diff options
Diffstat (limited to 'biology/bbmap')
| -rw-r--r-- | biology/bbmap/Makefile | 6 | ||||
| -rw-r--r-- | biology/bbmap/distinfo | 6 | ||||
| -rw-r--r-- | biology/bbmap/pkg-plist | 476 |
3 files changed, 417 insertions, 71 deletions
diff --git a/biology/bbmap/Makefile b/biology/bbmap/Makefile index f9adfeb4db4f..533216187a45 100644 --- a/biology/bbmap/Makefile +++ b/biology/bbmap/Makefile @@ -1,5 +1,5 @@ PORTNAME= bbmap -DISTVERSION= 39.15 +DISTVERSION= 39.34 CATEGORIES= biology java MASTER_SITES= SF/bbmap/ DISTNAME= BBMap_${PORTVERSION} @@ -14,8 +14,8 @@ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt RUN_DEPENDS= bash:shells/bash \ - pigz:archivers/pigz \ - pbzip2:archivers/pbzip2 + pbzip2:archivers/pbzip2 \ + pigz:archivers/pigz USES= java shebangfix diff --git a/biology/bbmap/distinfo b/biology/bbmap/distinfo index 1bec09ddc1f9..c65e1b09d3ef 100644 --- a/biology/bbmap/distinfo +++ b/biology/bbmap/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1737030117 -SHA256 (BBMap_39.15.tar.gz) = b6698469a2a90f4930537c575ff1f70332f88a933dd5e286c83ea0ff30802344 -SIZE (BBMap_39.15.tar.gz) = 12498916 +TIMESTAMP = 1755776772 +SHA256 (BBMap_39.34.tar.gz) = c9c096c6ce3cc87da5607b731532bb9ac0aaebea2bd8fbf0a56e235968c4fbf4 +SIZE (BBMap_39.34.tar.gz) = 13743574 diff --git a/biology/bbmap/pkg-plist b/biology/bbmap/pkg-plist index 1515769118ae..6dc7649290c2 100644 --- a/biology/bbmap/pkg-plist +++ b/biology/bbmap/pkg-plist @@ -11,11 +11,14 @@ libexec/bbmap/a_sample_mt.sh libexec/bbmap/addadapters.sh libexec/bbmap/addssu.sh libexec/bbmap/adjusthomopolymers.sh +libexec/bbmap/alignrandom.sh libexec/bbmap/alltoall.sh libexec/bbmap/analyzeaccession.sh libexec/bbmap/analyzegenes.sh libexec/bbmap/analyzesketchresults.sh libexec/bbmap/applyvariants.sh +libexec/bbmap/bandedaligner.sh +libexec/bbmap/bandedplusaligner.sh libexec/bbmap/bbcms.sh libexec/bbmap/bbcountunique.sh libexec/bbmap/bbcrisprfinder.sh @@ -45,8 +48,10 @@ libexec/bbmap/callgenes.sh libexec/bbmap/callpeaks.sh libexec/bbmap/callvariants.sh libexec/bbmap/callvariants2.sh +libexec/bbmap/cat.sh libexec/bbmap/cg2illumina.sh libexec/bbmap/checkstrand.sh +libexec/bbmap/cladeloader.sh libexec/bbmap/clumpify.sh libexec/bbmap/commonkmers.sh libexec/bbmap/comparegff.sh @@ -64,6 +69,7 @@ libexec/bbmap/countgc.sh libexec/bbmap/countsharedlines.sh libexec/bbmap/crossblock.sh libexec/bbmap/crosscontaminate.sh +libexec/bbmap/crosscutaligner.sh libexec/bbmap/cutgff.sh libexec/bbmap/cutprimers.sh libexec/bbmap/decontaminate.sh @@ -73,6 +79,8 @@ libexec/bbmap/dedupebymapping.sh libexec/bbmap/demuxbyname.sh libexec/bbmap/demuxserver.sh libexec/bbmap/diskbench.sh +libexec/bbmap/driftingaligner.sh +libexec/bbmap/driftingplusaligner.sh libexec/bbmap/estherfilter.sh libexec/bbmap/explodetree.sh libexec/bbmap/fetchproks.sh @@ -98,6 +106,8 @@ libexec/bbmap/getreads.sh libexec/bbmap/gi2ancestors.sh libexec/bbmap/gi2taxid.sh libexec/bbmap/gitable.sh +libexec/bbmap/glocalaligner.sh +libexec/bbmap/gradebins.sh libexec/bbmap/grademerge.sh libexec/bbmap/gradesam.sh libexec/bbmap/icecreamfinder.sh @@ -105,7 +115,9 @@ libexec/bbmap/icecreamgrader.sh libexec/bbmap/icecreammaker.sh libexec/bbmap/idmatrix.sh libexec/bbmap/idtree.sh +libexec/bbmap/indelfree.sh libexec/bbmap/invertkey.sh +libexec/bbmap/javasetup.sh libexec/bbmap/kapastats.sh libexec/bbmap/kcompress.sh libexec/bbmap/keepbestcopy.sh @@ -124,8 +136,10 @@ libexec/bbmap/loglog.sh libexec/bbmap/makechimeras.sh libexec/bbmap/makecontaminatedgenomes.sh libexec/bbmap/makepolymers.sh +libexec/bbmap/makequickbinvector.sh libexec/bbmap/mapPacBio.sh libexec/bbmap/matrixtocolumns.sh +libexec/bbmap/memdetect.sh libexec/bbmap/mergeOTUs.sh libexec/bbmap/mergebarcodes.sh libexec/bbmap/mergepgm.sh @@ -133,6 +147,7 @@ libexec/bbmap/mergeribo.sh libexec/bbmap/mergesam.sh libexec/bbmap/mergesketch.sh libexec/bbmap/mergesorted.sh +libexec/bbmap/microalign.sh libexec/bbmap/msa.sh libexec/bbmap/mutate.sh libexec/bbmap/muxbyname.sh @@ -153,11 +168,16 @@ libexec/bbmap/printtime.sh libexec/bbmap/processfrag.sh libexec/bbmap/processhi-c.sh libexec/bbmap/processspeed.sh +libexec/bbmap/quabblealigner.sh +libexec/bbmap/quantumaligner.sh libexec/bbmap/quickbin.sh +libexec/bbmap/quickclade.sh libexec/bbmap/randomgenome.sh libexec/bbmap/randomreads.sh +libexec/bbmap/randomreadsmg.sh libexec/bbmap/readlength.sh libexec/bbmap/readqc.sh +libexec/bbmap/reducecolumns.sh libexec/bbmap/reducesilva.sh libexec/bbmap/reformat.sh libexec/bbmap/reformatpb.sh @@ -168,7 +188,10 @@ libexec/bbmap/removehuman2.sh libexec/bbmap/removemicrobes.sh libexec/bbmap/removesmartbell.sh libexec/bbmap/rename.sh +libexec/bbmap/renamebymapping.sh +libexec/bbmap/renamebysketch.sh libexec/bbmap/renameimg.sh +libexec/bbmap/renameref.sh libexec/bbmap/repair.sh libexec/bbmap/replaceheaders.sh libexec/bbmap/representative.sh @@ -195,6 +218,7 @@ libexec/bbmap/splitsam.sh libexec/bbmap/splitsam4way.sh libexec/bbmap/splitsam6way.sh libexec/bbmap/stats.sh +libexec/bbmap/stats3.sh libexec/bbmap/statswrapper.sh libexec/bbmap/streamsam.sh libexec/bbmap/subsketch.sh @@ -215,6 +239,8 @@ libexec/bbmap/taxonomy.sh libexec/bbmap/taxserver.sh libexec/bbmap/taxsize.sh libexec/bbmap/taxtree.sh +libexec/bbmap/testaligners.sh +libexec/bbmap/testaligners2.sh libexec/bbmap/testfilesystem.sh libexec/bbmap/testformat.sh libexec/bbmap/testformat2.sh @@ -227,7 +253,11 @@ libexec/bbmap/trimcontigs.sh libexec/bbmap/unicode2ascii.sh libexec/bbmap/unzip.sh libexec/bbmap/vcf2gff.sh +libexec/bbmap/visualizealignment.sh +libexec/bbmap/wavefrontaligner.sh libexec/bbmap/webcheck.sh +libexec/bbmap/wobblealigner.sh +libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/align2/AbstractIndex.class %%JAVAJARDIR%%/bbmap/align2/AbstractIndex.java %%JAVAJARDIR%%/bbmap/align2/AbstractMapThread.class @@ -348,9 +378,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/align2/QuadHeap.java %%JAVAJARDIR%%/bbmap/align2/QualityTools.class %%JAVAJARDIR%%/bbmap/align2/QualityTools.java -%%JAVAJARDIR%%/bbmap/align2/RandomReads3$1.class -%%JAVAJARDIR%%/bbmap/align2/RandomReads3.class -%%JAVAJARDIR%%/bbmap/align2/RandomReads3.java +%%JAVAJARDIR%%/bbmap/align2/README.md %%JAVAJARDIR%%/bbmap/align2/RefToIndex.class %%JAVAJARDIR%%/bbmap/align2/RefToIndex.java %%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput.class @@ -363,6 +391,9 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/align2/SplitMappedReads.java %%JAVAJARDIR%%/bbmap/align2/TranslateColorspaceRead.class %%JAVAJARDIR%%/bbmap/align2/TranslateColorspaceRead.java +%%JAVAJARDIR%%/bbmap/aligner/AlignRandom$1.class +%%JAVAJARDIR%%/bbmap/aligner/AlignRandom.class +%%JAVAJARDIR%%/bbmap/aligner/AlignRandom.java %%JAVAJARDIR%%/bbmap/aligner/Aligner.class %%JAVAJARDIR%%/bbmap/aligner/Aligner.java %%JAVAJARDIR%%/bbmap/aligner/Alignment.class @@ -372,10 +403,84 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/aligner/AllToAll$ProcessThread.class %%JAVAJARDIR%%/bbmap/aligner/AllToAll.class %%JAVAJARDIR%%/bbmap/aligner/AllToAll.java +%%JAVAJARDIR%%/bbmap/aligner/BandedAligner.class +%%JAVAJARDIR%%/bbmap/aligner/BandedAligner.java +%%JAVAJARDIR%%/bbmap/aligner/BandedAlignerConcise.class +%%JAVAJARDIR%%/bbmap/aligner/BandedAlignerConcise.java +%%JAVAJARDIR%%/bbmap/aligner/BandedAlignerInt.class +%%JAVAJARDIR%%/bbmap/aligner/BandedAlignerInt.java +%%JAVAJARDIR%%/bbmap/aligner/BandedAlignerM.class +%%JAVAJARDIR%%/bbmap/aligner/BandedAlignerM.java +%%JAVAJARDIR%%/bbmap/aligner/BandedByteAligner.class +%%JAVAJARDIR%%/bbmap/aligner/BandedByteAligner.java +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAligner.class +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAligner.java +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAligner2.class +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAligner2.java +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAligner3.class +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAligner3.java +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAlignerInt.class +%%JAVAJARDIR%%/bbmap/aligner/BandedPlusAlignerInt.java +%%JAVAJARDIR%%/bbmap/aligner/ClippingTest.class +%%JAVAJARDIR%%/bbmap/aligner/ClippingTest.java +%%JAVAJARDIR%%/bbmap/aligner/CrossCutAligner.class +%%JAVAJARDIR%%/bbmap/aligner/CrossCutAligner.java +%%JAVAJARDIR%%/bbmap/aligner/DiagonalAligner$ExtzResult.class +%%JAVAJARDIR%%/bbmap/aligner/DiagonalAligner.class +%%JAVAJARDIR%%/bbmap/aligner/DiagonalAligner.java +%%JAVAJARDIR%%/bbmap/aligner/DriftingAligner.class +%%JAVAJARDIR%%/bbmap/aligner/DriftingAligner.java +%%JAVAJARDIR%%/bbmap/aligner/DriftingAlignerConcise.class +%%JAVAJARDIR%%/bbmap/aligner/DriftingAlignerConcise.java +%%JAVAJARDIR%%/bbmap/aligner/DriftingAlignerM.class +%%JAVAJARDIR%%/bbmap/aligner/DriftingAlignerM.java +%%JAVAJARDIR%%/bbmap/aligner/DriftingPlusAligner.class +%%JAVAJARDIR%%/bbmap/aligner/DriftingPlusAligner.java +%%JAVAJARDIR%%/bbmap/aligner/DriftingPlusAligner2.class +%%JAVAJARDIR%%/bbmap/aligner/DriftingPlusAligner2.java +%%JAVAJARDIR%%/bbmap/aligner/DriftingPlusAligner3.class +%%JAVAJARDIR%%/bbmap/aligner/DriftingPlusAligner3.java +%%JAVAJARDIR%%/bbmap/aligner/Eh.class +%%JAVAJARDIR%%/bbmap/aligner/Factory.class +%%JAVAJARDIR%%/bbmap/aligner/Factory.java %%JAVAJARDIR%%/bbmap/aligner/FlatAligner.class %%JAVAJARDIR%%/bbmap/aligner/FlatAligner.java %%JAVAJARDIR%%/bbmap/aligner/FlatAligner2.class %%JAVAJARDIR%%/bbmap/aligner/FlatAligner2.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalAligner.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalAligner.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalAlignerConcise.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalAlignerConcise.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalAlignerInt.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalAlignerInt.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalAlignerOld.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalAlignerOld.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner2.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner2.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner3.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner3.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner4.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner4.java +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner5.class +%%JAVAJARDIR%%/bbmap/aligner/GlocalPlusAligner5.java +%%JAVAJARDIR%%/bbmap/aligner/IDAligner.class +%%JAVAJARDIR%%/bbmap/aligner/IDAligner.java +%%JAVAJARDIR%%/bbmap/aligner/IndelFreeAligner$ProcessThread.class +%%JAVAJARDIR%%/bbmap/aligner/IndelFreeAligner.class +%%JAVAJARDIR%%/bbmap/aligner/IndelFreeAligner.java +%%JAVAJARDIR%%/bbmap/aligner/IntIndex.class +%%JAVAJARDIR%%/bbmap/aligner/IntIndex.java +%%JAVAJARDIR%%/bbmap/aligner/IntListAligner.class +%%JAVAJARDIR%%/bbmap/aligner/IntListAligner.java +%%JAVAJARDIR%%/bbmap/aligner/Ksw2gg$Cell.class +%%JAVAJARDIR%%/bbmap/aligner/Ksw2gg.class +%%JAVAJARDIR%%/bbmap/aligner/Ksw2gg.java +%%JAVAJARDIR%%/bbmap/aligner/KswGgJava.class +%%JAVAJARDIR%%/bbmap/aligner/KswGgJava.java +%%JAVAJARDIR%%/bbmap/aligner/MSAViz.class +%%JAVAJARDIR%%/bbmap/aligner/MSAViz.java %%JAVAJARDIR%%/bbmap/aligner/MicroAligner.class %%JAVAJARDIR%%/bbmap/aligner/MicroAligner.java %%JAVAJARDIR%%/bbmap/aligner/MicroAligner2.class @@ -384,6 +489,13 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/aligner/MicroAligner3.java %%JAVAJARDIR%%/bbmap/aligner/MicroIndex3.class %%JAVAJARDIR%%/bbmap/aligner/MicroIndex3.java +%%JAVAJARDIR%%/bbmap/aligner/MicroWrapper$ProcessThread.class +%%JAVAJARDIR%%/bbmap/aligner/MicroWrapper.class +%%JAVAJARDIR%%/bbmap/aligner/MicroWrapper.java +%%JAVAJARDIR%%/bbmap/aligner/MinHitsCalculator.class +%%JAVAJARDIR%%/bbmap/aligner/MinHitsCalculator.java +%%JAVAJARDIR%%/bbmap/aligner/MinHitsCalculatorOld.class +%%JAVAJARDIR%%/bbmap/aligner/MinHitsCalculatorOld.java %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter.class %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter.java %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter2.class @@ -392,6 +504,35 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter3.java %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.class %%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.java +%%JAVAJARDIR%%/bbmap/aligner/Parallelogram.class +%%JAVAJARDIR%%/bbmap/aligner/Parallelogram.java +%%JAVAJARDIR%%/bbmap/aligner/QuabbleAligner.class +%%JAVAJARDIR%%/bbmap/aligner/QuabbleAligner.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumAligner.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumAligner.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerConcise.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerConcise.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerConcise2.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerConcise2.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerM.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerM.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerQC.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumAlignerQC.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner2.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner2.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner3.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner3.java +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner4.class +%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner4.java +%%JAVAJARDIR%%/bbmap/aligner/Query.class +%%JAVAJARDIR%%/bbmap/aligner/Query.java +%%JAVAJARDIR%%/bbmap/aligner/README.md +%%JAVAJARDIR%%/bbmap/aligner/RelativeAligner.class +%%JAVAJARDIR%%/bbmap/aligner/RelativeAligner.java +%%JAVAJARDIR%%/bbmap/aligner/ScrabbleAligner.class +%%JAVAJARDIR%%/bbmap/aligner/ScrabbleAligner.java %%JAVAJARDIR%%/bbmap/aligner/SideChannel3.class %%JAVAJARDIR%%/bbmap/aligner/SideChannel3.java %%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat.class @@ -408,6 +549,39 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlatFloat.java %%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerPacBioAdapter.class %%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerPacBioAdapter.java +%%JAVAJARDIR%%/bbmap/aligner/Test$Runner.class +%%JAVAJARDIR%%/bbmap/aligner/Test.class +%%JAVAJARDIR%%/bbmap/aligner/Test.java +%%JAVAJARDIR%%/bbmap/aligner/TestAlignerSuite$Job.class +%%JAVAJARDIR%%/bbmap/aligner/TestAlignerSuite$Worker.class +%%JAVAJARDIR%%/bbmap/aligner/TestAlignerSuite.class +%%JAVAJARDIR%%/bbmap/aligner/TestAlignerSuite.java +%%JAVAJARDIR%%/bbmap/aligner/VisualizationConverter.class +%%JAVAJARDIR%%/bbmap/aligner/VisualizationConverter.java +%%JAVAJARDIR%%/bbmap/aligner/Visualizer.class +%%JAVAJARDIR%%/bbmap/aligner/Visualizer.java +%%JAVAJARDIR%%/bbmap/aligner/WaveFrontAligner.class +%%JAVAJARDIR%%/bbmap/aligner/WaveFrontAligner.java +%%JAVAJARDIR%%/bbmap/aligner/WaveFrontAligner2.class +%%JAVAJARDIR%%/bbmap/aligner/WaveFrontAligner2.java +%%JAVAJARDIR%%/bbmap/aligner/WaveFrontAlignerViz.class +%%JAVAJARDIR%%/bbmap/aligner/WaveFrontAlignerViz.java +%%JAVAJARDIR%%/bbmap/aligner/WobbleAligner.class +%%JAVAJARDIR%%/bbmap/aligner/WobbleAligner.java +%%JAVAJARDIR%%/bbmap/aligner/WobbleAlignerConcise.class +%%JAVAJARDIR%%/bbmap/aligner/WobbleAlignerConcise.java +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner.class +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner.java +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner2.class +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner2.java +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner3.class +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner3.java +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner4.class +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner4.java +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner5.class +%%JAVAJARDIR%%/bbmap/aligner/WobblePlusAligner5.java +%%JAVAJARDIR%%/bbmap/aligner/XDropHAligner.class +%%JAVAJARDIR%%/bbmap/aligner/XDropHAligner.java %%JAVAJARDIR%%/bbmap/assemble/AbstractBuildThread.class %%JAVAJARDIR%%/bbmap/assemble/AbstractBuildThread.java %%JAVAJARDIR%%/bbmap/assemble/AbstractExploreThread.class @@ -433,6 +607,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/assemble/KmerCompressor.java %%JAVAJARDIR%%/bbmap/assemble/Postfilter.class %%JAVAJARDIR%%/bbmap/assemble/Postfilter.java +%%JAVAJARDIR%%/bbmap/assemble/README.md %%JAVAJARDIR%%/bbmap/assemble/Rollback.class %%JAVAJARDIR%%/bbmap/assemble/Rollback.java %%JAVAJARDIR%%/bbmap/assemble/ShaveObject.class @@ -508,6 +683,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist$PopThread.class %%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist.class %%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist.java +%%JAVAJARDIR%%/bbmap/barcode/README.md %%JAVAJARDIR%%/bbmap/barcode/TagAndMerge.class %%JAVAJARDIR%%/bbmap/barcode/TagAndMerge.java %%JAVAJARDIR%%/bbmap/barcode/Transition.class @@ -520,40 +696,124 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixTile.java %%JAVAJARDIR%%/bbmap/bbmin/Minimizer.class %%JAVAJARDIR%%/bbmap/bbmin/Minimizer.java +%%JAVAJARDIR%%/bbmap/bbmin/README.md +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$EnsembleRefinerParams.class +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$EvidenceRefinerParams.class +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$GraphRefinerParams.class +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$RefinerParams.class +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner.class +%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner.java +%%JAVAJARDIR%%/bbmap/bin/AdjustEntropy.class +%%JAVAJARDIR%%/bbmap/bin/AdjustEntropy.java +%%JAVAJARDIR%%/bbmap/bin/AllToAllVectorMaker.class +%%JAVAJARDIR%%/bbmap/bin/AllToAllVectorMaker.java %%JAVAJARDIR%%/bbmap/bin/Bin.class %%JAVAJARDIR%%/bbmap/bin/Bin.java +%%JAVAJARDIR%%/bbmap/bin/BinComparator.class +%%JAVAJARDIR%%/bbmap/bin/BinComparator.java +%%JAVAJARDIR%%/bbmap/bin/BinMap.class +%%JAVAJARDIR%%/bbmap/bin/BinMap.java %%JAVAJARDIR%%/bbmap/bin/BinObject.class %%JAVAJARDIR%%/bbmap/bin/BinObject.java %%JAVAJARDIR%%/bbmap/bin/BinSketcher$ProcessThread.class %%JAVAJARDIR%%/bbmap/bin/BinSketcher.class %%JAVAJARDIR%%/bbmap/bin/BinSketcher.java +%%JAVAJARDIR%%/bbmap/bin/BinStats.class +%%JAVAJARDIR%%/bbmap/bin/BinStats.java +%%JAVAJARDIR%%/bbmap/bin/BinStatsComparator.class +%%JAVAJARDIR%%/bbmap/bin/BinStatsComparator.java +%%JAVAJARDIR%%/bbmap/bin/Binner$CompareThread.class %%JAVAJARDIR%%/bbmap/bin/Binner.class %%JAVAJARDIR%%/bbmap/bin/Binner.java +%%JAVAJARDIR%%/bbmap/bin/ChartMaker.class +%%JAVAJARDIR%%/bbmap/bin/ChartMaker.java +%%JAVAJARDIR%%/bbmap/bin/Clade.class +%%JAVAJARDIR%%/bbmap/bin/Clade.java +%%JAVAJARDIR%%/bbmap/bin/CladeIndex.class +%%JAVAJARDIR%%/bbmap/bin/CladeIndex.java +%%JAVAJARDIR%%/bbmap/bin/CladeLoader$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bin/CladeLoader.class +%%JAVAJARDIR%%/bbmap/bin/CladeLoader.java +%%JAVAJARDIR%%/bbmap/bin/CladeLoaderMF$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bin/CladeLoaderMF.class +%%JAVAJARDIR%%/bbmap/bin/CladeLoaderMF.java +%%JAVAJARDIR%%/bbmap/bin/CladeSearcher$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bin/CladeSearcher.class +%%JAVAJARDIR%%/bbmap/bin/CladeSearcher.java %%JAVAJARDIR%%/bbmap/bin/Cluster.class %%JAVAJARDIR%%/bbmap/bin/Cluster.java +%%JAVAJARDIR%%/bbmap/bin/Comparison.class +%%JAVAJARDIR%%/bbmap/bin/Comparison.java +%%JAVAJARDIR%%/bbmap/bin/ComparisonHeap$WorstFirstComparator.class +%%JAVAJARDIR%%/bbmap/bin/ComparisonHeap.class +%%JAVAJARDIR%%/bbmap/bin/ComparisonHeap.java +%%JAVAJARDIR%%/bbmap/bin/ConservationModel.class +%%JAVAJARDIR%%/bbmap/bin/ConservationModel.java +%%JAVAJARDIR%%/bbmap/bin/Contig$ContigIterator.class %%JAVAJARDIR%%/bbmap/bin/Contig.class %%JAVAJARDIR%%/bbmap/bin/Contig.java %%JAVAJARDIR%%/bbmap/bin/ContigRenamer$ProcessThread.class %%JAVAJARDIR%%/bbmap/bin/ContigRenamer$Scaf.class %%JAVAJARDIR%%/bbmap/bin/ContigRenamer.class %%JAVAJARDIR%%/bbmap/bin/ContigRenamer.java +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber$Centroid.class +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber.class +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber.java +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber2$Centroid.class +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber2.class +%%JAVAJARDIR%%/bbmap/bin/CrystalChamber2.java %%JAVAJARDIR%%/bbmap/bin/DataLoader.class %%JAVAJARDIR%%/bbmap/bin/DataLoader.java +%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner$ConsensusResult.class +%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner$RefinerResult.class +%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner.class +%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner.java +%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner$ContigStatus.class +%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner$DBSCANResult.class +%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner.class +%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner.java %%JAVAJARDIR%%/bbmap/bin/FileRenamer.class %%JAVAJARDIR%%/bbmap/bin/FileRenamer.java +%%JAVAJARDIR%%/bbmap/bin/GTDBLine.class +%%JAVAJARDIR%%/bbmap/bin/GTDBLine.java +%%JAVAJARDIR%%/bbmap/bin/GeneTools.class +%%JAVAJARDIR%%/bbmap/bin/GeneTools.java +%%JAVAJARDIR%%/bbmap/bin/GradeBins$CCLine.class +%%JAVAJARDIR%%/bbmap/bin/GradeBins$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bin/GradeBins.class +%%JAVAJARDIR%%/bbmap/bin/GradeBins.java +%%JAVAJARDIR%%/bbmap/bin/GraphRefiner$SimilarityGraph$Edge.class +%%JAVAJARDIR%%/bbmap/bin/GraphRefiner$SimilarityGraph.class +%%JAVAJARDIR%%/bbmap/bin/GraphRefiner.class +%%JAVAJARDIR%%/bbmap/bin/GraphRefiner.java +%%JAVAJARDIR%%/bbmap/bin/IDComparator.class +%%JAVAJARDIR%%/bbmap/bin/IDComparator.java +%%JAVAJARDIR%%/bbmap/bin/Key.class +%%JAVAJARDIR%%/bbmap/bin/Key.java +%%JAVAJARDIR%%/bbmap/bin/KeyValue.class +%%JAVAJARDIR%%/bbmap/bin/KeyValue.java +%%JAVAJARDIR%%/bbmap/bin/KmerProb.class +%%JAVAJARDIR%%/bbmap/bin/KmerProb.java +%%JAVAJARDIR%%/bbmap/bin/Oracle.class +%%JAVAJARDIR%%/bbmap/bin/Oracle.java %%JAVAJARDIR%%/bbmap/bin/QuickBin$ProcessThread.class %%JAVAJARDIR%%/bbmap/bin/QuickBin.class %%JAVAJARDIR%%/bbmap/bin/QuickBin.java -%%JAVAJARDIR%%/bbmap/bin/RandomReadsMG$Genome.class -%%JAVAJARDIR%%/bbmap/bin/RandomReadsMG$ProcessThread.class -%%JAVAJARDIR%%/bbmap/bin/RandomReadsMG.class -%%JAVAJARDIR%%/bbmap/bin/RandomReadsMG.java +%%JAVAJARDIR%%/bbmap/bin/README.md +%%JAVAJARDIR%%/bbmap/bin/SamLoader$LoadThread.class +%%JAVAJARDIR%%/bbmap/bin/SamLoader.class +%%JAVAJARDIR%%/bbmap/bin/SamLoader.java +%%JAVAJARDIR%%/bbmap/bin/ScoreComparator.class +%%JAVAJARDIR%%/bbmap/bin/ScoreComparator.java %%JAVAJARDIR%%/bbmap/bin/SimilarityMeasures.class %%JAVAJARDIR%%/bbmap/bin/SimilarityMeasures.java %%JAVAJARDIR%%/bbmap/bin/SketchRecord.class %%JAVAJARDIR%%/bbmap/bin/SketchRecord.java %%JAVAJARDIR%%/bbmap/bin/Sketchable.class %%JAVAJARDIR%%/bbmap/bin/Sketchable.java +%%JAVAJARDIR%%/bbmap/bin/SpectraCounter$LoadThread.class +%%JAVAJARDIR%%/bbmap/bin/SpectraCounter.class +%%JAVAJARDIR%%/bbmap/bin/SpectraCounter.java %%JAVAJARDIR%%/bbmap/bloom/BloomFilter.class %%JAVAJARDIR%%/bbmap/bloom/BloomFilter.java %%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrector.class @@ -616,6 +876,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/bloom/PolyFilter$ProcessThread.class %%JAVAJARDIR%%/bbmap/bloom/PolyFilter.class %%JAVAJARDIR%%/bbmap/bloom/PolyFilter.java +%%JAVAJARDIR%%/bbmap/bloom/README.md %%JAVAJARDIR%%/bbmap/bloom/ReadCounter$1.class %%JAVAJARDIR%%/bbmap/bloom/ReadCounter$CountThread.class %%JAVAJARDIR%%/bbmap/bloom/ReadCounter.class @@ -651,6 +912,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/cardinality/LogLog_old.java %%JAVAJARDIR%%/bbmap/cardinality/MultiLogLog.class %%JAVAJARDIR%%/bbmap/cardinality/MultiLogLog.java +%%JAVAJARDIR%%/bbmap/cardinality/README.md %%JAVAJARDIR%%/bbmap/clump/Clump.class %%JAVAJARDIR%%/bbmap/clump/Clump.java %%JAVAJARDIR%%/bbmap/clump/ClumpList$ClumpThread.class @@ -693,6 +955,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/clump/PivotSet$HashThread.class %%JAVAJARDIR%%/bbmap/clump/PivotSet.class %%JAVAJARDIR%%/bbmap/clump/PivotSet.java +%%JAVAJARDIR%%/bbmap/clump/README.md %%JAVAJARDIR%%/bbmap/clump/ReadKey.class %%JAVAJARDIR%%/bbmap/clump/ReadKey.java %%JAVAJARDIR%%/bbmap/clump/Splitter.class @@ -705,6 +968,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/cluster/ClusterTools.java %%JAVAJARDIR%%/bbmap/cluster/MergeReadHeaders.class %%JAVAJARDIR%%/bbmap/cluster/MergeReadHeaders.java +%%JAVAJARDIR%%/bbmap/cluster/README.md %%JAVAJARDIR%%/bbmap/cluster/ReadTag.class %%JAVAJARDIR%%/bbmap/cluster/ReadTag.java %%JAVAJARDIR%%/bbmap/cluster/ReclusterByKmer$ClusterThread.class @@ -730,6 +994,8 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/consensus/Lilypad$ProcessThread.class %%JAVAJARDIR%%/bbmap/consensus/Lilypad.class %%JAVAJARDIR%%/bbmap/consensus/Lilypad.java +%%JAVAJARDIR%%/bbmap/consensus/README.md +%%JAVAJARDIR%%/bbmap/covid/README.md %%JAVAJARDIR%%/bbmap/covid/SummarizeCoverage.class %%JAVAJARDIR%%/bbmap/covid/SummarizeCoverage.java %%JAVAJARDIR%%/bbmap/dna/AminoAcid.class @@ -762,6 +1028,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/dna/MotifProbsN.java %%JAVAJARDIR%%/bbmap/dna/MotifSimple.class %%JAVAJARDIR%%/bbmap/dna/MotifSimple.java +%%JAVAJARDIR%%/bbmap/dna/README.md %%JAVAJARDIR%%/bbmap/dna/ScafLoc.class %%JAVAJARDIR%%/bbmap/dna/ScafLoc.java %%JAVAJARDIR%%/bbmap/dna/Scaffold.class @@ -853,6 +1120,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/driver/ProcessSpeed2.java %%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.class %%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.java +%%JAVAJARDIR%%/bbmap/driver/README.md %%JAVAJARDIR%%/bbmap/driver/ReduceSilva.class %%JAVAJARDIR%%/bbmap/driver/ReduceSilva.java %%JAVAJARDIR%%/bbmap/driver/RenameAndMux$MuxThread.class @@ -928,6 +1196,8 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/fileIO/ChainLine.java %%JAVAJARDIR%%/bbmap/fileIO/CompressFiles.class %%JAVAJARDIR%%/bbmap/fileIO/CompressFiles.java +%%JAVAJARDIR%%/bbmap/fileIO/Concatenate.class +%%JAVAJARDIR%%/bbmap/fileIO/Concatenate.java %%JAVAJARDIR%%/bbmap/fileIO/CopyFile$1.class %%JAVAJARDIR%%/bbmap/fileIO/CopyFile.class %%JAVAJARDIR%%/bbmap/fileIO/CopyFile.java @@ -951,6 +1221,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/fileIO/PipeThread.java %%JAVAJARDIR%%/bbmap/fileIO/QuickFile.class %%JAVAJARDIR%%/bbmap/fileIO/QuickFile.java +%%JAVAJARDIR%%/bbmap/fileIO/README.md %%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$1.class %%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$WriteObjectThread.class %%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$WriteStringThread.class @@ -973,6 +1244,11 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/fun/DiskBench$WriteThread.class %%JAVAJARDIR%%/bbmap/fun/DiskBench.class %%JAVAJARDIR%%/bbmap/fun/DiskBench.java +%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer$1.class +%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer$2.class +%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer$DirSize.class +%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer.class +%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer.java %%JAVAJARDIR%%/bbmap/fun/Dongle.class %%JAVAJARDIR%%/bbmap/fun/Dongle.java %%JAVAJARDIR%%/bbmap/fun/FindPath$Edge.class @@ -1016,12 +1292,15 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/fun/Palindrome2$Drome.class %%JAVAJARDIR%%/bbmap/fun/Palindrome2.class %%JAVAJARDIR%%/bbmap/fun/Palindrome2.java +%%JAVAJARDIR%%/bbmap/fun/ParseDouble.class +%%JAVAJARDIR%%/bbmap/fun/ParseDouble.java %%JAVAJARDIR%%/bbmap/fun/ProbShared.class %%JAVAJARDIR%%/bbmap/fun/ProbShared.java %%JAVAJARDIR%%/bbmap/fun/ProbShared2.class %%JAVAJARDIR%%/bbmap/fun/ProbShared2.java %%JAVAJARDIR%%/bbmap/fun/ProbShared3.class %%JAVAJARDIR%%/bbmap/fun/ProbShared3.java +%%JAVAJARDIR%%/bbmap/fun/README.md %%JAVAJARDIR%%/bbmap/gff/CompareGff.class %%JAVAJARDIR%%/bbmap/gff/CompareGff.java %%JAVAJARDIR%%/bbmap/gff/CompareGff_old.class @@ -1039,8 +1318,11 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/gff/GbffLocus.java %%JAVAJARDIR%%/bbmap/gff/GffLine.class %%JAVAJARDIR%%/bbmap/gff/GffLine.java +%%JAVAJARDIR%%/bbmap/gff/GtfLine.class +%%JAVAJARDIR%%/bbmap/gff/GtfLine.java %%JAVAJARDIR%%/bbmap/gff/ParseCrispr.class %%JAVAJARDIR%%/bbmap/gff/ParseCrispr.java +%%JAVAJARDIR%%/bbmap/gff/README.md %%JAVAJARDIR%%/bbmap/gff/VcfToGff$1.class %%JAVAJARDIR%%/bbmap/gff/VcfToGff.class %%JAVAJARDIR%%/bbmap/gff/VcfToGff.java @@ -1075,6 +1357,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/hiseq/PlotHist.java %%JAVAJARDIR%%/bbmap/hiseq/PlotReadPosition.class %%JAVAJARDIR%%/bbmap/hiseq/PlotReadPosition.java +%%JAVAJARDIR%%/bbmap/hiseq/README.md %%JAVAJARDIR%%/bbmap/hiseq/ReadHeaderParser.class %%JAVAJARDIR%%/bbmap/hiseq/ReadHeaderParser.java %%JAVAJARDIR%%/bbmap/hiseq/Tile.class @@ -1087,6 +1370,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/hmm/HMMSearchReport.java %%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.class %%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.java +%%JAVAJARDIR%%/bbmap/hmm/README.md %%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.class %%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.java %%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJNI.class @@ -1105,6 +1389,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/icecream/PBHeader.java %%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.class %%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.java +%%JAVAJARDIR%%/bbmap/icecream/README.md %%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.class %%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.java %%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio$ProcessThread.class @@ -1114,49 +1399,22 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/icecream/ZMW.java %%JAVAJARDIR%%/bbmap/icecream/ZMWStreamer.class %%JAVAJARDIR%%/bbmap/icecream/ZMWStreamer.java -%%JAVAJARDIR%%/bbmap/jasper/Comparison.class -%%JAVAJARDIR%%/bbmap/jasper/Comparison.java -%%JAVAJARDIR%%/bbmap/jasper/DenseSimilarityMatrix.class -%%JAVAJARDIR%%/bbmap/jasper/DenseSimilarityMatrix.java -%%JAVAJARDIR%%/bbmap/jasper/DenseTree.class -%%JAVAJARDIR%%/bbmap/jasper/DenseTree.java -%%JAVAJARDIR%%/bbmap/jasper/DenseTreeValidate.class -%%JAVAJARDIR%%/bbmap/jasper/DenseTreeValidate.java %%JAVAJARDIR%%/bbmap/jasper/KmerPosition.class %%JAVAJARDIR%%/bbmap/jasper/KmerPosition.java %%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.class %%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.java -%%JAVAJARDIR%%/bbmap/jasper/NCBIComparison.class -%%JAVAJARDIR%%/bbmap/jasper/NCBIComparison.java -%%JAVAJARDIR%%/bbmap/jasper/NCBISparseSimilarityMatrix.class -%%JAVAJARDIR%%/bbmap/jasper/NCBISparseSimilarityMatrix.java -%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTree.class -%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTree.java -%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTreeValidate.class -%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTreeValidate.java -%%JAVAJARDIR%%/bbmap/jasper/NCBITreeNode.class -%%JAVAJARDIR%%/bbmap/jasper/NCBITreeNode.java -%%JAVAJARDIR%%/bbmap/jasper/Organism.class -%%JAVAJARDIR%%/bbmap/jasper/Organism.java -%%JAVAJARDIR%%/bbmap/jasper/SimilarityMatrix.class -%%JAVAJARDIR%%/bbmap/jasper/SimilarityMatrix.java -%%JAVAJARDIR%%/bbmap/jasper/SparseSimilarityMatrix.class -%%JAVAJARDIR%%/bbmap/jasper/SparseSimilarityMatrix.java -%%JAVAJARDIR%%/bbmap/jasper/SparseTree.class -%%JAVAJARDIR%%/bbmap/jasper/SparseTree.java -%%JAVAJARDIR%%/bbmap/jasper/SparseTreeValidate.class -%%JAVAJARDIR%%/bbmap/jasper/SparseTreeValidate.java -%%JAVAJARDIR%%/bbmap/jasper/TaxCompare.class -%%JAVAJARDIR%%/bbmap/jasper/TaxCompare.java -%%JAVAJARDIR%%/bbmap/jasper/TreeNode.class -%%JAVAJARDIR%%/bbmap/jasper/TreeNode.java +%%JAVAJARDIR%%/bbmap/jasper/README.md %%JAVAJARDIR%%/bbmap/jgi/AddAdapters.class %%JAVAJARDIR%%/bbmap/jgi/AddAdapters.java %%JAVAJARDIR%%/bbmap/jgi/AdjustHomopolymers.class %%JAVAJARDIR%%/bbmap/jgi/AdjustHomopolymers.java +%%JAVAJARDIR%%/bbmap/jgi/Assembly.class +%%JAVAJARDIR%%/bbmap/jgi/Assembly.java %%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2$Triple.class %%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2.class %%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2.java +%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats3.class +%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats3.java %%JAVAJARDIR%%/bbmap/jgi/AssemblyStatsWrapper.class %%JAVAJARDIR%%/bbmap/jgi/AssemblyStatsWrapper.java %%JAVAJARDIR%%/bbmap/jgi/BBDuk$LoadThread.class @@ -1189,6 +1447,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/CheckStrand.class %%JAVAJARDIR%%/bbmap/jgi/CheckStrand.java %%JAVAJARDIR%%/bbmap/jgi/CheckStrand2$ProcessThread.class +%%JAVAJARDIR%%/bbmap/jgi/CheckStrand2$Seq.class %%JAVAJARDIR%%/bbmap/jgi/CheckStrand2.class %%JAVAJARDIR%%/bbmap/jgi/CheckStrand2.java %%JAVAJARDIR%%/bbmap/jgi/Consect.class @@ -1216,9 +1475,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/CrisprFinder$ProcessThread.class %%JAVAJARDIR%%/bbmap/jgi/CrisprFinder.class %%JAVAJARDIR%%/bbmap/jgi/CrisprFinder.java -%%JAVAJARDIR%%/bbmap/jgi/CrossContaminate$Vessel.class -%%JAVAJARDIR%%/bbmap/jgi/CrossContaminate.class -%%JAVAJARDIR%%/bbmap/jgi/CrossContaminate.java %%JAVAJARDIR%%/bbmap/jgi/CutPrimers.class %%JAVAJARDIR%%/bbmap/jgi/CutPrimers.java %%JAVAJARDIR%%/bbmap/jgi/DecontaminateByNormalization.class @@ -1259,8 +1515,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/DemuxByName2.java %%JAVAJARDIR%%/bbmap/jgi/Difference.class %%JAVAJARDIR%%/bbmap/jgi/Difference.java -%%JAVAJARDIR%%/bbmap/jgi/FakeReads.class -%%JAVAJARDIR%%/bbmap/jgi/FakeReads.java %%JAVAJARDIR%%/bbmap/jgi/FilterByCoverage.class %%JAVAJARDIR%%/bbmap/jgi/FilterByCoverage.java %%JAVAJARDIR%%/bbmap/jgi/FilterBySequence$Code.class @@ -1281,8 +1535,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/FindString.java %%JAVAJARDIR%%/bbmap/jgi/FungalRelease.class %%JAVAJARDIR%%/bbmap/jgi/FungalRelease.java -%%JAVAJARDIR%%/bbmap/jgi/FuseSequence.class -%%JAVAJARDIR%%/bbmap/jgi/FuseSequence.java %%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$KapaEntry.class %%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$Plate.class %%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$TagData.class @@ -1323,10 +1575,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/KmerNormalize.java %%JAVAJARDIR%%/bbmap/jgi/KmerSample.class %%JAVAJARDIR%%/bbmap/jgi/KmerSample.java -%%JAVAJARDIR%%/bbmap/jgi/MakeChimeras.class -%%JAVAJARDIR%%/bbmap/jgi/MakeChimeras.java -%%JAVAJARDIR%%/bbmap/jgi/MakeContaminatedGenomes.class -%%JAVAJARDIR%%/bbmap/jgi/MakeContaminatedGenomes.java %%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram$1.class %%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.class %%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.java @@ -1336,12 +1584,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/MergeBarcodes.java %%JAVAJARDIR%%/bbmap/jgi/MergeSam.class %%JAVAJARDIR%%/bbmap/jgi/MergeSam.java -%%JAVAJARDIR%%/bbmap/jgi/MutateGenome$SmallVar.class -%%JAVAJARDIR%%/bbmap/jgi/MutateGenome.class -%%JAVAJARDIR%%/bbmap/jgi/MutateGenome.java -%%JAVAJARDIR%%/bbmap/jgi/MutateGenome2$SmallVar.class -%%JAVAJARDIR%%/bbmap/jgi/MutateGenome2.class -%%JAVAJARDIR%%/bbmap/jgi/MutateGenome2.java %%JAVAJARDIR%%/bbmap/jgi/Orf.class %%JAVAJARDIR%%/bbmap/jgi/Orf.java %%JAVAJARDIR%%/bbmap/jgi/PartitionReads$Partition.class @@ -1353,18 +1595,19 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/PickSubset$Node.class %%JAVAJARDIR%%/bbmap/jgi/PickSubset.class %%JAVAJARDIR%%/bbmap/jgi/PickSubset.java +%%JAVAJARDIR%%/bbmap/jgi/README.md %%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.class %%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.java %%JAVAJARDIR%%/bbmap/jgi/RQCFilterStats.class %%JAVAJARDIR%%/bbmap/jgi/RQCFilterStats.java -%%JAVAJARDIR%%/bbmap/jgi/RandomGenome.class -%%JAVAJARDIR%%/bbmap/jgi/RandomGenome.java %%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution$1.class %%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution$ProcessThread.class %%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution.class %%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution.java %%JAVAJARDIR%%/bbmap/jgi/RedirectTest.class %%JAVAJARDIR%%/bbmap/jgi/RedirectTest.java +%%JAVAJARDIR%%/bbmap/jgi/RefRenamer.class +%%JAVAJARDIR%%/bbmap/jgi/RefRenamer.java %%JAVAJARDIR%%/bbmap/jgi/ReformatReads.class %%JAVAJARDIR%%/bbmap/jgi/ReformatReads.java %%JAVAJARDIR%%/bbmap/jgi/RemapQuality.class @@ -1389,8 +1632,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/Seal.java %%JAVAJARDIR%%/bbmap/jgi/SealRefInfo.class %%JAVAJARDIR%%/bbmap/jgi/SealRefInfo.java -%%JAVAJARDIR%%/bbmap/jgi/Shred.class -%%JAVAJARDIR%%/bbmap/jgi/Shred.java %%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$CountComparator.class %%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$Kmer.class %%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$NumComparator.class @@ -1406,8 +1647,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/SplitSam6Way.java %%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.class %%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.java -%%JAVAJARDIR%%/bbmap/jgi/SynthMDA.class -%%JAVAJARDIR%%/bbmap/jgi/SynthMDA.java %%JAVAJARDIR%%/bbmap/jgi/TestFilesystem$WriteThread.class %%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.class %%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.java @@ -1418,6 +1657,10 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies$PrintThread.class %%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies.class %%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies.java +%%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies_old$Line.class +%%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies_old$PrintThread.class +%%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies_old.class +%%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies_old.java %%JAVAJARDIR%%/bbmap/jgi/TranslateSixFrames.class %%JAVAJARDIR%%/bbmap/jgi/TranslateSixFrames.java %%JAVAJARDIR%%/bbmap/jgi/TrimContigs$Range.class @@ -1433,6 +1676,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/json/JsonObject.java %%JAVAJARDIR%%/bbmap/json/JsonParser.class %%JAVAJARDIR%%/bbmap/json/JsonParser.java +%%JAVAJARDIR%%/bbmap/json/README.md %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable$AllocThread.class %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.class %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.java @@ -1476,6 +1720,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/kmer/KmerTableSet.java %%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.class %%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.java +%%JAVAJARDIR%%/bbmap/kmer/README.md %%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.class %%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.java %%JAVAJARDIR%%/bbmap/kmer/SimpleKmerTable.class @@ -1497,7 +1742,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/ml/CellNetParser.java %%JAVAJARDIR%%/bbmap/ml/CellNetReverseComparator.class %%JAVAJARDIR%%/bbmap/ml/CellNetReverseComparator.java -%%JAVAJARDIR%%/bbmap/ml/DataLoader$Pair.class +%%JAVAJARDIR%%/bbmap/ml/DataLoader$Triple.class %%JAVAJARDIR%%/bbmap/ml/DataLoader.class %%JAVAJARDIR%%/bbmap/ml/DataLoader.java %%JAVAJARDIR%%/bbmap/ml/ExtendedMSig.class @@ -1524,8 +1769,11 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders.java %%JAVAJARDIR%%/bbmap/ml/Profiler.class %%JAVAJARDIR%%/bbmap/ml/Profiler.java +%%JAVAJARDIR%%/bbmap/ml/README.md %%JAVAJARDIR%%/bbmap/ml/RSLog.class %%JAVAJARDIR%%/bbmap/ml/RSLog.java +%%JAVAJARDIR%%/bbmap/ml/ReduceColumns.class +%%JAVAJARDIR%%/bbmap/ml/ReduceColumns.java %%JAVAJARDIR%%/bbmap/ml/Sample.class %%JAVAJARDIR%%/bbmap/ml/Sample.java %%JAVAJARDIR%%/bbmap/ml/SampleErrorComparator.class @@ -1586,6 +1834,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized$Ssra.class %%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized.class %%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized.java +%%JAVAJARDIR%%/bbmap/pacbio/README.md %%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2$1.class %%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2$ProcessThread.class %%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2.class @@ -1648,6 +1897,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/prok/PGMTools.java %%JAVAJARDIR%%/bbmap/prok/ProkObject.class %%JAVAJARDIR%%/bbmap/prok/ProkObject.java +%%JAVAJARDIR%%/bbmap/prok/README.md %%JAVAJARDIR%%/bbmap/prok/RiboMaker$ProcessThread.class %%JAVAJARDIR%%/bbmap/prok/RiboMaker.class %%JAVAJARDIR%%/bbmap/prok/RiboMaker.java @@ -1675,14 +1925,30 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/repeat/RepeatSet.java %%JAVAJARDIR%%/bbmap/server/PercentEncoding.class %%JAVAJARDIR%%/bbmap/server/PercentEncoding.java +%%JAVAJARDIR%%/bbmap/server/README.md %%JAVAJARDIR%%/bbmap/server/ServerTools$1.class %%JAVAJARDIR%%/bbmap/server/ServerTools.class %%JAVAJARDIR%%/bbmap/server/ServerTools.java %%JAVAJARDIR%%/bbmap/server/SimpleHttpServer$GetHandler.class %%JAVAJARDIR%%/bbmap/server/SimpleHttpServer.class %%JAVAJARDIR%%/bbmap/server/SimpleHttpServer.java +%%JAVAJARDIR%%/bbmap/server/StressTest.class +%%JAVAJARDIR%%/bbmap/server/StressTest.java +%%JAVAJARDIR%%/bbmap/server/StressTest2$1.class +%%JAVAJARDIR%%/bbmap/server/StressTest2.class +%%JAVAJARDIR%%/bbmap/server/StressTest2.java +%%JAVAJARDIR%%/bbmap/server/StressTest3.class +%%JAVAJARDIR%%/bbmap/server/StressTest3.java %%JAVAJARDIR%%/bbmap/shared/Colors.class %%JAVAJARDIR%%/bbmap/shared/Colors.java +%%JAVAJARDIR%%/bbmap/shared/FastRandom.class +%%JAVAJARDIR%%/bbmap/shared/FastRandom.java +%%JAVAJARDIR%%/bbmap/shared/FastRandomAES.class +%%JAVAJARDIR%%/bbmap/shared/FastRandomAES.java +%%JAVAJARDIR%%/bbmap/shared/FastRandomSIMD.class +%%JAVAJARDIR%%/bbmap/shared/FastRandomSIMD.java +%%JAVAJARDIR%%/bbmap/shared/FastRandomXoshiro.class +%%JAVAJARDIR%%/bbmap/shared/FastRandomXoshiro.java %%JAVAJARDIR%%/bbmap/shared/KillSwitch.class %%JAVAJARDIR%%/bbmap/shared/KillSwitch.java %%JAVAJARDIR%%/bbmap/shared/LineParser.class @@ -1717,10 +1983,19 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/shared/PreParser.java %%JAVAJARDIR%%/bbmap/shared/Primes.class %%JAVAJARDIR%%/bbmap/shared/Primes.java +%%JAVAJARDIR%%/bbmap/shared/README.md %%JAVAJARDIR%%/bbmap/shared/SIMD.class %%JAVAJARDIR%%/bbmap/shared/SIMD.java +%%JAVAJARDIR%%/bbmap/shared/SIMDAlign.class +%%JAVAJARDIR%%/bbmap/shared/SIMDAlign.java +%%JAVAJARDIR%%/bbmap/shared/SIMDAlignByte.class +%%JAVAJARDIR%%/bbmap/shared/SIMDAlignByte.java +%%JAVAJARDIR%%/bbmap/shared/SIMDAlignOld.class +%%JAVAJARDIR%%/bbmap/shared/SIMDAlignOld.java %%JAVAJARDIR%%/bbmap/shared/Shared.class %%JAVAJARDIR%%/bbmap/shared/Shared.java +%%JAVAJARDIR%%/bbmap/shared/SyncHeart.class +%%JAVAJARDIR%%/bbmap/shared/SyncHeart.java %%JAVAJARDIR%%/bbmap/shared/Timer.class %%JAVAJARDIR%%/bbmap/shared/Timer.java %%JAVAJARDIR%%/bbmap/shared/Tools$1.class @@ -1770,8 +2045,6 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/sketch/Comparison.java %%JAVAJARDIR%%/bbmap/sketch/DisplayParams.class %%JAVAJARDIR%%/bbmap/sketch/DisplayParams.java -%%JAVAJARDIR%%/bbmap/sketch/GlocalAligner.class -%%JAVAJARDIR%%/bbmap/sketch/GlocalAligner.java %%JAVAJARDIR%%/bbmap/sketch/InvertKey.class %%JAVAJARDIR%%/bbmap/sketch/InvertKey.java %%JAVAJARDIR%%/bbmap/sketch/KmerLimit$ProcessThread.class @@ -1782,6 +2055,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/sketch/KmerLimit2.java %%JAVAJARDIR%%/bbmap/sketch/MergeSketch.class %%JAVAJARDIR%%/bbmap/sketch/MergeSketch.java +%%JAVAJARDIR%%/bbmap/sketch/README.md %%JAVAJARDIR%%/bbmap/sketch/Record.class %%JAVAJARDIR%%/bbmap/sketch/Record.java %%JAVAJARDIR%%/bbmap/sketch/RecordSet.class @@ -1831,6 +2105,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/sort/ContigLengthComparator.java %%JAVAJARDIR%%/bbmap/sort/MergeSorted.class %%JAVAJARDIR%%/bbmap/sort/MergeSorted.java +%%JAVAJARDIR%%/bbmap/sort/README.md %%JAVAJARDIR%%/bbmap/sort/ReadComparator.class %%JAVAJARDIR%%/bbmap/sort/ReadComparator.java %%JAVAJARDIR%%/bbmap/sort/ReadComparatorClump.class @@ -2053,6 +2328,8 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/structures/IntList3.java %%JAVAJARDIR%%/bbmap/structures/IntListCompressor.class %%JAVAJARDIR%%/bbmap/structures/IntListCompressor.java +%%JAVAJARDIR%%/bbmap/structures/IntListHashMap.class +%%JAVAJARDIR%%/bbmap/structures/IntListHashMap.java %%JAVAJARDIR%%/bbmap/structures/IntLongHashMap.class %%JAVAJARDIR%%/bbmap/structures/IntLongHashMap.java %%JAVAJARDIR%%/bbmap/structures/IntMap.class @@ -2098,10 +2375,17 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/structures/Point.java %%JAVAJARDIR%%/bbmap/structures/Quantizer.class %%JAVAJARDIR%%/bbmap/structures/Quantizer.java +%%JAVAJARDIR%%/bbmap/structures/README.md %%JAVAJARDIR%%/bbmap/structures/Range.class %%JAVAJARDIR%%/bbmap/structures/Range.java %%JAVAJARDIR%%/bbmap/structures/RawBitSet.class %%JAVAJARDIR%%/bbmap/structures/RawBitSet.java +%%JAVAJARDIR%%/bbmap/structures/RingBuffer.class +%%JAVAJARDIR%%/bbmap/structures/RingBuffer.java +%%JAVAJARDIR%%/bbmap/structures/RingBufferMask.class +%%JAVAJARDIR%%/bbmap/structures/RingBufferMask.java +%%JAVAJARDIR%%/bbmap/structures/RingBufferMod.class +%%JAVAJARDIR%%/bbmap/structures/RingBufferMod.java %%JAVAJARDIR%%/bbmap/structures/SeqCount.class %%JAVAJARDIR%%/bbmap/structures/SeqCount.java %%JAVAJARDIR%%/bbmap/structures/SeqCountM.class @@ -2128,6 +2412,41 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/structures/StringPair.java %%JAVAJARDIR%%/bbmap/structures/SuperLongList.class %%JAVAJARDIR%%/bbmap/structures/SuperLongList.java +%%JAVAJARDIR%%/bbmap/synth/CoverageModel.class +%%JAVAJARDIR%%/bbmap/synth/CoverageModel.java +%%JAVAJARDIR%%/bbmap/synth/CrossContaminate$Vessel.class +%%JAVAJARDIR%%/bbmap/synth/CrossContaminate.class +%%JAVAJARDIR%%/bbmap/synth/CrossContaminate.java +%%JAVAJARDIR%%/bbmap/synth/FakeReads.class +%%JAVAJARDIR%%/bbmap/synth/FakeReads.java +%%JAVAJARDIR%%/bbmap/synth/FuseSequence.class +%%JAVAJARDIR%%/bbmap/synth/FuseSequence.java +%%JAVAJARDIR%%/bbmap/synth/GCBias.class +%%JAVAJARDIR%%/bbmap/synth/GCBias.java +%%JAVAJARDIR%%/bbmap/synth/MakeChimeras.class +%%JAVAJARDIR%%/bbmap/synth/MakeChimeras.java +%%JAVAJARDIR%%/bbmap/synth/MakeContaminatedGenomes.class +%%JAVAJARDIR%%/bbmap/synth/MakeContaminatedGenomes.java +%%JAVAJARDIR%%/bbmap/synth/MutateGenome$SmallVar.class +%%JAVAJARDIR%%/bbmap/synth/MutateGenome.class +%%JAVAJARDIR%%/bbmap/synth/MutateGenome.java +%%JAVAJARDIR%%/bbmap/synth/MutateGenome2$SmallVar.class +%%JAVAJARDIR%%/bbmap/synth/MutateGenome2.class +%%JAVAJARDIR%%/bbmap/synth/MutateGenome2.java +%%JAVAJARDIR%%/bbmap/synth/RandomGenome.class +%%JAVAJARDIR%%/bbmap/synth/RandomGenome.java +%%JAVAJARDIR%%/bbmap/synth/RandomHexamer.class +%%JAVAJARDIR%%/bbmap/synth/RandomHexamer.java +%%JAVAJARDIR%%/bbmap/synth/RandomReads3$1.class +%%JAVAJARDIR%%/bbmap/synth/RandomReads3.class +%%JAVAJARDIR%%/bbmap/synth/RandomReads3.java +%%JAVAJARDIR%%/bbmap/synth/RandomReadsMG$ProcessThread.class +%%JAVAJARDIR%%/bbmap/synth/RandomReadsMG.class +%%JAVAJARDIR%%/bbmap/synth/RandomReadsMG.java +%%JAVAJARDIR%%/bbmap/synth/Shred.class +%%JAVAJARDIR%%/bbmap/synth/Shred.java +%%JAVAJARDIR%%/bbmap/synth/SynthMDA.class +%%JAVAJARDIR%%/bbmap/synth/SynthMDA.java %%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid$HashThread.class %%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid.class %%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid.java @@ -2139,6 +2458,8 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession.java %%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession_ST.class %%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession_ST.java +%%JAVAJARDIR%%/bbmap/tax/CanonicalLineage.class +%%JAVAJARDIR%%/bbmap/tax/CanonicalLineage.java %%JAVAJARDIR%%/bbmap/tax/ExplodeTree.class %%JAVAJARDIR%%/bbmap/tax/ExplodeTree.java %%JAVAJARDIR%%/bbmap/tax/FilterByTaxa.class @@ -2157,10 +2478,13 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/tax/ImgRecord.java %%JAVAJARDIR%%/bbmap/tax/ImgRecord2.class %%JAVAJARDIR%%/bbmap/tax/ImgRecord2.java +%%JAVAJARDIR%%/bbmap/tax/Lineage.class +%%JAVAJARDIR%%/bbmap/tax/Lineage.java %%JAVAJARDIR%%/bbmap/tax/PrintTaxonomy.class %%JAVAJARDIR%%/bbmap/tax/PrintTaxonomy.java %%JAVAJARDIR%%/bbmap/tax/Query.class %%JAVAJARDIR%%/bbmap/tax/Query.java +%%JAVAJARDIR%%/bbmap/tax/README.md %%JAVAJARDIR%%/bbmap/tax/RenameGiToTaxid.class %%JAVAJARDIR%%/bbmap/tax/RenameGiToTaxid.java %%JAVAJARDIR%%/bbmap/tax/RenameIMG.class @@ -2230,6 +2554,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/template/BBTool_ST.java %%JAVAJARDIR%%/bbmap/template/DoWorker.class %%JAVAJARDIR%%/bbmap/template/DoWorker.java +%%JAVAJARDIR%%/bbmap/template/README.md %%JAVAJARDIR%%/bbmap/template/ThreadPoolJob.class %%JAVAJARDIR%%/bbmap/template/ThreadPoolJob.java %%JAVAJARDIR%%/bbmap/template/ThreadWaiter.class @@ -2288,6 +2613,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/ukmer/KmerTableSetU.java %%JAVAJARDIR%%/bbmap/ukmer/OwnershipThread.class %%JAVAJARDIR%%/bbmap/ukmer/OwnershipThread.java +%%JAVAJARDIR%%/bbmap/ukmer/README.md %%JAVAJARDIR%%/bbmap/ukmer/WalkerU.class %%JAVAJARDIR%%/bbmap/ukmer/WalkerU.java %%JAVAJARDIR%%/bbmap/var/ApplyVarsToReference$1.class @@ -2307,6 +2633,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/var/GenerateVarlets3$ProcessThread.class %%JAVAJARDIR%%/bbmap/var/GenerateVarlets3.class %%JAVAJARDIR%%/bbmap/var/GenerateVarlets3.java +%%JAVAJARDIR%%/bbmap/var/README.md %%JAVAJARDIR%%/bbmap/var/StackVariations$1.class %%JAVAJARDIR%%/bbmap/var/StackVariations$SVThread.class %%JAVAJARDIR%%/bbmap/var/StackVariations.class @@ -2321,8 +2648,12 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/var/Variation.java %%JAVAJARDIR%%/bbmap/var/Varlet.class %%JAVAJARDIR%%/bbmap/var/Varlet.java +%%JAVAJARDIR%%/bbmap/var2/AnalyzeVars.class +%%JAVAJARDIR%%/bbmap/var2/AnalyzeVars.java %%JAVAJARDIR%%/bbmap/var2/ApplyVariants.class %%JAVAJARDIR%%/bbmap/var2/ApplyVariants.java +%%JAVAJARDIR%%/bbmap/var2/CVOutputWriter.class +%%JAVAJARDIR%%/bbmap/var2/CVOutputWriter.java %%JAVAJARDIR%%/bbmap/var2/CallVariants$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/CallVariants.class %%JAVAJARDIR%%/bbmap/var2/CallVariants.java @@ -2332,6 +2663,8 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/var2/CallVariants2.java %%JAVAJARDIR%%/bbmap/var2/CompareVCF.class %%JAVAJARDIR%%/bbmap/var2/CompareVCF.java +%%JAVAJARDIR%%/bbmap/var2/FeatureVectorMaker.class +%%JAVAJARDIR%%/bbmap/var2/FeatureVectorMaker.java %%JAVAJARDIR%%/bbmap/var2/FilterSam$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/FilterSam.class %%JAVAJARDIR%%/bbmap/var2/FilterSam.java @@ -2341,6 +2674,7 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/var2/MergeSamples$MergeThread.class %%JAVAJARDIR%%/bbmap/var2/MergeSamples.class %%JAVAJARDIR%%/bbmap/var2/MergeSamples.java +%%JAVAJARDIR%%/bbmap/var2/README.md %%JAVAJARDIR%%/bbmap/var2/Realign$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/Realign.class %%JAVAJARDIR%%/bbmap/var2/Realign.java @@ -2363,15 +2697,27 @@ libexec/bbmap/webcheck.sh %%JAVAJARDIR%%/bbmap/var2/Var.java %%JAVAJARDIR%%/bbmap/var2/VarFilter.class %%JAVAJARDIR%%/bbmap/var2/VarFilter.java +%%JAVAJARDIR%%/bbmap/var2/VarHelper.class +%%JAVAJARDIR%%/bbmap/var2/VarHelper.java %%JAVAJARDIR%%/bbmap/var2/VarKey.class %%JAVAJARDIR%%/bbmap/var2/VarKey.java %%JAVAJARDIR%%/bbmap/var2/VarMap$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/VarMap$VarMapIterator.class %%JAVAJARDIR%%/bbmap/var2/VarMap.class %%JAVAJARDIR%%/bbmap/var2/VarMap.java +%%JAVAJARDIR%%/bbmap/var2/VarProb.class +%%JAVAJARDIR%%/bbmap/var2/VarProb.java %%JAVAJARDIR%%/bbmap/var2/VcfLoader$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/VcfLoader.class %%JAVAJARDIR%%/bbmap/var2/VcfLoader.java +%%JAVAJARDIR%%/bbmap/var2/VcfToVar.class +%%JAVAJARDIR%%/bbmap/var2/VcfToVar.java %%JAVAJARDIR%%/bbmap/var2/VcfWriter$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/VcfWriter.class %%JAVAJARDIR%%/bbmap/var2/VcfWriter.java +%%JAVAJARDIR%%/bbmap/var2/VectorDonovan$QuantileTransformer.class +%%JAVAJARDIR%%/bbmap/var2/VectorDonovan.class +%%JAVAJARDIR%%/bbmap/var2/VectorDonovan.java +%%JAVAJARDIR%%/bbmap/var2/VectorElba$ElbaMinMaxValues.class +%%JAVAJARDIR%%/bbmap/var2/VectorElba.class +%%JAVAJARDIR%%/bbmap/var2/VectorElba.java |