam4Way.java
vendor/bbmap/current/jgi/SplitSam6Way.java
vendor/bbmap/current/jgi/SplitSamFile.java
vendor/bbmap/current/jgi/StringCount.java
vendor/bbmap/current/jgi/SynthMDA.java
vendor/bbmap/current/jgi/TestFilesystem.java
vendor/bbmap/current/jgi/TestFormat.java
vendor/bbmap/current/jgi/TetramerFrequencies.java
vendor/bbmap/current/jgi/TranslateSixFrames.java
vendor/bbmap/current/jgi/UnicodeToAscii.java
vendor/bbmap/current/jgi/Unzip.java
vendor/bbmap/current/json/JsonLiteral.java
vendor/bbmap/current/json/JsonObject.java
vendor/bbmap/current/json/JsonParser.java
vendor/bbmap/current/kmer/AbstractKmerTable.java
vendor/bbmap/current/kmer/AbstractKmerTableSet.java
vendor/bbmap/current/kmer/DumpThread.java
vendor/bbmap/current/kmer/HashArray.java
vendor/bbmap/current/kmer/HashArray1D.java
vendor/bbmap/current/kmer/HashArray2D.java
vendor/bbmap/current/kmer/HashArrayHybrid.java
vendor/bbmap/current/kmer/HashArrayHybridFast.java
vendor/bbmap/current/kmer/HashBuffer.java
vendor/bbmap/current/kmer/HashForest.java
vendor/bbmap/current/kmer/HistogramMaker.java
vendor/bbmap/current/kmer/KmerBuffer.java
vendor/bbmap/current/kmer/KmerLink.java
vendor/bbmap/current/kmer/KmerNode.java
vendor/bbmap/current/kmer/KmerNode1D.java
vendor/bbmap/current/kmer/KmerNode2D.java
vendor/bbmap/current/kmer/KmerTable.java
vendor/bbmap/current/kmer/KmerTableSet.java
vendor/bbmap/current/kmer/OwnershipThread.java
vendor/bbmap/current/kmer/ScheduleMaker.java
vendor/bbmap/current/kmer/SimpleKmerTable.java
vendor/bbmap/current/kmer/TableLoaderLockFree.java
vendor/bbmap/current/kmer/TableReader.java
vendor/bbmap/current/kmer/Walker.java
vendor/bbmap/current/ml/Bell.java
vendor/bbmap/current/ml/Cell.java
vendor/bbmap/current/ml/CellNet.java
vendor/bbmap/current/ml/CellNetParser.java
vendor/bbmap/current/ml/CellNetReverseComparator.java
vendor/bbmap/current/ml/DataLoader.java
vendor/bbmap/current/ml/ExtendedMSig.java
vendor/bbmap/current/ml/ExtendedSigmoid.java
vendor/bbmap/current/ml/Function.java
vendor/bbmap/current/ml/Functions.java
vendor/bbmap/current/ml/JobData.java
vendor/bbmap/current/ml/JobResults.java
vendor/bbmap/current/ml/MSig.java
vendor/bbmap/current/ml/Matrix.java
vendor/bbmap/current/ml/NetFilter.java
vendor/bbmap/current/ml/ProcessBBMergeHeaders.java
vendor/bbmap/current/ml/Profiler.java
vendor/bbmap/current/ml/RSLog.java
vendor/bbmap/current/ml/Sample.java
vendor/bbmap/current/ml/SampleErrorComparator.java
vendor/bbmap/current/ml/SampleSet.java
vendor/bbmap/current/ml/SampleValueComparator.java
vendor/bbmap/current/ml/ScannerThread.java
vendor/bbmap/current/ml/ScoreSequence.java
vendor/bbmap/current/ml/Seed.java
vendor/bbmap/current/ml/SequenceToVector.java
vendor/bbmap/current/ml/Sigmoid.java
vendor/bbmap/current/ml/Source.java
vendor/bbmap/current/ml/Status.java
vendor/bbmap/current/ml/Subset.java
vendor/bbmap/current/ml/Swish.java
vendor/bbmap/current/ml/Tanh.java
vendor/bbmap/current/ml/Trainer.java
vendor/bbmap/current/ml/TrainerThread.java
vendor/bbmap/current/ml/WorkerThread.java
vendor/bbmap/current/pacbio/CalcCoverageFromSites.java
vendor/bbmap/current/pacbio/GenerateMultiChrom.java
vendor/bbmap/current/pacbio/MakePacBioScript.java
vendor/bbmap/current/pacbio/MergeFastaContigs.java
vendor/bbmap/current/pacbio/MergeReadsAndGenome.java
vendor/bbmap/current/pacbio/PartitionFastaFile.java
vendor/bbmap/current/pacbio/PartitionReads.java
vendor/bbmap/current/pacbio/ProcessStackedSitesNormalized.java
vendor/bbmap/current/pacbio/RemoveAdapters2.java
vendor/bbmap/current/pacbio/RemoveAdapters3.java
vendor/bbmap/current/pacbio/SiteR.java
vendor/bbmap/current/pacbio/SortSites.java
vendor/bbmap/current/pacbio/SplitOffPerfectContigs.java
vendor/bbmap/current/pacbio/StackSites.java
vendor/bbmap/current/pacbio/StackSites2.java
vendor/bbmap/current/prok/AnalyzeGenes.java
vendor/bbmap/current/prok/CallGenes.java
vendor/bbmap/current/prok/FetchProks.java
vendor/bbmap/current/prok/FilterSilva.java
vendor/bbmap/current/prok/FrameStats.java
vendor/bbmap/current/prok/GeneCaller.java
vendor/bbmap/current/prok/GeneModel.java
vendor/bbmap/current/prok/GeneModelParser.java
vendor/bbmap/current/prok/MergeRibo.java
vendor/bbmap/current/prok/MergeRibo_Fast.java
vendor/bbmap/current/prok/Orf.java
vendor/bbmap/current/prok/PFeature.java
vendor/bbmap/current/prok/PGMTools.java
vendor/bbmap/current/prok/ProkObject.java
vendor/bbmap/current/prok/RiboMaker.java
vendor/bbmap/current/prok/ScafData.java
vendor/bbmap/current/prok/ScoreTracker.java
vendor/bbmap/current/prok/SplitRibo.java
vendor/bbmap/current/prok/StatsContainer.java
vendor/bbmap/current/repeat/Palindrome.java
vendor/bbmap/current/repeat/PalindromeFinder.java
vendor/bbmap/current/repeat/Repeat.java
vendor/bbmap/current/repeat/RepeatFinder.java
vendor/bbmap/current/repeat/RepeatSet.java
vendor/bbmap/current/server/PercentEncoding.java
vendor/bbmap/current/server/ServerTools.java
vendor/bbmap/current/server/SimpleHttpServer.java
vendor/bbmap/current/shared/Colors.java
vendor/bbmap/current/shared/KillSwitch.java
vendor/bbmap/current/shared/LineParser.java
vendor/bbmap/current/shared/LineParser1.java
vendor/bbmap/current/shared/LineParser2.java
vendor/bbmap/current/shared/LineParserS.java
vendor/bbmap/current/shared/LineParserS1.java
vendor/bbmap/current/shared/LineParserS2.java
vendor/bbmap/current/shared/LineParserS3.java
vendor/bbmap/current/shared/LineParserS4.java
vendor/bbmap/current/shared/LineParserS4Reverse.java
vendor/bbmap/current/shared/LineParserSimple.java
vendor/bbmap/current/shared/MetadataWriter.java
vendor/bbmap/current/shared/Parse.java
vendor/bbmap/current/shared/Parser.java
vendor/bbmap/current/shared/PreParser.java
vendor/bbmap/current/shared/Primes.java
vendor/bbmap/current/shared/SIMD.java
vendor/bbmap/current/shared/Shared.java
vendor/bbmap/current/shared/Timer.java
vendor/bbmap/current/shared/Tools.java
vendor/bbmap/current/shared/TrimRead.java
vendor/bbmap/current/shared/Vector.java
vendor/bbmap/current/sketch/AddSSU.java
vendor/bbmap/current/sketch/AlignmentJob.java
vendor/bbmap/current/sketch/AlignmentThreadPool.java
vendor/bbmap/current/sketch/AnalyzeSketchResults.java
vendor/bbmap/current/sketch/Blacklist.java
vendor/bbmap/current/sketch/BlacklistMaker.java
vendor/bbmap/current/sketch/BlacklistMaker2.java
vendor/bbmap/current/sketch/CompareBuffer.java
vendor/bbmap/current/sketch/CompareSSU.java
vendor/bbmap/current/sketch/CompareSketch.java
vendor/bbmap/current/sketch/Comparison.java
vendor/bbmap/current/sketch/DisplayParams.java
vendor/bbmap/current/sketch/GlocalAligner.java
vendor/bbmap/current/sketch/InvertKey.java
vendor/bbmap/current/sketch/KmerLimit.java
vendor/bbmap/current/sketch/KmerLimit2.java
vendor/bbmap/current/sketch/MergeSketch.java
vendor/bbmap/current/sketch/Record.java
vendor/bbmap/current/sketch/RecordSet.java
vendor/bbmap/current/sketch/ResultLineParser.java
vendor/bbmap/current/sketch/SSUMap.java
vendor/bbmap/current/sketch/SendSketch.java
vendor/bbmap/current/sketch/Sketch.java
vendor/bbmap/current/sketch/SketchHeap.java
vendor/bbmap/current/sketch/SketchIdComparator.java
vendor/bbmap/current/sketch/SketchIndex.java
vendor/bbmap/current/sketch/SketchMaker.java
vendor/bbmap/current/sketch/SketchMakerMini.java
vendor/bbmap/current/sketch/SketchObject.java
vendor/bbmap/current/sketch/SketchResults.java
vendor/bbmap/current/sketch/SketchSearcher.java
vendor/bbmap/current/sketch/SketchTool.java
vendor/bbmap/current/sketch/SubSketch.java
vendor/bbmap/current/sketch/SummarizeSketchStats.java
vendor/bbmap/current/sketch/Whitelist.java
vendor/bbmap/current/sort/ContigLengthComparator.java
vendor/bbmap/current/sort/MergeSorted.java
vendor/bbmap/current/sort/ReadComparator.java
vendor/bbmap/current/sort/ReadComparatorClump.java
vendor/bbmap/current/sort/ReadComparatorCrispr.java
vendor/bbmap/current/sort/ReadComparatorFlowcell.java
vendor/bbmap/current/sort/ReadComparatorID.java
vendor/bbmap/current/sort/ReadComparatorList.java
vendor/bbmap/current/sort/ReadComparatorMapping.java
vendor/bbmap/current/sort/ReadComparatorName.java
vendor/bbmap/current/sort/ReadComparatorPosition.java
vendor/bbmap/current/sort/ReadComparatorRandom.java
vendor/bbmap/current/sort/ReadComparatorTaxa.java
vendor/bbmap/current/sort/ReadComparatorTopological.java
vendor/bbmap/current/sort/ReadComparatorTopological5Bit.java
vendor/bbmap/current/sort/ReadErrorComparator.java
vendor/bbmap/current/sort/ReadLengthComparator.java
vendor/bbmap/current/sort/ReadQualityComparator.java
vendor/bbmap/current/sort/Shuffle.java
vendor/bbmap/current/sort/Shuffle2.java
vendor/bbmap/current/sort/SortByName.java
vendor/bbmap/current/sort/SortReadsByID.java
vendor/bbmap/current/stream/ArrayListSet.java
vendor/bbmap/current/stream/BufferedMultiCros.java
vendor/bbmap/current/stream/ConcurrentCollectionReadInputStream.java
vendor/bbmap/current/stream/ConcurrentDepot.java
vendor/bbmap/current/stream/ConcurrentGenericReadInputStream.java
vendor/bbmap/current/stream/ConcurrentGenericReadOutputStream.java
vendor/bbmap/current/stream/ConcurrentLegacyReadInputStream.java
vendor/bbmap/current/stream/ConcurrentReadInputStream.java
vendor/bbmap/current/stream/ConcurrentReadInputStreamD.java
vendor/bbmap/current/stream/ConcurrentReadListDepot.java
vendor/bbmap/current/stream/ConcurrentReadOutputStream.java
vendor/bbmap/current/stream/ConcurrentReadOutputStreamD.java
vendor/bbmap/current/stream/ConcurrentReadStreamInterface.java
vendor/bbmap/current/stream/CrisContainer.java
vendor/bbmap/current/stream/CrisWrapper.java
vendor/bbmap/current/stream/CustomHeader.java
vendor/bbmap/current/stream/DualCris.java
vendor/bbmap/current/stream/EmblReadInputStream.java
vendor/bbmap/current/stream/FASTQ.java
vendor/bbmap/current/stream/FastaQualReadInputStream.java
vendor/bbmap/current/stream/FastaReadInputStream.java
vendor/bbmap/current/stream/FastaShredInputStream.java
vendor/bbmap/current/stream/FastqReadInputStream.java
vendor/bbmap/current/stream/GbkReadInputStream.java
vendor/bbmap/current/stream/HeaderInputStream.java
vendor/bbmap/current/stream/MDWalker.java
vendor/bbmap/current/stream/MultiCros.java
vendor/bbmap/current/stream/MultiCros2.java
vendor/bbmap/current/stream/MultiCros3.java
vendor/bbmap/current/stream/MultiCros4.java
vendor/bbmap/current/stream/MultiCros5.java
vendor/bbmap/current/stream/MultiCros6.java
vendor/bbmap/current/stream/NullOutputStream.java
vendor/bbmap/current/stream/OnelineReadInputStream.java
vendor/bbmap/current/stream/RTextInputStream.java
vendor/bbmap/current/stream/RandomReadInputStream3.java
vendor/bbmap/current/stream/Read.java
vendor/bbmap/current/stream/ReadInputStream.java
vendor/bbmap/current/stream/ReadStreamByteWriter.java
vendor/bbmap/current/stream/ReadStreamWriter.java
vendor/bbmap/current/stream/SamHeader.java
vendor/bbmap/current/stream/SamLine.java
vendor/bbmap/current/stream/SamLineStreamer.java
vendor/bbmap/current/stream/SamReadInputStream.java
vendor/bbmap/current/stream/SamReadStreamer.java
vendor/bbmap/current/stream/SamStreamer.java
vendor/bbmap/current/stream/SamStreamerMF.java
vendor/bbmap/current/stream/SamStreamerWrapper.java
vendor/bbmap/current/stream/ScaffoldCoordinates.java
vendor/bbmap/current/stream/ScarfReadInputStream.java
vendor/bbmap/current/stream/SequentialReadInputStream.java
vendor/bbmap/current/stream/SiteScore.java
vendor/bbmap/current/stream/SiteScoreR.java
vendor/bbmap/current/structures/AbstractBitSet.java
vendor/bbmap/current/structures/AbstractIntHashMap.java
vendor/bbmap/current/structures/AtomicBitSet.java
vendor/bbmap/current/structures/ByteBuilder.java
vendor/bbmap/current/structures/CRange.java
vendor/bbmap/current/structures/CoverageArray.java
vendor/bbmap/current/structures/CoverageArray2.java
vendor/bbmap/current/structures/CoverageArray2A.java
vendor/bbmap/current/structures/CoverageArray3.java
vendor/bbmap/current/structures/CoverageArray3A.java
vendor/bbmap/current/structures/Crispr.java
vendor/bbmap/current/structures/DoubleList.java
vendor/bbmap/current/structures/Feature.java
vendor/bbmap/current/structures/FloatList.java
vendor/bbmap/current/structures/Heap.java
vendor/bbmap/current/structures/HeapLoc.java
vendor/bbmap/current/structures/IntHashMap.java
vendor/bbmap/current/structures/IntHashMapBinary.java
vendor/bbmap/current/structures/IntHashSet.java
vendor/bbmap/current/structures/IntHashSetList.java
vendor/bbmap/current/structures/IntList.java
vendor/bbmap/current/structures/IntList2.java
vendor/bbmap/current/structures/IntList3.java
vendor/bbmap/current/structures/IntListCompressor.java
vendor/bbmap/current/structures/IntLongHashMap.java
vendor/bbmap/current/structures/IntMap.java
vendor/bbmap/current/structures/ListNum.java
vendor/bbmap/current/structures/LongArrayListHashMap.java
vendor/bbmap/current/structures/LongHashMap.java
vendor/bbmap/current/structures/LongHashSet.java
vendor/bbmap/current/structures/LongHeap.java
vendor/bbmap/current/structures/LongHeapMap.java
vendor/bbmap/current/structures/LongHeapSet.java
vendor/bbmap/current/structures/LongHeapSetInterface.java
vendor/bbmap/current/structures/LongList.java
vendor/bbmap/current/structures/LongList2.java
vendor/bbmap/current/structures/LongList3.java
vendor/bbmap/current/structures/LongListSet.java
vendor/bbmap/current/structures/LongLongHashMap.java
vendor/bbmap/current/structures/LongLongListHashMap.java
vendor/bbmap/current/structures/LongM.java
vendor/bbmap/current/structures/LongPair.java
vendor/bbmap/current/structures/MultiBitSet.java
vendor/bbmap/current/structures/Quantizer.java
vendor/bbmap/current/structures/Range.java
vendor/bbmap/current/structures/RawBitSet.java
vendor/bbmap/current/structures/SeqCount.java
vendor/bbmap/current/structures/SeqCountM.java
vendor/bbmap/current/structures/SeqMap.java
vendor/bbmap/current/structures/SeqPos.java
vendor/bbmap/current/structures/SeqPosM.java
vendor/bbmap/current/structures/SetLoc.java
vendor/bbmap/current/structures/StandardDeviator.java
vendor/bbmap/current/structures/StringNum.java
vendor/bbmap/current/structures/StringPair.java
vendor/bbmap/current/structures/SuperLongList.java
vendor/bbmap/current/tax/AccessionToTaxid.java
vendor/bbmap/current/tax/AccessionToTaxid_old.java
vendor/bbmap/current/tax/AnalyzeAccession.java
vendor/bbmap/current/tax/AnalyzeAccession_ST.java
vendor/bbmap/current/tax/ExplodeTree.java
vendor/bbmap/current/tax/FilterByTaxa.java
vendor/bbmap/current/tax/FindAncestor.java
vendor/bbmap/current/tax/GiToTaxid.java
vendor/bbmap/current/tax/GiToTaxidInt.java
vendor/bbmap/current/tax/IDNode.java
vendor/bbmap/current/tax/IDTree.java
vendor/bbmap/current/tax/ImgRecord.java
vendor/bbmap/current/tax/ImgRecord2.java
vendor/bbmap/current/tax/PrintTaxonomy.java
vendor/bbmap/current/tax/Query.java
vendor/bbmap/current/tax/RenameGiToTaxid.java
vendor/bbmap/current/tax/RenameIMG.java
vendor/bbmap/current/tax/ShrinkAccession.java
vendor/bbmap/current/tax/SplitByTaxa.java
vendor/bbmap/current/tax/TaxClient.java
vendor/bbmap/current/tax/TaxFilter.java
vendor/bbmap/current/tax/TaxNode.java
vendor/bbmap/current/tax/TaxServer.java
vendor/bbmap/current/tax/TaxSize.java
vendor/bbmap/current/tax/TaxTree.java
vendor/bbmap/current/template/A_Sample.java
vendor/bbmap/current/template/A_Sample2.java
vendor/bbmap/current/template/A_SampleBasic.java
vendor/bbmap/current/template/A_SampleBasic2.java
vendor/bbmap/current/template/A_SampleByteFile.java
vendor/bbmap/current/template/A_SampleByteFileMT.java
vendor/bbmap/current/template/A_SampleD.java
vendor/bbmap/current/template/A_SampleMT.java
vendor/bbmap/current/template/A_SampleMultipleInput.java
vendor/bbmap/current/template/A_SampleSamStreamer.java
vendor/bbmap/current/template/A_SampleSummary.java
vendor/bbmap/current/template/A_Sample_Generator.java
vendor/bbmap/current/template/A_Sample_Unpaired.java
vendor/bbmap/current/template/Accumulator.java
vendor/bbmap/current/template/BBTool_ST.java
vendor/bbmap/current/template/DoWorker.java
vendor/bbmap/current/template/ThreadPoolJob.java
vendor/bbmap/current/template/ThreadWaiter.java
vendor/bbmap/current/tracker/AdapterTracker.java
vendor/bbmap/current/tracker/CrisprTracker.java
vendor/bbmap/current/tracker/EntropyTracker.java
vendor/bbmap/current/tracker/PalindromeTracker.java
vendor/bbmap/current/tracker/PolymerTracker.java
vendor/bbmap/current/tracker/QualityTracker.java
vendor/bbmap/current/tracker/ReadStats.java
vendor/bbmap/current/tracker/SealStats.java
vendor/bbmap/current/ukmer/AbstractKmerTableU.java
vendor/bbmap/current/ukmer/DumpThreadU.java
vendor/bbmap/current/ukmer/HashArrayU.java
vendor/bbmap/current/ukmer/HashArrayU1D.java
vendor/bbmap/current/ukmer/HashArrayU2D.java
vendor/bbmap/current/ukmer/HashArrayUHybrid.java
vendor/bbmap/current/ukmer/HashBufferU.java
vendor/bbmap/current/ukmer/HashForestU.java
vendor/bbmap/current/ukmer/HistogramMakerU.java
vendor/bbmap/current/ukmer/Kmer.java
vendor/bbmap/current/ukmer/KmerBufferU.java
vendor/bbmap/current/ukmer/KmerNodeU.java
vendor/bbmap/current/ukmer/KmerNodeU1D.java
vendor/bbmap/current/ukmer/KmerNodeU2D.java
vendor/bbmap/current/ukmer/KmerTableSetU.java
vendor/bbmap/current/ukmer/OwnershipThread.java
vendor/bbmap/current/ukmer/WalkerU.java
vendor/bbmap/current/var2/ApplyVariants.java
vendor/bbmap/current/var2/CallVariants.java
vendor/bbmap/current/var2/CallVariants2.java
vendor/bbmap/current/var2/CompareVCF.java
vendor/bbmap/current/var2/FilterSam.java
vendor/bbmap/current/var2/FilterVCF.java
vendor/bbmap/current/var2/MergeSamples.java
vendor/bbmap/current/var2/Realign.java
vendor/bbmap/current/var2/Realigner.java
vendor/bbmap/current/var2/SamFilter.java
vendor/bbmap/current/var2/ScafMap.java
vendor/bbmap/current/var2/Scaffold.java
vendor/bbmap/current/var2/SoftClipper.java
vendor/bbmap/current/var2/VCFFile.java
vendor/bbmap/current/var2/VCFLine.java
vendor/bbmap/current/var2/Var.java
vendor/bbmap/current/var2/VarFilter.java
vendor/bbmap/current/var2/VarKey.java
vendor/bbmap/current/var2/VarMap.java
vendor/bbmap/current/var2/VcfLoader.java
vendor/bbmap/current/var2/VcfWriter.java
vendor/bbmap/docs/Legal.txt
vendor/bbmap/docs/Legal_Illumina.txt
vendor/bbmap/docs/RestartingServers.txt
vendor/bbmap/docs/TableOfContents.txt
vendor/bbmap/docs/ToolDescriptions.txt
vendor/bbmap/docs/UsageGuide.txt
vendor/bbmap/docs/bbcms.txt
vendor/bbmap/docs/changelog.txt
vendor/bbmap/docs/citation.txt
vendor/bbmap/docs/compiling.txt
vendor/bbmap/docs/git.txt
vendor/bbmap/docs/readme.txt
vendor/bbmap/docs/readme_config.txt
vendor/bbmap/docs/readme_filetypes.txt
vendor/bbmap/docs/guides/A_SampleGuide.txt
vendor/bbmap/docs/guides/AddAdaptersGuide.txt
vendor/bbmap/docs/guides/BBDukGuide.txt
vendor/bbmap/docs/guides/BBMapGuide.txt
vendor/bbmap/docs/guides/BBMap_old_readme.txt
vendor/bbmap/docs/guides/BBMaskGuide.txt
vendor/bbmap/docs/guides/BBMergeGuide.txt
vendor/bbmap/docs/guides/BBNormGuide.txt
vendor/bbmap/docs/guides/BBSketchGuide.txt
vendor/bbmap/docs/guides/CalcUniquenessGuide.txt
vendor/bbmap/docs/guides/CallVariantsGuide.txt
vendor/bbmap/docs/guides/ClumpifyGuide.txt
vendor/bbmap/docs/guides/DedupeGuide.txt
vendor/bbmap/docs/guides/FilterByTileGuide.txt
vendor/bbmap/docs/guides/PreprocessingGuide.txt
vendor/bbmap/docs/guides/ReformatGuide.txt
vendor/bbmap/docs/guides/RepairGuide.txt
vendor/bbmap/docs/guides/SealGuide.txt
vendor/bbmap/docs/guides/SplitNexteraGuide.txt
vendor/bbmap/docs/guides/StatsGuide.txt
vendor/bbmap/docs/guides/TadpoleGuide.txt
vendor/bbmap/docs/guides/TaxonomyGuide.txt
vendor/bbmap/jni/BBMergeOverlapper.c
vendor/bbmap/jni/BBMergeOverlapper.o
vendor/bbmap/jni/BandedAlignerJNI.c
vendor/bbmap/jni/BandedAlignerJNI.o
vendor/bbmap/jni/CMakeLists.txt
vendor/bbmap/jni/IceCreamAlignerJNI.c
vendor/bbmap/jni/IceCreamAlignerJNI.o
vendor/bbmap/jni/MultiStateAligner11tsJNI.c
vendor/bbmap/jni/MultiStateAligner11tsJNI.o
vendor/bbmap/jni/README.txt
vendor/bbmap/jni/align2_BandedAlignerJNI.h
vendor/bbmap/jni/align2_MultiStateAligner11tsJNI.h
vendor/bbmap/jni/icecream_IceCreamAlignerJNI.h
vendor/bbmap/jni/jgi_BBMergeOverlapper.h
vendor/bbmap/jni/libbbtoolsjni.dylib
vendor/bbmap/jni/makefile.linux
vendor/bbmap/jni/makefile.osx
vendor/bbmap/jni/run.sh
vendor/bbmap/pipelines/assembleMito_Illumina.sh
vendor/bbmap/pipelines/assembleMito_PacBio.sh
vendor/bbmap/pipelines/assemblyPipeline.sh
vendor/bbmap/pipelines/callInsertions.sh
vendor/bbmap/pipelines/crisprPipeline.sh
vendor/bbmap/pipelines/cutRna.sh
vendor/bbmap/pipelines/makeRiboKmers.sh
vendor/bbmap/pipelines/processIMG.sh
vendor/bbmap/pipelines/testPlatformQuality.sh
vendor/bbmap/pipelines/testsketch.sh
vendor/bbmap/pipelines/variantPipeline.sh
vendor/bbmap/pipelines/covid/makeSummary.sh
vendor/bbmap/pipelines/covid/processCorona.sh
vendor/bbmap/pipelines/covid/processCoronaWrapper.sh
vendor/bbmap/pipelines/covid/readme.txt
vendor/bbmap/pipelines/covid/recal.sh
vendor/bbmap/pipelines/fetch/fetchMito.sh
vendor/bbmap/pipelines/fetch/fetchNt.sh
vendor/bbmap/pipelines/fetch/fetchNtOuter.sh
vendor/bbmap/pipelines/fetch/fetchPlasmid.sh
vendor/bbmap/pipelines/fetch/fetchPlastid.sh
vendor/bbmap/pipelines/fetch/fetchProkByGenus.sh
vendor/bbmap/pipelines/fetch/fetchRefSeq.sh
vendor/bbmap/pipelines/fetch/fetchRefSeqClades.sh
vendor/bbmap/pipelines/fetch/fetchRefSeqCladesOuter.sh
vendor/bbmap/pipelines/fetch/fetchSilva.sh
vendor/bbmap/pipelines/fetch/fetchTaxonomy.sh
vendor/bbmap/pipelines/fetch/runRefSeqProtein.sh
vendor/bbmap/pipelines/fetch/sketchRefSeq.sh
vendor/bbmap/pipelines/server/startNtServerVM.sh
vendor/bbmap/pipelines/server/startProteinServerVM.sh
vendor/bbmap/pipelines/server/startRefseqServerVM.sh
vendor/bbmap/pipelines/server/startSilvaServerVM.sh
vendor/bbmap/pipelines/server/startTaxServerVM.sh
vendor/bbmap/pipelines/silva/fetchSilva.sh
vendor/bbmap/pipelines/silva/make15mers.sh
vendor/bbmap/pipelines/silva/makeCoveringSetLsu.sh
vendor/bbmap/pipelines/silva/makeCoveringSetSsu.sh
vendor/bbmap/pipelines/silva/makeRep.sh
vendor/bbmap/pytools/.gitignore
vendor/bbmap/pytools/ReadMe
vendor/bbmap/pytools/filter.py
vendor/bbmap/pytools/readqc.py
vendor/bbmap/pytools/css/report.css
vendor/bbmap/pytools/filter_desc/3primerna.txt
vendor/bbmap/pytools/filter_desc/bisulphite.txt
vendor/bbmap/pytools/filter_desc/cell-enrichment.txt
vendor/bbmap/pytools/filter_desc/chip-seq.txt
vendor/bbmap/pytools/filter_desc/clip-pe.txt
vendor/bbmap/pytools/filter_desc/clrs.txt
vendor/bbmap/pytools/filter_desc/dna.txt
vendor/bbmap/pytools/filter_desc/filter.json
vendor/bbmap/pytools/filter_desc/filter_mt.json
vendor/bbmap/pytools/filter_desc/filter_nextera.json
vendor/bbmap/pytools/filter_desc/filter_report.txt
vendor/bbmap/pytools/filter_desc/fungal.txt
vendor/bbmap/pytools/filter_desc/iso.txt
vendor/bbmap/pytools/filter_desc/itag.txt
vendor/bbmap/pytools/filter_desc/lfpe.txt
vendor/bbmap/pytools/filter_desc/metagenome.txt
vendor/bbmap/pytools/filter_desc/microtrans.txt
vendor/bbmap/pytools/filter_desc/mtaa.txt
vendor/bbmap/pytools/filter_desc/nextera-lmp.txt
vendor/bbmap/pytools/filter_desc/plant-2x150.txt
vendor/bbmap/pytools/filter_desc/plant-2x250.txt
vendor/bbmap/pytools/filter_desc/rna.txt
vendor/bbmap/pytools/filter_desc/rnawohuman.txt
vendor/bbmap/pytools/filter_desc/sag.txt
vendor/bbmap/pytools/filter_desc/smrna.txt
vendor/bbmap/pytools/filter_desc/sop_list.txt
vendor/bbmap/pytools/filter_desc/viral-metagenome.txt
vendor/bbmap/pytools/filter_param/3primerna.config
vendor/bbmap/pytools/filter_param/bisulphite.config
vendor/bbmap/pytools/filter_param/cell-enrichment.config
vendor/bbmap/pytools/filter_param/chip-seq.config
vendor/bbmap/pytools/filter_param/clip-pe.config
vendor/bbmap/pytools/filter_param/clrs.config
vendor/bbmap/pytools/filter_param/dna.config
vendor/bbmap/pytools/filter_param/fungal.config
vendor/bbmap/pytools/filter_param/iso.config
vendor/bbmap/pytools/filter_param/itag.config
vendor/bbmap/pytools/filter_param/lfpe.config
vendor/bbmap/pytools/filter_param/metagenome.config
vendor/bbmap/pytools/filter_param/microtrans.config
vendor/bbmap/pytools/filter_param/mtaa.config
vendor/bbmap/pytools/filter_param/nextera-lmp.config
vendor/bbmap/pytools/filter_param/nextseq.config
vendor/bbmap/pytools/filter_param/plant-2x150.config
vendor/bbmap/pytools/filter_param/plant-2x250.config
vendor/bbmap/pytools/filter_param/rna.config
vendor/bbmap/pytools/filter_param/rnawohuman.config
vendor/bbmap/pytools/filter_param/sag.config
vendor/bbmap/pytools/filter_param/smrna.config
vendor/bbmap/pytools/filter_param/viral-metagenome.config
vendor/bbmap/pytools/images/JGI_logo.jpg
vendor/bbmap/pytools/images/favicon.ico
vendor/bbmap/pytools/images/jgi_log_transparent.png
vendor/bbmap/pytools/template/filter_body_template.html
vendor/bbmap/pytools/template/readqc_artifacts.html
vendor/bbmap/pytools/template/readqc_body_template.html
vendor/bbmap/pytools/template/template.html
vendor/bbmap/pytools/tools/patterN_fastq.pl
vendor/bbmap/resources/16S_15mers.fa
vendor/bbmap/resources/16S_consensus_sequence.fa
vendor/bbmap/resources/18S_15mers.fa
vendor/bbmap/resources/18S_consensus_sequence.fa
vendor/bbmap/resources/23S_15mers.fa
vendor/bbmap/resources/23S_consensus_sequence.fa
vendor/bbmap/resources/5S_10mers.fa
vendor/bbmap/resources/5S_11mers.fa
vendor/bbmap/resources/5S_12mers.fa
vendor/bbmap/resources/5S_15mers.fa
vendor/bbmap/resources/5S_9mers.fa
vendor/bbmap/resources/5S_consensus_sequence.fa
vendor/bbmap/resources/Covid19_ref.fa
vendor/bbmap/resources/ITS_animal_consensus_sequence.fq
vendor/bbmap/resources/ITS_consensus_sequence.fq
vendor/bbmap/resources/ITS_fungi_consensus_sequence.fq
vendor/bbmap/resources/ITS_nonfungi_consensus_sequence.fq
vendor/bbmap/resources/ITS_other_consensus_sequence.fq
vendor/bbmap/resources/ITS_plant_consensus_sequence.fq
vendor/bbmap/resources/ITS_universal_consensus_sequence.fq
vendor/bbmap/resources/PacBioAdapter.fa
vendor/bbmap/resources/SIP_spikeins.fa.gz
vendor/bbmap/resources/adapters.fa
vendor/bbmap/resources/adapters_no_transposase.fa.gz
vendor/bbmap/resources/artic3.fasta
vendor/bbmap/resources/bbmerge.bbnet
vendor/bbmap/resources/blacklist_nt_merged.sketch
vendor/bbmap/resources/blacklist_prokprot_merged.sketch
vendor/bbmap/resources/blacklist_refseq_merged.sketch
vendor/bbmap/resources/blacklist_silva_merged.sketch
vendor/bbmap/resources/contents.txt
vendor/bbmap/resources/crelox.fa.gz
vendor/bbmap/resources/crispr.bbnet.gz
vendor/bbmap/resources/crisprs.fa.gz
vendor/bbmap/resources/favicon.ico
vendor/bbmap/resources/kapatags.L40.fa
vendor/bbmap/resources/lambda.fa.gz
vendor/bbmap/resources/lfpe.linker.fa.gz
vendor/bbmap/resources/lsu_15mers.fa
vendor/bbmap/resources/m16S_consensus_sequence.fa
vendor/bbmap/resources/m18S_consensus_sequence.fa
vendor/bbmap/resources/minorAlleleCount.txt
vendor/bbmap/resources/model.pgm
vendor/bbmap/resources/mtst.fa
vendor/bbmap/resources/nextera.fa.gz
vendor/bbmap/resources/nextera_LMP_adapter.fa.gz
vendor/bbmap/resources/nextera_LMP_linker.fa.gz
vendor/bbmap/resources/p16S_consensus_sequence.fa
vendor/bbmap/resources/pJET1.2.fa
vendor/bbmap/resources/phix174_ill.ref.fa.gz
vendor/bbmap/resources/phix_adapters.fa.gz
vendor/bbmap/resources/polyA.fa.gz
vendor/bbmap/resources/primes.txt.gz
vendor/bbmap/resources/remote_files.txt
vendor/bbmap/resources/remote_files_old.txt
vendor/bbmap/resources/sample1.fq.gz
vendor/bbmap/resources/sample2.fq.gz
vendor/bbmap/resources/sequencing_artifacts.fa.gz
vendor/bbmap/resources/short.fa
vendor/bbmap/resources/ssu_15mers.fa
vendor/bbmap/resources/tRNA_10mers.fa
vendor/bbmap/resources/tRNA_11mers.fa
vendor/bbmap/resources/tRNA_15mers.fa
vendor/bbmap/resources/tRNA_16mers.fa
vendor/bbmap/resources/tRNA_consensus_sequence.fa
vendor/bbmap/resources/tax_server.html
vendor/bbmap/resources/truseq.fa.gz
vendor/bbmap/resources/truseq_rna.fa.gz