├── .gitignore ├── BB_User-Meeting-2014-poster-FINAL.pdf ├── README.md ├── bbmap-help-Biostar.md ├── bitbucket-pipelines.yml ├── config ├── cluster16s.txt ├── filter16s.txt ├── histograms.txt ├── recalibrate.txt ├── rnaseq.txt └── trimadapters.txt ├── current ├── align2 │ ├── AbstractIndex.java │ ├── AbstractMapThread.java │ ├── AbstractMapper.java │ ├── BBIndex.java │ ├── BBIndex5.java │ ├── BBIndexAcc.java │ ├── BBIndexPacBio.java │ ├── BBIndexPacBioSkimmer.java │ ├── BBMap.java │ ├── BBMap5.java │ ├── BBMapAcc.java │ ├── BBMapPacBio.java │ ├── BBMapPacBioSkimmer.java │ ├── BBMapThread.java │ ├── BBMapThread5.java │ ├── BBMapThreadAcc.java │ ├── BBMapThreadPacBio.java │ ├── BBMapThreadPacBioSkimmer.java │ ├── BBSplitter.java │ ├── BBWrap.java │ ├── BandedAligner.java │ ├── BandedAlignerConcrete.java │ ├── BandedAlignerJNI.java │ ├── Blacklist.java │ ├── Block.java │ ├── ChromLoadThread.java │ ├── CompareSamFiles.java │ ├── CompressString.java │ ├── Evaluate.java │ ├── GapTools.java │ ├── GradeSamFile.java │ ├── Index.java │ ├── IndexMaker4.java │ ├── IndexMaker5.java │ ├── KeyRing.java │ ├── MSA.java │ ├── MakeQualityHistogram.java │ ├── MakeRocCurve.java │ ├── MultiStateAligner10ts.java │ ├── MultiStateAligner11ts.java │ ├── MultiStateAligner11tsJNI.java │ ├── MultiStateAligner9Flat.java │ ├── MultiStateAligner9PacBio.java │ ├── MultiStateAligner9PacBioAdapter.java │ ├── MultiStateAligner9PacBioAdapter2.java │ ├── MultiStateAligner9PacBioAdapter_WithBarriers.java │ ├── MultiStateAligner9XFlat.java │ ├── MultiStateAligner9ts.java │ ├── NeedlemanWunsch.java │ ├── PackedHeap.java │ ├── Pointer.java │ ├── PrintTime.java │ ├── Quad.java │ ├── Quad64.java │ ├── Quad64Heap.java │ ├── QuadHeap.java │ ├── QualityTools.java │ ├── RandomReads3.java │ ├── ReadComparatorID.java │ ├── ReadComparatorMapping.java │ ├── ReadComparatorName.java │ ├── ReadComparatorTopological.java │ ├── ReadErrorComparator.java │ ├── ReadLengthComparator.java │ ├── ReadStats.java │ ├── RefToIndex.java │ ├── ReformatBatchOutput.java │ ├── ReformatBatchOutput2.java │ ├── Shared.java │ ├── Solver.java │ ├── SortReadsByID.java │ ├── SortReadsByMapping.java │ ├── SortReadsTopologically.java │ ├── SplitMappedReads.java │ ├── Tools.java │ ├── TranslateColorspaceRead.java │ └── TrimRead.java ├── aligner │ ├── Aligner.java │ ├── Alignment.java │ ├── AlignmentResult.java │ ├── AllToAll.java │ ├── FlatAligner.java │ ├── FlatAligner2.java │ ├── MultiStateAligner9PacBioAdapter.java │ ├── MultiStateAligner9PacBioAdapter2.java │ ├── MultiStateAligner9PacBioAdapter3.java │ ├── MultiStateAligner9PacBioAdapter_WithBarriers.java │ ├── SingleStateAlignerFlat.java │ ├── SingleStateAlignerFlat2.java │ ├── SingleStateAlignerFlat2Amino.java │ ├── SingleStateAlignerFlat2_1D.java │ ├── SingleStateAlignerFlat3.java │ ├── SingleStateAlignerFlatFloat.java │ └── SingleStateAlignerPacBioAdapter.java ├── assemble │ ├── AbstractBuildThread.java │ ├── AbstractExploreThread.java │ ├── AbstractProcessContigThread.java │ ├── AbstractRemoveThread.java │ ├── AbstractShaveThread.java │ ├── BubblePopper.java │ ├── Contig.java │ ├── Edge.java │ ├── ErrorTracker.java │ ├── KmerCompressor.java │ ├── Postfilter.java │ ├── Rollback.java │ ├── ShaveObject.java │ ├── Shaver.java │ ├── Shaver1.java │ ├── Shaver2.java │ ├── TadPipe.java │ ├── Tadpole.java │ ├── Tadpole1.java │ ├── Tadpole2.java │ └── TadpoleWrapper.java ├── bloom │ ├── BloomFilter.java │ ├── BloomFilterCorrector.java │ ├── BloomFilterCorrectorWrapper.java │ ├── BloomFilterWrapper.java │ ├── ErrorCorrect.java │ ├── KCountArray.java │ ├── KCountArray2.java │ ├── KCountArray3.java │ ├── KCountArray4.java │ ├── KCountArray4MT.java │ ├── KCountArray5MT.java │ ├── KCountArray6MT.java │ ├── KCountArray7MT.java │ ├── KCountArray7MTA.java │ ├── KCountArray8MT.java │ ├── KmerCount3.java │ ├── KmerCount4.java │ ├── KmerCount5.java │ ├── KmerCount6.java │ ├── KmerCount6MT.java │ ├── KmerCount7MT.java │ ├── KmerCount7MTA.java │ ├── KmerCountAbstract.java │ ├── LargeKmerCount.java │ ├── LargeKmerCount2.java │ └── TestLargeKmer.java ├── cardinality │ ├── BBLog.java │ ├── BBLog_simple.java │ ├── CardinalityTracker.java │ ├── LogLog.java │ ├── LogLog16.java │ ├── LogLog2.java │ ├── LogLog8.java │ ├── LogLog8_simple.java │ ├── LogLogWrapper.java │ ├── LogLog_old.java │ └── MultiLogLog.java ├── clump │ ├── Clump.java │ ├── ClumpList.java │ ├── ClumpTools.java │ ├── Clumpify.java │ ├── Condensor.java │ ├── KmerComparator.java │ ├── KmerComparator2.java │ ├── KmerComparatorX.java │ ├── KmerComparatorY.java │ ├── KmerComparator_original.java │ ├── KmerReduce.java │ ├── KmerSort.java │ ├── KmerSort1.java │ ├── KmerSort2.java │ ├── KmerSort3.java │ ├── KmerSplit.java │ ├── PivotSet.java │ ├── ReadKey.java │ ├── Splitter.java │ └── StreamToOutput.java ├── cluster │ ├── Cluster.java │ ├── ClusterTools.java │ ├── MergeReadHeaders.java │ ├── ReadTag.java │ └── ReclusterByKmer.java ├── consensus │ ├── BaseGraph.java │ ├── BaseGraphPart.java │ ├── BaseNode.java │ ├── ConsensusMaker.java │ ├── ConsensusObject.java │ ├── FixScaffoldGaps.java │ └── Lilypad.java ├── covid │ └── SummarizeCoverage.java ├── dna │ ├── AminoAcid.java │ ├── ChromArrayMaker.java │ ├── ChromToFasta.java │ ├── ChromosomeArray.java │ ├── Coverage.java │ ├── CoverageArray.java │ ├── CoverageArray2.java │ ├── CoverageArray3.java │ ├── Data.java │ ├── Exon.java │ ├── FastaToChromArrays2.java │ ├── Gene.java │ ├── GeneSet.java │ ├── IntMap.java │ ├── IntMapFlex.java │ ├── Matrix.java │ ├── Motif.java │ ├── MotifMulti.java │ ├── MotifProbsN.java │ ├── MotifSimple.java │ ├── Parser.java │ ├── Range.java │ ├── ScafLoc.java │ ├── Scaffold.java │ └── Timer.java ├── driver │ ├── A_Sample_Textfile.java │ ├── BBVersion.java │ ├── ClearRam.java │ ├── CollateSpikeIn.java │ ├── CompareReferenceGenomes.java │ ├── CompareSequences.java │ ├── ConcatenateFiles.java │ ├── ConcatenateTextFiles.java │ ├── Concatenator.java │ ├── ConvertSamToAln.java │ ├── CorrelateIdentity.java │ ├── CountRNAs.java │ ├── CountSharedLines.java │ ├── EstherFilter.java │ ├── FilterAssemblySummary.java │ ├── FilterLines.java │ ├── FilterReadsByName.java │ ├── FindMotifs.java │ ├── FixChr.java │ ├── FixDumbFile.java │ ├── GenerateNoCallsFromCoverage.java │ ├── GetSequence.java │ ├── GetUniquePrefixes.java │ ├── Grep.java │ ├── Life.java │ ├── LineCount.java │ ├── LoadReads.java │ ├── LookAtID.java │ ├── MakeTestScript.java │ ├── MakeTestScriptScoreOnly.java │ ├── MeasureGene.java │ ├── MergeBigelow.java │ ├── MergeCoverageOTU.java │ ├── MergeTextFiles.java │ ├── MergeTextFiles2.java │ ├── MoveFiles.java │ ├── ParseCrossblockResults.java │ ├── PlotGC.java │ ├── PrintEnv.java │ ├── ProcessFragMerging.java │ ├── ProcessSpeed.java │ ├── ProcessSpeed2.java │ ├── ProcessWebcheck.java │ ├── ReduceSilva.java │ ├── RenameAndMux.java │ ├── RenameByHeader.java │ ├── RenameNcbiToTid.java │ ├── RenameRefseqFiles.java │ ├── Sample.java │ ├── Search.java │ ├── SelectReads.java │ ├── SniffSplices.java │ ├── SortByQuality.java │ ├── SummarizeContamReport.java │ ├── SummarizeCoverage.java │ ├── SummarizeCrossblock.java │ ├── SummarizeMSDIN.java │ ├── SummarizeQuast.java │ ├── SummarizeSealStats.java │ ├── TestCompressionSpeed.java │ ├── TestLockSpeed.java │ ├── Translator.java │ ├── Translator2.java │ ├── TransposeTextFile.java │ └── TrimSamFile.java ├── fileIO │ ├── ArrayFile.java │ ├── ByteFile.java │ ├── ByteFile1.java │ ├── ByteFile2.java │ ├── ByteStreamWriter.java │ ├── ChainBlock.java │ ├── ChainLine.java │ ├── CompressFiles.java │ ├── CopyFile.java │ ├── CopyFiles.java │ ├── CopyFiles2.java │ ├── FileFormat.java │ ├── FindFiles.java │ ├── GenericTextFile.java │ ├── LoadThread.java │ ├── MatrixFile.java │ ├── OpenFile.java │ ├── PipeThread.java │ ├── QuickFile.java │ ├── ReadWrite.java │ ├── SummaryFile.java │ ├── TextFile.java │ └── TextStreamWriter.java ├── fun │ ├── Calc.java │ ├── Chance.java │ ├── DiskBench.java │ ├── FindPath.java │ ├── Genetic.java │ ├── Life.java │ ├── MakeAdjacencyList.java │ ├── Palindrome.java │ ├── ProbShared.java │ ├── ProbShared2.java │ └── ProbShared3.java ├── gff │ ├── CompareGff.java │ ├── CompareGff_old.java │ ├── CutGff.java │ ├── CutGff_ST.java │ ├── GbffFeature.java │ ├── GbffFile.java │ ├── GbffLocus.java │ ├── GffLine.java │ └── VcfToGff.java ├── hiseq │ ├── AnalyzeFlowCell.java │ ├── CycleTracker.java │ ├── FlowCell.java │ ├── FlowcellCoordinate.java │ ├── IlluminaHeaderParser.java │ ├── Lane.java │ ├── MicroTile.java │ ├── PlotFlowCell.java │ └── Tile.java ├── hmm │ ├── HMMSearchLine.java │ ├── HMMSearchReport.java │ └── ProteinSummary.java ├── icecream │ ├── IceCreamAligner.java │ ├── IceCreamAlignerJNI.java │ ├── IceCreamAlignerJava.java │ ├── IceCreamFinder.java │ ├── IceCreamGrader.java │ ├── IceCreamMaker.java │ ├── PBHeader.java │ ├── PolymerTrimmer.java │ ├── ReadBuilder.java │ ├── ReformatPacBio.java │ ├── ZMW.java │ └── ZMWStreamer.java ├── jasper │ ├── Comparison.java │ ├── DenseSimilarityMatrix.java │ ├── DenseTree.java │ ├── DenseTreeValidate.java │ ├── KmerPosition.java │ ├── KmerPosition3.java │ ├── NCBIComparison.java │ ├── NCBISparseSimilarityMatrix.java │ ├── NCBISparseTree.java │ ├── NCBISparseTreeValidate.java │ ├── NCBITreeNode.java │ ├── Organism.java │ ├── SimilarityMatrix.java │ ├── SparseSimilarityMatrix.java │ ├── SparseTree.java │ ├── SparseTreeValidate.java │ ├── TaxCompare.java │ └── TreeNode.java ├── jgi │ ├── A_Sample.java │ ├── A_Sample2.java │ ├── A_SampleByteFile.java │ ├── A_SampleD.java │ ├── A_SampleMT.java │ ├── A_Sample_Unpaired.java │ ├── AddAdapters.java │ ├── AdjustHomopolymers.java │ ├── AssemblyStats2.java │ ├── AssemblyStatsWrapper.java │ ├── BBDuk.java │ ├── BBDuk2.java │ ├── BBDukF.java │ ├── BBMask.java │ ├── BBMask_noSam.java │ ├── BBMerge.java │ ├── BBMergeOverlapper.java │ ├── BBQC.java │ ├── BBTool_ST.java │ ├── CalcTrueQuality.java │ ├── CalcTrueQuality_single.java │ ├── CalcUniqueness.java │ ├── CallPeaks.java │ ├── Consect.java │ ├── CorrelateBarcodes.java │ ├── CountBarcodes.java │ ├── CountGC.java │ ├── CountUniqueness.java │ ├── CovStatsLine.java │ ├── CoveragePileup.java │ ├── CrossContaminate.java │ ├── CutPrimers.java │ ├── DecontaminateByNormalization.java │ ├── Dedupe.java │ ├── Dedupe2.java │ ├── DedupeByMapping.java │ ├── DedupeProtein.java │ ├── DemuxByName.java │ ├── DemuxByName2.java │ ├── Difference.java │ ├── ErrorCorrect.java │ ├── FakeReads.java │ ├── FilterByCoverage.java │ ├── FilterBySequence.java │ ├── FilterReadsWithSubs.java │ ├── FindHiCJunctions.java │ ├── FindPrimers.java │ ├── FindPrimers_old.java │ ├── FindString.java │ ├── FungalRelease.java │ ├── FuseSequence.java │ ├── GatherKapaStats.java │ ├── GetReads.java │ ├── GradeMergedReads.java │ ├── GreedyBarCodeFinder.java │ ├── IdentityMatrix.java │ ├── Info.java │ ├── KExpand.java │ ├── KeepBestCopy.java │ ├── KmerCountExact.java │ ├── KmerCountMulti.java │ ├── KmerCoverage.java │ ├── KmerFilterSetMaker.java │ ├── KmerNormalize.java │ ├── KmerSample.java │ ├── LogLog.java │ ├── MakeChimeras.java │ ├── MakeContaminatedGenomes.java │ ├── MakeCoverageHistogram.java │ ├── MakeLengthHistogram.java │ ├── MakePolymers.java │ ├── MateReadsMT.java │ ├── MergeBarcodes.java │ ├── MergeSam.java │ ├── MutateGenome.java │ ├── MutateGenome2.java │ ├── NormAndCorrectWrapper.java │ ├── Orf.java │ ├── PartitionReads.java │ ├── PhylipToFasta.java │ ├── RQCFilter.java │ ├── RQCFilter2.java │ ├── RQCFilterStats.java │ ├── RandomGenome.java │ ├── ReadKmerDepthDistribution.java │ ├── RedirectTest.java │ ├── ReformatReads.java │ ├── RemapQuality.java │ ├── RemoveBadBarcodes.java │ ├── RenameReads.java │ ├── ReplaceHeaders.java │ ├── RepresentativeSet.java │ ├── SamToEst.java │ ├── Seal.java │ ├── Shred.java │ ├── Shuffle.java │ ├── SmallKmerFrequency.java │ ├── SplitNexteraLMP.java │ ├── SplitPairsAndSingles.java │ ├── SplitSam4Way.java │ ├── SplitSam6Way.java │ ├── SplitSamFile.java │ ├── StringCount.java │ ├── SynthMDA.java │ ├── TestFilesystem.java │ ├── TestFormat.java │ ├── TetramerFrequencies.java │ ├── TranslateSixFrames.java │ ├── UnicodeToAscii.java │ └── Unzip.java ├── json │ ├── JsonLiteral.java │ ├── JsonObject.java │ └── JsonParser.java ├── kmer │ ├── AbstractKmerTable.java │ ├── AbstractKmerTableSet.java │ ├── AtomicShortArray.java │ ├── DumpThread.java │ ├── HashArray.java │ ├── HashArray1D.java │ ├── HashArray2D.java │ ├── HashArrayHybrid.java │ ├── HashArrayHybridFast.java │ ├── HashBuffer.java │ ├── HashForest.java │ ├── HistogramMaker.java │ ├── KmerBuffer.java │ ├── KmerLink.java │ ├── KmerNode.java │ ├── KmerNode1D.java │ ├── KmerNode2D.java │ ├── KmerTable.java │ ├── KmerTableSet.java │ ├── OwnershipThread.java │ ├── Primes.java │ ├── ScheduleMaker.java │ ├── TableLoaderLockFree.java │ ├── TableReader.java │ └── Walker.java ├── ml │ └── ProcessBBMergeHeaders.java ├── pacbio │ ├── CalcCoverageFromSites.java │ ├── GenerateMultiChrom.java │ ├── MakePacBioScript.java │ ├── MergeFastaContigs.java │ ├── MergeReadsAndGenome.java │ ├── PartitionFastaFile.java │ ├── PartitionReads.java │ ├── ProcessStackedSitesNormalized.java │ ├── RemoveAdapters2.java │ ├── RemoveAdapters3.java │ ├── RemoveNFromChromosome.java │ ├── SiteR.java │ ├── SortSites.java │ ├── SplitOffPerfectContigs.java │ ├── StackSites.java │ └── StackSites2.java ├── prok │ ├── AnalyzeGenes.java │ ├── CallGenes.java │ ├── Feature.java │ ├── FetchProks.java │ ├── FilterSilva.java │ ├── FrameStats.java │ ├── GeneCaller.java │ ├── GeneModel.java │ ├── GeneModelParser.java │ ├── MergeRibo.java │ ├── MergeRibo_Fast.java │ ├── Orf.java │ ├── PGMTools.java │ ├── ProkObject.java │ ├── RiboMaker.java │ ├── ScafData.java │ ├── ScoreTracker.java │ ├── SplitRibo.java │ └── StatsContainer.java ├── server │ ├── PercentEncoding.java │ ├── ServerTools.java │ └── SimpleHttpServer.java ├── shared │ ├── Colors.java │ ├── KillSwitch.java │ ├── MetadataWriter.java │ ├── Parse.java │ ├── Parser.java │ ├── PreParser.java │ ├── Primes.java │ ├── ReadStats.java │ ├── Shared.java │ ├── Timer.java │ ├── Tools.java │ └── TrimRead.java ├── sketch │ ├── AddSSU.java │ ├── AlignmentJob.java │ ├── AlignmentThreadPool.java │ ├── AnalyzeSketchResults.java │ ├── Blacklist.java │ ├── BlacklistMaker.java │ ├── BlacklistMaker2.java │ ├── CompareBuffer.java │ ├── CompareSSU.java │ ├── CompareSketch.java │ ├── Comparison.java │ ├── DisplayParams.java │ ├── GlocalAligner.java │ ├── InvertKey.java │ ├── KmerLimit.java │ ├── KmerLimit2.java │ ├── MergeSketch.java │ ├── Record.java │ ├── RecordSet.java │ ├── ResultLineParser.java │ ├── SSUMap.java │ ├── SendSketch.java │ ├── Sketch.java │ ├── SketchHeap.java │ ├── SketchIdComparator.java │ ├── SketchIndex.java │ ├── SketchMaker.java │ ├── SketchMakerMini.java │ ├── SketchObject.java │ ├── SketchResults.java │ ├── SketchSearcher.java │ ├── SketchTool.java │ ├── SubSketch.java │ ├── SummarizeSketchStats.java │ └── Whitelist.java ├── sort │ ├── ContigLengthComparator.java │ ├── MergeSorted.java │ ├── ReadComparator.java │ ├── ReadComparatorFlowcell.java │ ├── ReadComparatorID.java │ ├── ReadComparatorList.java │ ├── ReadComparatorMapping.java │ ├── ReadComparatorName.java │ ├── ReadComparatorPosition.java │ ├── ReadComparatorRandom.java │ ├── ReadComparatorTaxa.java │ ├── ReadComparatorTopological.java │ ├── ReadErrorComparator.java │ ├── ReadLengthComparator.java │ ├── ReadQualityComparator.java │ ├── Shuffle.java │ ├── Shuffle2.java │ ├── SortByName.java │ └── SortReadsByID.java ├── stream │ ├── ArrayListSet.java │ ├── BufferedMultiCros.java │ ├── ByteBuilder.java │ ├── ConcurrentCollectionReadInputStream.java │ ├── ConcurrentDepot.java │ ├── ConcurrentGenericReadInputStream.java │ ├── ConcurrentGenericReadOutputStream.java │ ├── ConcurrentLegacyReadInputStream.java │ ├── ConcurrentReadInputStream.java │ ├── ConcurrentReadInputStreamD.java │ ├── ConcurrentReadListDepot.java │ ├── ConcurrentReadOutputStream.java │ ├── ConcurrentReadOutputStreamD.java │ ├── ConcurrentReadStreamInterface.java │ ├── CrisContainer.java │ ├── CrisWrapper.java │ ├── DualCris.java │ ├── EmblReadInputStream.java │ ├── FASTQ.java │ ├── FastaQualReadInputStream.java │ ├── FastaReadInputStream.java │ ├── FastaReadInputStream2.java │ ├── FastaShredInputStream.java │ ├── FastqReadInputStream.java │ ├── GbkReadInputStream.java │ ├── Header.java │ ├── HeaderInputStream.java │ ├── KillSwitch.java │ ├── MDWalker.java │ ├── MultiCros.java │ ├── MultiCros2.java │ ├── MultiCros3.java │ ├── NullOutputStream.java │ ├── OnelineReadInputStream.java │ ├── RTextInputStream.java │ ├── RandomReadInputStream3.java │ ├── Read.java │ ├── ReadInputStream.java │ ├── ReadStreamByteWriter.java │ ├── ReadStreamStringWriter.java │ ├── ReadStreamWriter.java │ ├── SamHeader.java │ ├── SamLine.java │ ├── SamLineStreamer.java │ ├── SamReadInputStream.java │ ├── SamReadStreamer.java │ ├── SamStreamer.java │ ├── SamStreamerMF.java │ ├── SamStreamerWrapper.java │ ├── ScaffoldCoordinates.java │ ├── ScarfReadInputStream.java │ ├── SequentialReadInputStream.java │ ├── SiteScore.java │ └── SiteScoreR.java ├── structures │ ├── AbstractBitSet.java │ ├── AbstractIntHashMap.java │ ├── AtomicBitSet.java │ ├── ByteBuilder.java │ ├── CoverageArray.java │ ├── CoverageArray2.java │ ├── CoverageArray3.java │ ├── CoverageArray3A.java │ ├── DoubleList.java │ ├── EntropyTracker.java │ ├── FloatList.java │ ├── Heap.java │ ├── IntHashMap.java │ ├── IntHashMapBinary.java │ ├── IntHashSet.java │ ├── IntHashSetList.java │ ├── IntList.java │ ├── IntList2.java │ ├── IntList3.java │ ├── IntListCompressor.java │ ├── IntLongHashMap.java │ ├── IntMap.java │ ├── ListNum.java │ ├── LongHashMap.java │ ├── LongHashSet.java │ ├── LongHeap.java │ ├── LongHeapMap.java │ ├── LongHeapSet.java │ ├── LongHeapSetInterface.java │ ├── LongList.java │ ├── LongListSet.java │ ├── LongLongHashMap.java │ ├── LongM.java │ ├── LongPair.java │ ├── MultiBitSet.java │ ├── PolymerTracker.java │ ├── Quantizer.java │ ├── Range.java │ ├── RawBitSet.java │ ├── StringNum.java │ ├── StringPair.java │ └── SuperLongList.java ├── tax │ ├── AccessionToTaxid.java │ ├── AccessionToTaxid_old.java │ ├── AnalyzeAccession.java │ ├── AnalyzeAccession_ST.java │ ├── ExplodeTree.java │ ├── FilterByTaxa.java │ ├── FindAncestor.java │ ├── GiToNcbi.java │ ├── GiToTaxid.java │ ├── IDNode.java │ ├── IDTree.java │ ├── ImgRecord.java │ ├── ImgRecord2.java │ ├── PrintTaxonomy.java │ ├── Query.java │ ├── RenameGiToNcbi.java │ ├── RenameGiToTaxid.java │ ├── RenameIMG.java │ ├── ShrinkAccession.java │ ├── SortByTaxa.java │ ├── SplitByTaxa.java │ ├── TaxApp.java │ ├── TaxClient.java │ ├── TaxFilter.java │ ├── TaxNode.java │ ├── TaxServer.java │ ├── TaxSize.java │ └── TaxTree.java ├── template │ ├── A_Sample.java │ ├── A_Sample2.java │ ├── A_SampleBasic.java │ ├── A_SampleBasic2.java │ ├── A_SampleByteFile.java │ ├── A_SampleD.java │ ├── A_SampleMT.java │ ├── A_SampleSamStreamer.java │ ├── A_SampleSummary.java │ ├── A_Sample_Generator.java │ ├── A_Sample_Unpaired.java │ ├── Accumulator.java │ ├── BBTool_ST.java │ ├── DoWorker.java │ ├── ThreadPoolJob.java │ └── ThreadWaiter.java ├── ukmer │ ├── AbstractKmerTableU.java │ ├── DumpThreadU.java │ ├── HashArrayU.java │ ├── HashArrayU1D.java │ ├── HashArrayU2D.java │ ├── HashArrayUHybrid.java │ ├── HashBufferU.java │ ├── HashForestU.java │ ├── HistogramMakerU.java │ ├── Kmer.java │ ├── KmerBufferU.java │ ├── KmerNodeU.java │ ├── KmerNodeU1D.java │ ├── KmerNodeU2D.java │ ├── KmerTableSetU.java │ ├── OwnershipThread.java │ └── WalkerU.java ├── var │ ├── ApplyVarsToReference.java │ ├── GenerateConsensusVariations.java │ ├── GenerateVarlets.java │ ├── GenerateVarlets2.java │ ├── GenerateVarlets3.java │ ├── StackVariations.java │ ├── StackVariations2.java │ ├── VarLine.java │ ├── Variation.java │ └── Varlet.java └── var2 │ ├── ApplyVariants.java │ ├── CallVariants.java │ ├── CallVariants2.java │ ├── CompareVCF.java │ ├── FilterSam.java │ ├── FilterVCF.java │ ├── MergeSamples.java │ ├── Realign.java │ ├── Realigner.java │ ├── SamFilter.java │ ├── ScafMap.java │ ├── Scaffold.java │ ├── SoftClipper.java │ ├── VCFFile.java │ ├── VCFLine.java │ ├── Var.java │ ├── VarFilter.java │ ├── VarKey.java │ ├── VarMap.java │ ├── VcfLoader.java │ └── VcfWriter.java ├── docs ├── Legal.txt ├── Legal_Illumina.txt ├── RestartingServers.txt ├── TableOfContents.txt ├── ToolDescriptions.txt ├── UsageGuide.txt ├── bbcms.txt ├── changelog.txt ├── citation.txt ├── compiling.txt ├── git.txt ├── guides │ ├── A_SampleGuide.txt │ ├── AddAdaptersGuide.txt │ ├── BBDukGuide.txt │ ├── BBMapGuide.txt │ ├── BBMap_old_readme.txt │ ├── BBMaskGuide.txt │ ├── BBMergeGuide.txt │ ├── BBNormGuide.txt │ ├── BBSketchGuide.txt │ ├── CalcUniquenessGuide.txt │ ├── CallVariantsGuide.txt │ ├── ClumpifyGuide.txt │ ├── DedupeGuide.txt │ ├── FilterByTileGuide.txt │ ├── PreprocessingGuide.txt │ ├── ReformatGuide.txt │ ├── RepairGuide.txt │ ├── SealGuide.txt │ ├── SplitNexteraGuide.txt │ ├── StatsGuide.txt │ ├── TadpoleGuide.txt │ └── TaxonomyGuide.txt ├── readme.txt ├── readme_config.txt └── readme_filetypes.txt ├── jni ├── BBMergeOverlapper.c ├── BBMergeOverlapper.o ├── BandedAlignerJNI.c ├── BandedAlignerJNI.o ├── CMakeLists.txt ├── IceCreamAlignerJNI.c ├── IceCreamAlignerJNI.o ├── MultiStateAligner11tsJNI.c ├── MultiStateAligner11tsJNI.o ├── README.txt ├── align2_BandedAlignerJNI.h ├── align2_MultiStateAligner11tsJNI.h ├── icecream_IceCreamAlignerJNI.h ├── jgi_BBMergeOverlapper.h ├── libbbtoolsjni.dylib ├── libbbtoolsjni.so ├── makefile.linux ├── makefile.osx └── run.sh ├── license.txt ├── pipelines ├── assembleMito_Illumina.sh ├── assembleMito_PacBio.sh ├── assemblyPipeline.sh ├── callInsertions.sh ├── covid │ ├── makeSummary.sh │ ├── processCorona.sh │ ├── processCoronaWrapper.sh │ ├── readme.txt │ └── recal.sh ├── cutRna.sh ├── fetch │ ├── fetchMito.sh │ ├── fetchNt.sh │ ├── fetchNtOuter.sh │ ├── fetchPlasmid.sh │ ├── fetchPlastid.sh │ ├── fetchProkByGenus.sh │ ├── fetchRefSeq.sh │ ├── fetchRefSeqClades.sh │ ├── fetchRefSeqCladesOuter.sh │ ├── fetchSilva.sh │ ├── fetchTaxonomy.sh │ ├── runRefSeqProtein.sh │ └── sketchRefSeq.sh ├── makeRiboKmers.sh ├── processIMG.sh ├── server │ ├── startNtServerVM.sh │ ├── startProteinServerVM.sh │ ├── startRefseqServerVM.sh │ ├── startSilvaServerVM.sh │ └── startTaxServerVM.sh ├── silva │ ├── fetchSilva.sh │ ├── make15mers.sh │ ├── makeCoveringSetLsu.sh │ ├── makeCoveringSetSsu.sh │ └── makeRep.sh ├── testPlatformQuality.sh ├── testsketch.sh └── variantPipeline.sh ├── pytools ├── .gitignore ├── ReadMe ├── css │ └── report.css ├── filter.py ├── filter_desc │ ├── 3primerna.txt │ ├── bisulphite.txt │ ├── cell-enrichment.txt │ ├── chip-seq.txt │ ├── clip-pe.txt │ ├── clrs.txt │ ├── dna.txt │ ├── filter.json │ ├── filter_mt.json │ ├── filter_nextera.json │ ├── filter_report.txt │ ├── fungal.txt │ ├── iso.txt │ ├── itag.txt │ ├── lfpe.txt │ ├── metagenome.txt │ ├── microtrans.txt │ ├── mtaa.txt │ ├── nextera-lmp.txt │ ├── plant-2x150.txt │ ├── plant-2x250.txt │ ├── rna.txt │ ├── rnawohuman.txt │ ├── sag.txt │ ├── smrna.txt │ ├── sop_list.txt │ └── viral-metagenome.txt ├── filter_param │ ├── 3primerna.config │ ├── bisulphite.config │ ├── cell-enrichment.config │ ├── chip-seq.config │ ├── clip-pe.config │ ├── clrs.config │ ├── dna.config │ ├── fungal.config │ ├── iso.config │ ├── itag.config │ ├── lfpe.config │ ├── metagenome.config │ ├── microtrans.config │ ├── mtaa.config │ ├── nextera-lmp.config │ ├── nextseq.config │ ├── plant-2x150.config │ ├── plant-2x250.config │ ├── rna.config │ ├── rnawohuman.config │ ├── sag.config │ ├── smrna.config │ └── viral-metagenome.config ├── images │ ├── JGI_logo.jpg │ ├── favicon.ico │ └── jgi_log_transparent.png ├── lib │ ├── common.py │ ├── html_utility.py │ ├── kmercount_pos.py │ ├── os_utility.py │ ├── readSeq.py │ ├── readqc_constants.py │ ├── readqc_report.py │ ├── readqc_utils.py │ ├── rqc_constants.py │ ├── rqc_fastq.py │ └── rqc_utility.py ├── readqc.py ├── template │ ├── filter_body_template.html │ ├── readqc_artifacts.html │ ├── readqc_body_template.html │ └── template.html └── tools │ └── patterN_fastq.pl ├── resources ├── 16S_15mers.fa ├── 16S_consensus_sequence.fa ├── 18S_15mers.fa ├── 18S_consensus_sequence.fa ├── 23S_15mers.fa ├── 23S_consensus_sequence.fa ├── 5S_10mers.fa ├── 5S_11mers.fa ├── 5S_12mers.fa ├── 5S_15mers.fa ├── 5S_9mers.fa ├── 5S_consensus_sequence.fa ├── Covid19_ref.fa ├── ITS_animal_consensus_sequence.fq ├── ITS_consensus_sequence.fq ├── ITS_fungi_consensus_sequence.fq ├── ITS_nonfungi_consensus_sequence.fq ├── ITS_other_consensus_sequence.fq ├── ITS_plant_consensus_sequence.fq ├── ITS_universal_consensus_sequence.fq ├── adapters.fa ├── adapters_no_transposase.fa.gz ├── artic3.fasta ├── blacklist_nt_merged.sketch ├── blacklist_prokprot_merged.sketch ├── blacklist_refseq_merged.sketch ├── blacklist_silva_merged.sketch ├── contents.txt ├── crelox.fa.gz ├── favicon.ico ├── kapatags.L40.fa ├── lambda.fa.gz ├── lfpe.linker.fa.gz ├── lsu_15mers.fa ├── m16S_consensus_sequence.fa ├── m18S_consensus_sequence.fa ├── model.pgm ├── mtst.fa ├── nextera.fa.gz ├── nextera_LMP_adapter.fa.gz ├── nextera_LMP_linker.fa.gz ├── p16S_consensus_sequence.fa ├── pJET1.2.fa ├── phix174_ill.ref.fa.gz ├── phix_adapters.fa.gz ├── polyA.fa.gz ├── primes.txt.gz ├── remote_files.txt ├── remote_files_old.txt ├── sample1.fq.gz ├── sample2.fq.gz ├── sequencing_artifacts.fa.gz ├── short.fa ├── ssu_15mers.fa ├── tRNA_10mers.fa ├── tRNA_11mers.fa ├── tRNA_15mers.fa ├── tRNA_16mers.fa ├── tRNA_consensus_sequence.fa ├── tax_server.html ├── truseq.fa.gz └── truseq_rna.fa.gz └── sh ├── a_sample_mt.sh ├── addadapters.sh ├── addssu.sh ├── adjusthomopolymers.sh ├── alltoall.sh ├── analyzeaccession.sh ├── analyzegenes.sh ├── analyzesketchresults.sh ├── applyvariants.sh ├── bbcms.sh ├── bbcountunique.sh ├── bbduk.sh ├── bbduk2.sh ├── bbest.sh ├── bbfakereads.sh ├── bbmap.sh ├── bbmapskimmer.sh ├── bbmask.sh ├── bbmerge-auto.sh ├── bbmerge.sh ├── bbnorm.sh ├── bbrealign.sh ├── bbrename.sh ├── bbsketch.sh ├── bbsplit.sh ├── bbsplitpairs.sh ├── bbstats.sh ├── bbversion.sh ├── bbwrap.sh ├── bloomfilter.sh ├── calcmem.sh ├── calctruequality.sh ├── callgenes.sh ├── callpeaks.sh ├── callvariants.sh ├── callvariants2.sh ├── clumpify.sh ├── commonkmers.sh ├── comparegff.sh ├── comparesketch.sh ├── comparessu.sh ├── comparevcf.sh ├── consect.sh ├── consensus.sh ├── countbarcodes.sh ├── countgc.sh ├── countsharedlines.sh ├── crossblock.sh ├── crosscontaminate.sh ├── current ├── cutgff.sh ├── cutprimers.sh ├── decontaminate.sh ├── dedupe.sh ├── dedupe2.sh ├── dedupebymapping.sh ├── demuxbyname.sh ├── diskbench.sh ├── ecc.sh ├── estherfilter.sh ├── explodetree.sh ├── fetchproks.sh ├── filterassemblysummary.sh ├── filterbarcodes.sh ├── filterbycoverage.sh ├── filterbyname.sh ├── filterbysequence.sh ├── filterbytaxa.sh ├── filterbytile.sh ├── filterlines.sh ├── filterqc.sh ├── filtersam.sh ├── filtersilva.sh ├── filtersubs.sh ├── filtervcf.sh ├── fixgaps.sh ├── fungalrelease.sh ├── fuse.sh ├── gbff2gff.sh ├── getreads.sh ├── gi2ancestors.sh ├── gi2taxid.sh ├── gitable.sh ├── grademerge.sh ├── gradesam.sh ├── icecreamfinder.sh ├── icecreamgrader.sh ├── icecreammaker.sh ├── idmatrix.sh ├── idtree.sh ├── invertkey.sh ├── kapastats.sh ├── kcompress.sh ├── keepbestcopy.sh ├── khist.sh ├── kmercountexact.sh ├── kmercountmulti.sh ├── kmercoverage.sh ├── kmerfilterset.sh ├── kmerlimit.sh ├── kmerlimit2.sh ├── kmerposition.sh ├── kmutate.sh ├── lilypad.sh ├── loadreads.sh ├── loglog.sh ├── makechimeras.sh ├── makecontaminatedgenomes.sh ├── makepolymers.sh ├── mapPacBio.sh ├── matrixtocolumns.sh ├── mergeOTUs.sh ├── mergebarcodes.sh ├── mergepgm.sh ├── mergeribo.sh ├── mergesam.sh ├── mergesketch.sh ├── mergesorted.sh ├── msa.sh ├── mutate.sh ├── muxbyname.sh ├── partition.sh ├── phylip2fasta.sh ├── pileup.sh ├── plotflowcell.sh ├── plotgc.sh ├── postfilter.sh ├── printtime.sh ├── processfrag.sh ├── processhi-c.sh ├── processspeed.sh ├── randomgenome.sh ├── randomreads.sh ├── readlength.sh ├── readqc.sh ├── reducesilva.sh ├── reformat.sh ├── reformatpb.sh ├── removebadbarcodes.sh ├── removecatdogmousehuman.sh ├── removehuman.sh ├── removehuman2.sh ├── removemicrobes.sh ├── removesmartbell.sh ├── rename.sh ├── renameimg.sh ├── repair.sh ├── replaceheaders.sh ├── representative.sh ├── rqcfilter.sh ├── rqcfilter2.sh ├── runhmm.sh ├── samtoroc.sh ├── seal.sh ├── sendsketch.sh ├── shred.sh ├── shrinkaccession.sh ├── shuffle.sh ├── shuffle2.sh ├── sketch.sh ├── sketchblacklist.sh ├── sketchblacklist2.sh ├── sortbyname.sh ├── sortbytaxa.sh ├── splitbytaxa.sh ├── splitnextera.sh ├── splitribo.sh ├── splitsam.sh ├── splitsam4way.sh ├── splitsam6way.sh ├── stats.sh ├── statswrapper.sh ├── streamsam.sh ├── subsketch.sh ├── summarizecontam.sh ├── summarizecoverage.sh ├── summarizecrossblock.sh ├── summarizemerge.sh ├── summarizequast.sh ├── summarizescafstats.sh ├── summarizeseal.sh ├── summarizesketch.sh ├── synthmda.sh ├── tadpipe.sh ├── tadpole.sh ├── tadwrapper.sh ├── taxonomy.sh ├── taxserver.sh ├── taxsize.sh ├── taxtree.sh ├── testfilesystem.sh ├── testformat.sh ├── testformat2.sh ├── tetramerfreq.sh ├── textfile.sh ├── translate6frames.sh ├── unicode2ascii.sh ├── unzip.sh ├── upd.sh ├── vcf2gff.sh └── webcheck.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioInfoTools/BBMap/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/BioInfoTools/BBMap/HEAD/README.md -------------------------------------------------------------------------------- /bbmap-help-Biostar.md: -------------------------------------------------------------------------------- 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