mirror of https://git.FreeBSD.org/ports.git
biology/bbmap: Update to 39.34
A few improvements and fixes
Changes:
https://bitbucket.org/berkeleylab/jgi-bbtools/commits/branch/master
Reported by: portscout
This commit is contained in:
Jason W. Bacon
parent
c70cbe40b0
commit
5d8f84ce55
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@ -1,5 +1,5 @@
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PORTNAME= bbmap
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DISTVERSION= 39.33
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DISTVERSION= 39.34
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CATEGORIES= biology java
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MASTER_SITES= SF/bbmap/
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DISTNAME= BBMap_${PORTVERSION}
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@ -1,3 +1,3 @@
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TIMESTAMP = 1753598961
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SHA256 (BBMap_39.33.tar.gz) = b82d06579e118467b5f129f06c93991196d25cc7e43cd233aeb777f85507175e
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SIZE (BBMap_39.33.tar.gz) = 13433045
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TIMESTAMP = 1755776772
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SHA256 (BBMap_39.34.tar.gz) = c9c096c6ce3cc87da5607b731532bb9ac0aaebea2bd8fbf0a56e235968c4fbf4
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SIZE (BBMap_39.34.tar.gz) = 13743574
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@ -378,6 +378,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/align2/QuadHeap.java
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%%JAVAJARDIR%%/bbmap/align2/QualityTools.class
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%%JAVAJARDIR%%/bbmap/align2/QualityTools.java
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%%JAVAJARDIR%%/bbmap/align2/README.md
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%%JAVAJARDIR%%/bbmap/align2/RefToIndex.class
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%%JAVAJARDIR%%/bbmap/align2/RefToIndex.java
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%%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput.class
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@ -527,6 +528,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/aligner/QuantumPlusAligner4.java
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%%JAVAJARDIR%%/bbmap/aligner/Query.class
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%%JAVAJARDIR%%/bbmap/aligner/Query.java
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%%JAVAJARDIR%%/bbmap/aligner/README.md
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%%JAVAJARDIR%%/bbmap/aligner/RelativeAligner.class
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%%JAVAJARDIR%%/bbmap/aligner/RelativeAligner.java
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%%JAVAJARDIR%%/bbmap/aligner/ScrabbleAligner.class
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@ -605,6 +607,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/assemble/KmerCompressor.java
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%%JAVAJARDIR%%/bbmap/assemble/Postfilter.class
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%%JAVAJARDIR%%/bbmap/assemble/Postfilter.java
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%%JAVAJARDIR%%/bbmap/assemble/README.md
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%%JAVAJARDIR%%/bbmap/assemble/Rollback.class
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%%JAVAJARDIR%%/bbmap/assemble/Rollback.java
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%%JAVAJARDIR%%/bbmap/assemble/ShaveObject.class
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@ -680,6 +683,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist$PopThread.class
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%%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist.class
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%%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist.java
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%%JAVAJARDIR%%/bbmap/barcode/README.md
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%%JAVAJARDIR%%/bbmap/barcode/TagAndMerge.class
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%%JAVAJARDIR%%/bbmap/barcode/TagAndMerge.java
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%%JAVAJARDIR%%/bbmap/barcode/Transition.class
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@ -692,6 +696,11 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixTile.java
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%%JAVAJARDIR%%/bbmap/bbmin/Minimizer.class
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%%JAVAJARDIR%%/bbmap/bbmin/Minimizer.java
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%%JAVAJARDIR%%/bbmap/bbmin/README.md
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%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$EnsembleRefinerParams.class
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%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$EvidenceRefinerParams.class
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%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$GraphRefinerParams.class
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%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$RefinerParams.class
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%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner.class
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%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner.java
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%%JAVAJARDIR%%/bbmap/bin/AdjustEntropy.class
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@ -750,8 +759,19 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/bin/CrystalChamber$Centroid.class
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%%JAVAJARDIR%%/bbmap/bin/CrystalChamber.class
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%%JAVAJARDIR%%/bbmap/bin/CrystalChamber.java
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%%JAVAJARDIR%%/bbmap/bin/CrystalChamber2$Centroid.class
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%%JAVAJARDIR%%/bbmap/bin/CrystalChamber2.class
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%%JAVAJARDIR%%/bbmap/bin/CrystalChamber2.java
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%%JAVAJARDIR%%/bbmap/bin/DataLoader.class
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%%JAVAJARDIR%%/bbmap/bin/DataLoader.java
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%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner$ConsensusResult.class
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%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner$RefinerResult.class
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%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner.class
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%%JAVAJARDIR%%/bbmap/bin/EnsembleRefiner.java
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%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner$ContigStatus.class
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%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner$DBSCANResult.class
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%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner.class
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%%JAVAJARDIR%%/bbmap/bin/EvidenceRefiner.java
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%%JAVAJARDIR%%/bbmap/bin/FileRenamer.class
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%%JAVAJARDIR%%/bbmap/bin/FileRenamer.java
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%%JAVAJARDIR%%/bbmap/bin/GTDBLine.class
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@ -762,6 +782,10 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/bin/GradeBins$ProcessThread.class
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%%JAVAJARDIR%%/bbmap/bin/GradeBins.class
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%%JAVAJARDIR%%/bbmap/bin/GradeBins.java
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%%JAVAJARDIR%%/bbmap/bin/GraphRefiner$SimilarityGraph$Edge.class
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%%JAVAJARDIR%%/bbmap/bin/GraphRefiner$SimilarityGraph.class
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%%JAVAJARDIR%%/bbmap/bin/GraphRefiner.class
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%%JAVAJARDIR%%/bbmap/bin/GraphRefiner.java
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%%JAVAJARDIR%%/bbmap/bin/IDComparator.class
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%%JAVAJARDIR%%/bbmap/bin/IDComparator.java
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%%JAVAJARDIR%%/bbmap/bin/Key.class
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@ -775,6 +799,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/bin/QuickBin$ProcessThread.class
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%%JAVAJARDIR%%/bbmap/bin/QuickBin.class
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%%JAVAJARDIR%%/bbmap/bin/QuickBin.java
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%%JAVAJARDIR%%/bbmap/bin/README.md
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%%JAVAJARDIR%%/bbmap/bin/SamLoader$LoadThread.class
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%%JAVAJARDIR%%/bbmap/bin/SamLoader.class
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%%JAVAJARDIR%%/bbmap/bin/SamLoader.java
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@ -851,6 +876,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/bloom/PolyFilter$ProcessThread.class
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%%JAVAJARDIR%%/bbmap/bloom/PolyFilter.class
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%%JAVAJARDIR%%/bbmap/bloom/PolyFilter.java
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%%JAVAJARDIR%%/bbmap/bloom/README.md
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%%JAVAJARDIR%%/bbmap/bloom/ReadCounter$1.class
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%%JAVAJARDIR%%/bbmap/bloom/ReadCounter$CountThread.class
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%%JAVAJARDIR%%/bbmap/bloom/ReadCounter.class
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@ -886,6 +912,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/cardinality/LogLog_old.java
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%%JAVAJARDIR%%/bbmap/cardinality/MultiLogLog.class
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%%JAVAJARDIR%%/bbmap/cardinality/MultiLogLog.java
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%%JAVAJARDIR%%/bbmap/cardinality/README.md
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%%JAVAJARDIR%%/bbmap/clump/Clump.class
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%%JAVAJARDIR%%/bbmap/clump/Clump.java
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%%JAVAJARDIR%%/bbmap/clump/ClumpList$ClumpThread.class
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@ -928,6 +955,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/clump/PivotSet$HashThread.class
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%%JAVAJARDIR%%/bbmap/clump/PivotSet.class
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%%JAVAJARDIR%%/bbmap/clump/PivotSet.java
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%%JAVAJARDIR%%/bbmap/clump/README.md
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%%JAVAJARDIR%%/bbmap/clump/ReadKey.class
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%%JAVAJARDIR%%/bbmap/clump/ReadKey.java
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%%JAVAJARDIR%%/bbmap/clump/Splitter.class
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@ -940,6 +968,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/cluster/ClusterTools.java
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%%JAVAJARDIR%%/bbmap/cluster/MergeReadHeaders.class
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%%JAVAJARDIR%%/bbmap/cluster/MergeReadHeaders.java
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%%JAVAJARDIR%%/bbmap/cluster/README.md
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%%JAVAJARDIR%%/bbmap/cluster/ReadTag.class
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%%JAVAJARDIR%%/bbmap/cluster/ReadTag.java
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%%JAVAJARDIR%%/bbmap/cluster/ReclusterByKmer$ClusterThread.class
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@ -965,6 +994,8 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/consensus/Lilypad$ProcessThread.class
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%%JAVAJARDIR%%/bbmap/consensus/Lilypad.class
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%%JAVAJARDIR%%/bbmap/consensus/Lilypad.java
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%%JAVAJARDIR%%/bbmap/consensus/README.md
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%%JAVAJARDIR%%/bbmap/covid/README.md
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%%JAVAJARDIR%%/bbmap/covid/SummarizeCoverage.class
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%%JAVAJARDIR%%/bbmap/covid/SummarizeCoverage.java
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%%JAVAJARDIR%%/bbmap/dna/AminoAcid.class
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@ -997,6 +1028,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/dna/MotifProbsN.java
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%%JAVAJARDIR%%/bbmap/dna/MotifSimple.class
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%%JAVAJARDIR%%/bbmap/dna/MotifSimple.java
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%%JAVAJARDIR%%/bbmap/dna/README.md
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%%JAVAJARDIR%%/bbmap/dna/ScafLoc.class
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%%JAVAJARDIR%%/bbmap/dna/ScafLoc.java
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%%JAVAJARDIR%%/bbmap/dna/Scaffold.class
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@ -1088,6 +1120,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed2.java
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%%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.class
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%%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.java
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%%JAVAJARDIR%%/bbmap/driver/README.md
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%%JAVAJARDIR%%/bbmap/driver/ReduceSilva.class
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%%JAVAJARDIR%%/bbmap/driver/ReduceSilva.java
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%%JAVAJARDIR%%/bbmap/driver/RenameAndMux$MuxThread.class
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@ -1188,6 +1221,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/fileIO/PipeThread.java
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%%JAVAJARDIR%%/bbmap/fileIO/QuickFile.class
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%%JAVAJARDIR%%/bbmap/fileIO/QuickFile.java
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%%JAVAJARDIR%%/bbmap/fileIO/README.md
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%%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$1.class
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%%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$WriteObjectThread.class
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%%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$WriteStringThread.class
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@ -1266,6 +1300,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/fun/ProbShared2.java
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%%JAVAJARDIR%%/bbmap/fun/ProbShared3.class
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%%JAVAJARDIR%%/bbmap/fun/ProbShared3.java
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%%JAVAJARDIR%%/bbmap/fun/README.md
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%%JAVAJARDIR%%/bbmap/gff/CompareGff.class
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%%JAVAJARDIR%%/bbmap/gff/CompareGff.java
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%%JAVAJARDIR%%/bbmap/gff/CompareGff_old.class
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@ -1287,6 +1322,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/gff/GtfLine.java
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%%JAVAJARDIR%%/bbmap/gff/ParseCrispr.class
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%%JAVAJARDIR%%/bbmap/gff/ParseCrispr.java
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%%JAVAJARDIR%%/bbmap/gff/README.md
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%%JAVAJARDIR%%/bbmap/gff/VcfToGff$1.class
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%%JAVAJARDIR%%/bbmap/gff/VcfToGff.class
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%%JAVAJARDIR%%/bbmap/gff/VcfToGff.java
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@ -1321,6 +1357,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/hiseq/PlotHist.java
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%%JAVAJARDIR%%/bbmap/hiseq/PlotReadPosition.class
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%%JAVAJARDIR%%/bbmap/hiseq/PlotReadPosition.java
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%%JAVAJARDIR%%/bbmap/hiseq/README.md
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%%JAVAJARDIR%%/bbmap/hiseq/ReadHeaderParser.class
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%%JAVAJARDIR%%/bbmap/hiseq/ReadHeaderParser.java
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%%JAVAJARDIR%%/bbmap/hiseq/Tile.class
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@ -1333,6 +1370,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/hmm/HMMSearchReport.java
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%%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.class
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%%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.java
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%%JAVAJARDIR%%/bbmap/hmm/README.md
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%%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.class
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%%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.java
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%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJNI.class
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@ -1351,6 +1389,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/icecream/PBHeader.java
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%%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.class
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%%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.java
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%%JAVAJARDIR%%/bbmap/icecream/README.md
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%%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.class
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%%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.java
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%%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio$ProcessThread.class
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@ -1364,6 +1403,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/jasper/KmerPosition.java
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%%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.class
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%%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.java
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%%JAVAJARDIR%%/bbmap/jasper/README.md
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%%JAVAJARDIR%%/bbmap/jgi/AddAdapters.class
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%%JAVAJARDIR%%/bbmap/jgi/AddAdapters.java
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%%JAVAJARDIR%%/bbmap/jgi/AdjustHomopolymers.class
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@ -1555,6 +1595,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/jgi/PickSubset$Node.class
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%%JAVAJARDIR%%/bbmap/jgi/PickSubset.class
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%%JAVAJARDIR%%/bbmap/jgi/PickSubset.java
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%%JAVAJARDIR%%/bbmap/jgi/README.md
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%%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.class
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%%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.java
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%%JAVAJARDIR%%/bbmap/jgi/RQCFilterStats.class
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@ -1635,6 +1676,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/json/JsonObject.java
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%%JAVAJARDIR%%/bbmap/json/JsonParser.class
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%%JAVAJARDIR%%/bbmap/json/JsonParser.java
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%%JAVAJARDIR%%/bbmap/json/README.md
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%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable$AllocThread.class
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%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.class
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%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.java
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@ -1678,6 +1720,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet.java
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%%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.class
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%%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.java
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%%JAVAJARDIR%%/bbmap/kmer/README.md
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%%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.class
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%%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.java
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%%JAVAJARDIR%%/bbmap/kmer/SimpleKmerTable.class
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@ -1726,6 +1769,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders.java
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%%JAVAJARDIR%%/bbmap/ml/Profiler.class
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%%JAVAJARDIR%%/bbmap/ml/Profiler.java
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%%JAVAJARDIR%%/bbmap/ml/README.md
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%%JAVAJARDIR%%/bbmap/ml/RSLog.class
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%%JAVAJARDIR%%/bbmap/ml/RSLog.java
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%%JAVAJARDIR%%/bbmap/ml/ReduceColumns.class
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@ -1790,6 +1834,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized$Ssra.class
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%%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized.class
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%%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized.java
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%%JAVAJARDIR%%/bbmap/pacbio/README.md
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%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2$1.class
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%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2$ProcessThread.class
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%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2.class
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@ -1852,6 +1897,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/prok/PGMTools.java
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%%JAVAJARDIR%%/bbmap/prok/ProkObject.class
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%%JAVAJARDIR%%/bbmap/prok/ProkObject.java
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%%JAVAJARDIR%%/bbmap/prok/README.md
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%%JAVAJARDIR%%/bbmap/prok/RiboMaker$ProcessThread.class
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%%JAVAJARDIR%%/bbmap/prok/RiboMaker.class
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%%JAVAJARDIR%%/bbmap/prok/RiboMaker.java
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@ -1879,6 +1925,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/repeat/RepeatSet.java
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%%JAVAJARDIR%%/bbmap/server/PercentEncoding.class
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%%JAVAJARDIR%%/bbmap/server/PercentEncoding.java
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%%JAVAJARDIR%%/bbmap/server/README.md
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%%JAVAJARDIR%%/bbmap/server/ServerTools$1.class
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%%JAVAJARDIR%%/bbmap/server/ServerTools.class
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%%JAVAJARDIR%%/bbmap/server/ServerTools.java
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@ -1936,6 +1983,7 @@ libexec/bbmap/wobbleplusaligner.sh
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%%JAVAJARDIR%%/bbmap/shared/PreParser.java
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%%JAVAJARDIR%%/bbmap/shared/Primes.class
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%%JAVAJARDIR%%/bbmap/shared/Primes.java
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%%JAVAJARDIR%%/bbmap/shared/README.md
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%%JAVAJARDIR%%/bbmap/shared/SIMD.class
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%%JAVAJARDIR%%/bbmap/shared/SIMD.java
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%%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
|
||||
|
|
|
|||
Loading…
Reference in New Issue