diff options
Diffstat (limited to 'biology/bbmap')
| -rw-r--r-- | biology/bbmap/Makefile | 2 | ||||
| -rw-r--r-- | biology/bbmap/distinfo | 6 | ||||
| -rw-r--r-- | biology/bbmap/pkg-plist | 64 |
3 files changed, 68 insertions, 4 deletions
diff --git a/biology/bbmap/Makefile b/biology/bbmap/Makefile index f002e215a910..533216187a45 100644 --- a/biology/bbmap/Makefile +++ b/biology/bbmap/Makefile @@ -1,5 +1,5 @@ PORTNAME= bbmap -DISTVERSION= 39.33 +DISTVERSION= 39.34 CATEGORIES= biology java MASTER_SITES= SF/bbmap/ DISTNAME= BBMap_${PORTVERSION} diff --git a/biology/bbmap/distinfo b/biology/bbmap/distinfo index c2fdad3c90f0..c65e1b09d3ef 100644 --- a/biology/bbmap/distinfo +++ b/biology/bbmap/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1753598961 -SHA256 (BBMap_39.33.tar.gz) = b82d06579e118467b5f129f06c93991196d25cc7e43cd233aeb777f85507175e -SIZE (BBMap_39.33.tar.gz) = 13433045 +TIMESTAMP = 1755776772 +SHA256 (BBMap_39.34.tar.gz) = c9c096c6ce3cc87da5607b731532bb9ac0aaebea2bd8fbf0a56e235968c4fbf4 +SIZE (BBMap_39.34.tar.gz) = 13743574 diff --git a/biology/bbmap/pkg-plist b/biology/bbmap/pkg-plist index 9a9e248eafa3..6dc7649290c2 100644 --- a/biology/bbmap/pkg-plist +++ b/biology/bbmap/pkg-plist @@ -378,6 +378,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/align2/QuadHeap.java %%JAVAJARDIR%%/bbmap/align2/QualityTools.class %%JAVAJARDIR%%/bbmap/align2/QualityTools.java +%%JAVAJARDIR%%/bbmap/align2/README.md %%JAVAJARDIR%%/bbmap/align2/RefToIndex.class %%JAVAJARDIR%%/bbmap/align2/RefToIndex.java %%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput.class @@ -527,6 +528,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner4.java %%JAVAJARDIR%%/bbmap/aligner/Query.class %%JAVAJARDIR%%/bbmap/aligner/Query.java +%%JAVAJARDIR%%/bbmap/aligner/README.md %%JAVAJARDIR%%/bbmap/aligner/RelativeAligner.class %%JAVAJARDIR%%/bbmap/aligner/RelativeAligner.java %%JAVAJARDIR%%/bbmap/aligner/ScrabbleAligner.class @@ -605,6 +607,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/assemble/KmerCompressor.java %%JAVAJARDIR%%/bbmap/assemble/Postfilter.class %%JAVAJARDIR%%/bbmap/assemble/Postfilter.java +%%JAVAJARDIR%%/bbmap/assemble/README.md %%JAVAJARDIR%%/bbmap/assemble/Rollback.class %%JAVAJARDIR%%/bbmap/assemble/Rollback.java %%JAVAJARDIR%%/bbmap/assemble/ShaveObject.class @@ -680,6 +683,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist$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 @@ -692,6 +696,11 @@ libexec/bbmap/wobbleplusaligner.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 @@ -750,8 +759,19 @@ libexec/bbmap/wobbleplusaligner.sh %%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 @@ -762,6 +782,10 @@ libexec/bbmap/wobbleplusaligner.sh %%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 @@ -775,6 +799,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/bin/QuickBin$ProcessThread.class %%JAVAJARDIR%%/bbmap/bin/QuickBin.class %%JAVAJARDIR%%/bbmap/bin/QuickBin.java +%%JAVAJARDIR%%/bbmap/bin/README.md %%JAVAJARDIR%%/bbmap/bin/SamLoader$LoadThread.class %%JAVAJARDIR%%/bbmap/bin/SamLoader.class %%JAVAJARDIR%%/bbmap/bin/SamLoader.java @@ -851,6 +876,7 @@ libexec/bbmap/wobbleplusaligner.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 @@ -886,6 +912,7 @@ libexec/bbmap/wobbleplusaligner.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$ClumpThread.class @@ -928,6 +955,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/clump/PivotSet$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 @@ -940,6 +968,7 @@ libexec/bbmap/wobbleplusaligner.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$ClusterThread.class @@ -965,6 +994,8 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/consensus/Lilypad$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 @@ -997,6 +1028,7 @@ libexec/bbmap/wobbleplusaligner.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 @@ -1088,6 +1120,7 @@ libexec/bbmap/wobbleplusaligner.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 @@ -1188,6 +1221,7 @@ libexec/bbmap/wobbleplusaligner.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 @@ -1266,6 +1300,7 @@ libexec/bbmap/wobbleplusaligner.sh %%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 @@ -1287,6 +1322,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/gff/GtfLine.java %%JAVAJARDIR%%/bbmap/gff/ParseCrispr.class %%JAVAJARDIR%%/bbmap/gff/ParseCrispr.java +%%JAVAJARDIR%%/bbmap/gff/README.md %%JAVAJARDIR%%/bbmap/gff/VcfToGff$1.class %%JAVAJARDIR%%/bbmap/gff/VcfToGff.class %%JAVAJARDIR%%/bbmap/gff/VcfToGff.java @@ -1321,6 +1357,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/hiseq/PlotHist.java %%JAVAJARDIR%%/bbmap/hiseq/PlotReadPosition.class %%JAVAJARDIR%%/bbmap/hiseq/PlotReadPosition.java +%%JAVAJARDIR%%/bbmap/hiseq/README.md %%JAVAJARDIR%%/bbmap/hiseq/ReadHeaderParser.class %%JAVAJARDIR%%/bbmap/hiseq/ReadHeaderParser.java %%JAVAJARDIR%%/bbmap/hiseq/Tile.class @@ -1333,6 +1370,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/hmm/HMMSearchReport.java %%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.class %%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.java +%%JAVAJARDIR%%/bbmap/hmm/README.md %%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.class %%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.java %%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJNI.class @@ -1351,6 +1389,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/icecream/PBHeader.java %%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.class %%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.java +%%JAVAJARDIR%%/bbmap/icecream/README.md %%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.class %%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.java %%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio$ProcessThread.class @@ -1364,6 +1403,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/jasper/KmerPosition.java %%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.class %%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.java +%%JAVAJARDIR%%/bbmap/jasper/README.md %%JAVAJARDIR%%/bbmap/jgi/AddAdapters.class %%JAVAJARDIR%%/bbmap/jgi/AddAdapters.java %%JAVAJARDIR%%/bbmap/jgi/AdjustHomopolymers.class @@ -1555,6 +1595,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/jgi/PickSubset$Node.class %%JAVAJARDIR%%/bbmap/jgi/PickSubset.class %%JAVAJARDIR%%/bbmap/jgi/PickSubset.java +%%JAVAJARDIR%%/bbmap/jgi/README.md %%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.class %%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.java %%JAVAJARDIR%%/bbmap/jgi/RQCFilterStats.class @@ -1635,6 +1676,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/json/JsonObject.java %%JAVAJARDIR%%/bbmap/json/JsonParser.class %%JAVAJARDIR%%/bbmap/json/JsonParser.java +%%JAVAJARDIR%%/bbmap/json/README.md %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable$AllocThread.class %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.class %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.java @@ -1678,6 +1720,7 @@ libexec/bbmap/wobbleplusaligner.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 @@ -1726,6 +1769,7 @@ libexec/bbmap/wobbleplusaligner.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 @@ -1790,6 +1834,7 @@ libexec/bbmap/wobbleplusaligner.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 @@ -1852,6 +1897,7 @@ libexec/bbmap/wobbleplusaligner.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 @@ -1879,6 +1925,7 @@ libexec/bbmap/wobbleplusaligner.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 @@ -1936,6 +1983,7 @@ libexec/bbmap/wobbleplusaligner.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 @@ -2007,6 +2055,7 @@ libexec/bbmap/wobbleplusaligner.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 @@ -2056,6 +2105,7 @@ libexec/bbmap/wobbleplusaligner.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 @@ -2325,6 +2375,7 @@ libexec/bbmap/wobbleplusaligner.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 @@ -2433,6 +2484,7 @@ libexec/bbmap/wobbleplusaligner.sh %%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 @@ -2502,6 +2554,7 @@ libexec/bbmap/wobbleplusaligner.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 @@ -2560,6 +2613,7 @@ libexec/bbmap/wobbleplusaligner.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$1.class @@ -2579,6 +2633,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/var/GenerateVarlets3$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 @@ -2608,6 +2663,8 @@ libexec/bbmap/wobbleplusaligner.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$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/FilterSam.class %%JAVAJARDIR%%/bbmap/var2/FilterSam.java @@ -2617,6 +2674,7 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/var2/MergeSamples$MergeThread.class %%JAVAJARDIR%%/bbmap/var2/MergeSamples.class %%JAVAJARDIR%%/bbmap/var2/MergeSamples.java +%%JAVAJARDIR%%/bbmap/var2/README.md %%JAVAJARDIR%%/bbmap/var2/Realign$ProcessThread.class %%JAVAJARDIR%%/bbmap/var2/Realign.class %%JAVAJARDIR%%/bbmap/var2/Realign.java @@ -2657,3 +2715,9 @@ libexec/bbmap/wobbleplusaligner.sh %%JAVAJARDIR%%/bbmap/var2/VcfWriter$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 |