Jason W. Bacon
5d8f84ce55
A few improvements and fixes
Changes:
https://bitbucket.org/berkeleylab/jgi-bbtools/commits/branch/master
Reported by: portscout
2724 lines
123 KiB
Plaintext
2724 lines
123 KiB
Plaintext
bin/bbduk.sh
|
|
bin/bbmap.sh
|
|
bin/bbmerge.sh
|
|
bin/bbnorm.sh
|
|
bin/bloomfilter.sh
|
|
bin/dedupe.sh
|
|
bin/reformat.sh
|
|
bin/tadpole.sh
|
|
libexec/bbmap/Xcalcmem.sh
|
|
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
|
|
libexec/bbmap/bbduk.sh
|
|
libexec/bbmap/bbest.sh
|
|
libexec/bbmap/bbfakereads.sh
|
|
libexec/bbmap/bbmap.sh
|
|
libexec/bbmap/bbmapskimmer.sh
|
|
libexec/bbmap/bbmask.sh
|
|
libexec/bbmap/bbmerge-auto.sh
|
|
libexec/bbmap/bbmerge.sh
|
|
libexec/bbmap/bbnorm.sh
|
|
libexec/bbmap/bbrealign.sh
|
|
libexec/bbmap/bbrename.sh
|
|
libexec/bbmap/bbsketch.sh
|
|
libexec/bbmap/bbsort.sh
|
|
libexec/bbmap/bbsplit.sh
|
|
libexec/bbmap/bbsplitpairs.sh
|
|
libexec/bbmap/bbstats.sh
|
|
libexec/bbmap/bbversion.sh
|
|
libexec/bbmap/bbwrap.sh
|
|
libexec/bbmap/bloomfilter.sh
|
|
libexec/bbmap/bloomfilterparser.sh
|
|
libexec/bbmap/calcmem.sh
|
|
libexec/bbmap/calctruequality.sh
|
|
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
|
|
libexec/bbmap/comparelabels.sh
|
|
libexec/bbmap/comparesketch.sh
|
|
libexec/bbmap/comparessu.sh
|
|
libexec/bbmap/comparevcf.sh
|
|
libexec/bbmap/consect.sh
|
|
libexec/bbmap/consensus.sh
|
|
libexec/bbmap/copyfile.sh
|
|
libexec/bbmap/countbarcodes.sh
|
|
libexec/bbmap/countbarcodes2.sh
|
|
libexec/bbmap/countduplicates.sh
|
|
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
|
|
libexec/bbmap/dedupe.sh
|
|
libexec/bbmap/dedupe2.sh
|
|
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
|
|
libexec/bbmap/filterassemblysummary.sh
|
|
libexec/bbmap/filterbarcodes.sh
|
|
libexec/bbmap/filterbycoverage.sh
|
|
libexec/bbmap/filterbyname.sh
|
|
libexec/bbmap/filterbysequence.sh
|
|
libexec/bbmap/filterbytaxa.sh
|
|
libexec/bbmap/filterbytile.sh
|
|
libexec/bbmap/filterlines.sh
|
|
libexec/bbmap/filterqc.sh
|
|
libexec/bbmap/filtersam.sh
|
|
libexec/bbmap/filtersilva.sh
|
|
libexec/bbmap/filtersubs.sh
|
|
libexec/bbmap/filtervcf.sh
|
|
libexec/bbmap/findrepeats.sh
|
|
libexec/bbmap/fixgaps.sh
|
|
libexec/bbmap/fungalrelease.sh
|
|
libexec/bbmap/fuse.sh
|
|
libexec/bbmap/gbff2gff.sh
|
|
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
|
|
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
|
|
libexec/bbmap/khist.sh
|
|
libexec/bbmap/kmercountexact.sh
|
|
libexec/bbmap/kmercountmulti.sh
|
|
libexec/bbmap/kmercoverage.sh
|
|
libexec/bbmap/kmerfilterset.sh
|
|
libexec/bbmap/kmerlimit.sh
|
|
libexec/bbmap/kmerlimit2.sh
|
|
libexec/bbmap/kmerposition.sh
|
|
libexec/bbmap/kmutate.sh
|
|
libexec/bbmap/lilypad.sh
|
|
libexec/bbmap/loadreads.sh
|
|
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
|
|
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
|
|
libexec/bbmap/netfilter.sh
|
|
libexec/bbmap/novademux.sh
|
|
libexec/bbmap/partition.sh
|
|
libexec/bbmap/phylip2fasta.sh
|
|
libexec/bbmap/picksubset.sh
|
|
libexec/bbmap/pileup.sh
|
|
libexec/bbmap/pileup2.sh
|
|
libexec/bbmap/plotflowcell.sh
|
|
libexec/bbmap/plotgc.sh
|
|
libexec/bbmap/plothist.sh
|
|
libexec/bbmap/plotreadposition.sh
|
|
libexec/bbmap/polyfilter.sh
|
|
libexec/bbmap/postfilter.sh
|
|
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
|
|
libexec/bbmap/removebadbarcodes.sh
|
|
libexec/bbmap/removecatdogmousehuman.sh
|
|
libexec/bbmap/removehuman.sh
|
|
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
|
|
libexec/bbmap/rqcfilter.sh
|
|
libexec/bbmap/rqcfilter2.sh
|
|
libexec/bbmap/runhmm.sh
|
|
libexec/bbmap/samtoroc.sh
|
|
libexec/bbmap/scoresequence.sh
|
|
libexec/bbmap/seal.sh
|
|
libexec/bbmap/sendsketch.sh
|
|
libexec/bbmap/seqtovec.sh
|
|
libexec/bbmap/shred.sh
|
|
libexec/bbmap/shrinkaccession.sh
|
|
libexec/bbmap/shuffle.sh
|
|
libexec/bbmap/shuffle2.sh
|
|
libexec/bbmap/sketch.sh
|
|
libexec/bbmap/sketchblacklist.sh
|
|
libexec/bbmap/sketchblacklist2.sh
|
|
libexec/bbmap/sortbyname.sh
|
|
libexec/bbmap/splitbytaxa.sh
|
|
libexec/bbmap/splitnextera.sh
|
|
libexec/bbmap/splitribo.sh
|
|
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
|
|
libexec/bbmap/summarizecontam.sh
|
|
libexec/bbmap/summarizecoverage.sh
|
|
libexec/bbmap/summarizecrossblock.sh
|
|
libexec/bbmap/summarizemerge.sh
|
|
libexec/bbmap/summarizequast.sh
|
|
libexec/bbmap/summarizescafstats.sh
|
|
libexec/bbmap/summarizeseal.sh
|
|
libexec/bbmap/summarizesketch.sh
|
|
libexec/bbmap/synthmda.sh
|
|
libexec/bbmap/tadpipe.sh
|
|
libexec/bbmap/tadpole.sh
|
|
libexec/bbmap/tadwrapper.sh
|
|
libexec/bbmap/tagandmerge.sh
|
|
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
|
|
libexec/bbmap/tetramerfreq.sh
|
|
libexec/bbmap/textfile.sh
|
|
libexec/bbmap/tiledump.sh
|
|
libexec/bbmap/train.sh
|
|
libexec/bbmap/translate6frames.sh
|
|
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
|
|
%%JAVAJARDIR%%/bbmap/align2/AbstractMapThread.java
|
|
%%JAVAJARDIR%%/bbmap/align2/AbstractMapper.class
|
|
%%JAVAJARDIR%%/bbmap/align2/AbstractMapper.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBIndex.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBIndex.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBIndex5.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBIndex5.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBIndexAcc.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBIndexAcc.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBIndexPacBio.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBIndexPacBio.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBIndexPacBioSkimmer.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBIndexPacBioSkimmer.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMap.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMap.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMap5.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMap5.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapAcc.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapAcc.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapPacBio.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapPacBio.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapPacBioSkimmer.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapPacBioSkimmer.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapThread$1.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapThread.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapThread.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapThread5$1.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapThread5.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapThread5.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadAcc$1.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadAcc.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadAcc.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadPacBio$1.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadPacBio.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadPacBio.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadPacBioSkimmer.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBMapThreadPacBioSkimmer.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBSplitter$1.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBSplitter$SetCount.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBSplitter.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBSplitter.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BBWrap.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BBWrap.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BandedAligner.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BandedAligner.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BandedAlignerConcrete.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BandedAlignerConcrete.java
|
|
%%JAVAJARDIR%%/bbmap/align2/BandedAlignerJNI.class
|
|
%%JAVAJARDIR%%/bbmap/align2/BandedAlignerJNI.java
|
|
%%JAVAJARDIR%%/bbmap/align2/Blacklist.class
|
|
%%JAVAJARDIR%%/bbmap/align2/Blacklist.java
|
|
%%JAVAJARDIR%%/bbmap/align2/Block.class
|
|
%%JAVAJARDIR%%/bbmap/align2/Block.java
|
|
%%JAVAJARDIR%%/bbmap/align2/ChromLoadThread.class
|
|
%%JAVAJARDIR%%/bbmap/align2/ChromLoadThread.java
|
|
%%JAVAJARDIR%%/bbmap/align2/CompareSamFiles$1.class
|
|
%%JAVAJARDIR%%/bbmap/align2/CompareSamFiles.class
|
|
%%JAVAJARDIR%%/bbmap/align2/CompareSamFiles.java
|
|
%%JAVAJARDIR%%/bbmap/align2/CompressString.class
|
|
%%JAVAJARDIR%%/bbmap/align2/CompressString.java
|
|
%%JAVAJARDIR%%/bbmap/align2/GapTools$Range.class
|
|
%%JAVAJARDIR%%/bbmap/align2/GapTools.class
|
|
%%JAVAJARDIR%%/bbmap/align2/GapTools.java
|
|
%%JAVAJARDIR%%/bbmap/align2/GradeSamFile$1.class
|
|
%%JAVAJARDIR%%/bbmap/align2/GradeSamFile.class
|
|
%%JAVAJARDIR%%/bbmap/align2/GradeSamFile.java
|
|
%%JAVAJARDIR%%/bbmap/align2/Index.class
|
|
%%JAVAJARDIR%%/bbmap/align2/Index.java
|
|
%%JAVAJARDIR%%/bbmap/align2/IndexMaker4$BlockMaker$CountThread.class
|
|
%%JAVAJARDIR%%/bbmap/align2/IndexMaker4$BlockMaker.class
|
|
%%JAVAJARDIR%%/bbmap/align2/IndexMaker4.class
|
|
%%JAVAJARDIR%%/bbmap/align2/IndexMaker4.java
|
|
%%JAVAJARDIR%%/bbmap/align2/IndexMaker5$BlockMaker$CountThread.class
|
|
%%JAVAJARDIR%%/bbmap/align2/IndexMaker5$BlockMaker.class
|
|
%%JAVAJARDIR%%/bbmap/align2/IndexMaker5.class
|
|
%%JAVAJARDIR%%/bbmap/align2/IndexMaker5.java
|
|
%%JAVAJARDIR%%/bbmap/align2/KeyRing.class
|
|
%%JAVAJARDIR%%/bbmap/align2/KeyRing.java
|
|
%%JAVAJARDIR%%/bbmap/align2/MSA.class
|
|
%%JAVAJARDIR%%/bbmap/align2/MSA.java
|
|
%%JAVAJARDIR%%/bbmap/align2/MakeQualityHistogram.class
|
|
%%JAVAJARDIR%%/bbmap/align2/MakeQualityHistogram.java
|
|
%%JAVAJARDIR%%/bbmap/align2/MakeRocCurve$1.class
|
|
%%JAVAJARDIR%%/bbmap/align2/MakeRocCurve.class
|
|
%%JAVAJARDIR%%/bbmap/align2/MakeRocCurve.java
|
|
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner10ts.class
|
|
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner10ts.java
|
|
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner11ts.class
|
|
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner11ts.java
|
|
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner11tsJNI.class
|
|
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner11tsJNI.java
|
|
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9Flat.class
|
|
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9Flat.java
|
|
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9PacBio.class
|
|
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9PacBio.java
|
|
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9XFlat.class
|
|
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9XFlat.java
|
|
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9ts.class
|
|
%%JAVAJARDIR%%/bbmap/align2/MultiStateAligner9ts.java
|
|
%%JAVAJARDIR%%/bbmap/align2/NeedlemanWunsch.class
|
|
%%JAVAJARDIR%%/bbmap/align2/NeedlemanWunsch.java
|
|
%%JAVAJARDIR%%/bbmap/align2/PackedHeap.class
|
|
%%JAVAJARDIR%%/bbmap/align2/PackedHeap.java
|
|
%%JAVAJARDIR%%/bbmap/align2/Pointer.class
|
|
%%JAVAJARDIR%%/bbmap/align2/Pointer.java
|
|
%%JAVAJARDIR%%/bbmap/align2/PrintTime.class
|
|
%%JAVAJARDIR%%/bbmap/align2/PrintTime.java
|
|
%%JAVAJARDIR%%/bbmap/align2/Quad.class
|
|
%%JAVAJARDIR%%/bbmap/align2/Quad.java
|
|
%%JAVAJARDIR%%/bbmap/align2/Quad64.class
|
|
%%JAVAJARDIR%%/bbmap/align2/Quad64.java
|
|
%%JAVAJARDIR%%/bbmap/align2/Quad64Heap.class
|
|
%%JAVAJARDIR%%/bbmap/align2/Quad64Heap.java
|
|
%%JAVAJARDIR%%/bbmap/align2/QuadHeap.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput.java
|
|
%%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput2.class
|
|
%%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput2.java
|
|
%%JAVAJARDIR%%/bbmap/align2/Solver.class
|
|
%%JAVAJARDIR%%/bbmap/align2/Solver.java
|
|
%%JAVAJARDIR%%/bbmap/align2/SplitMappedReads.class
|
|
%%JAVAJARDIR%%/bbmap/align2/SplitMappedReads.java
|
|
%%JAVAJARDIR%%/bbmap/align2/TranslateColorspaceRead.class
|
|
%%JAVAJARDIR%%/bbmap/align2/TranslateColorspaceRead.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/AlignRandom$1.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/AlignRandom.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/AlignRandom.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/Aligner.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/Aligner.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/Alignment.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/Alignment.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/AlignmentResult.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/AlignmentResult.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/AllToAll$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$Cell.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/Ksw2gg.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/Ksw2gg.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/KswGgJava.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/KswGgJava.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/MSAViz.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/MSAViz.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/MicroAligner.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/MicroAligner.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/MicroAligner2.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/MicroAligner2.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/MicroAligner3.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/MicroAligner3.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/MicroIndex3.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/MicroIndex3.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/MicroWrapper$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
|
|
%%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter2.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/MultiStateAligner9PacBioAdapter3.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat2.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat2.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat2Amino.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat2Amino.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat2_1D.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat2_1D.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat3.class
|
|
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlat3.java
|
|
%%JAVAJARDIR%%/bbmap/aligner/SingleStateAlignerFlatFloat.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/assemble/AbstractExploreThread.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/AbstractProcessContigThread.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/AbstractProcessContigThread.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/AbstractRemoveThread$RemoveThread1.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/AbstractRemoveThread$RemoveThread2.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/AbstractRemoveThread.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/AbstractRemoveThread.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/AbstractShaveThread.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/AbstractShaveThread.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/BubblePopper.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/BubblePopper.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/Contig.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Contig.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/Edge.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Edge.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/ErrorTracker.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/ErrorTracker.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/KmerCompressor$BuildThread.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/KmerCompressor.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/assemble/ShaveObject.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/Shaver.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Shaver.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/Shaver1$ExploreThread.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Shaver1$ShaveThread.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Shaver1.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Shaver1.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/Shaver2$ExploreThread.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Shaver2$ShaveThread.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Shaver2.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Shaver2.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/TadPipe.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/TadPipe.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/Tadpole$DumpKmersThread.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Tadpole$ExtendThread.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Tadpole$MakeKhistThread.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Tadpole.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Tadpole.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/Tadpole1$BuildThread.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Tadpole1$ProcessContigThread.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Tadpole1.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Tadpole1.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/Tadpole2$BuildThread.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Tadpole2$ProcessContigThread.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Tadpole2.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/Tadpole2.java
|
|
%%JAVAJARDIR%%/bbmap/assemble/TadpoleWrapper$1.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/TadpoleWrapper$Record.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/TadpoleWrapper.class
|
|
%%JAVAJARDIR%%/bbmap/assemble/TadpoleWrapper.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/AnalyzeBarcodes.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/AnalyzeBarcodes.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/Barcode.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/Barcode.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/BarcodeCounter.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/BarcodeCounter.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/BarcodeMappingStats.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/BarcodeMappingStats.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/BarcodeStats.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/BarcodeStats.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/CompareLabels$Label.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/CompareLabels.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/CompareLabels.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/CorrelateBarcodes.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/CorrelateBarcodes.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/CountBarcodes.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/CountBarcodes.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/CountBarcodes2.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/CountBarcodes2.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/DemuxClient.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/DemuxClient.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/DemuxData.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/DemuxData.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$BaseHandler.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$DemuxHandler.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$IconHandler.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$KillHandler.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$Pair.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer$StatsHandler.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/DemuxServer.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/LegacyFileWriter$QTag.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/LegacyFileWriter.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/LegacyFileWriter.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/NovaDemux.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/NovaDemux.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/PCRMatrix$MapLine.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/PCRMatrix.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/PCRMatrix.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/PCRMatrixHDist$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
|
|
%%JAVAJARDIR%%/bbmap/barcode/Transition.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixProb.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixProb.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixProbAbstract.class
|
|
%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixProbAbstract.java
|
|
%%JAVAJARDIR%%/bbmap/barcode/stub/PCRMatrixTile.class
|
|
%%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$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/bin/QuickBin.class
|
|
%%JAVAJARDIR%%/bbmap/bin/QuickBin.java
|
|
%%JAVAJARDIR%%/bbmap/bin/README.md
|
|
%%JAVAJARDIR%%/bbmap/bin/SamLoader$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$LoadThread.class
|
|
%%JAVAJARDIR%%/bbmap/bin/SpectraCounter.class
|
|
%%JAVAJARDIR%%/bbmap/bin/SpectraCounter.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/BloomFilter.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/BloomFilter.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrector.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrector.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrectorWrapper$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrectorWrapper.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrectorWrapper.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterWrapper$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterWrapper.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/BloomFilterWrapper.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/ErrorCorrect$1.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/ErrorCorrect.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/ErrorCorrect.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/IndexCounter$CountThread.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/IndexCounter.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/IndexCounter.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray$AllocThread.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray2.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray2.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray3.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray3.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray4.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray4.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray4MT$WriteThread.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray4MT.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray4MT.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray5MT$WriteThread.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray5MT.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray5MT.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray6MT$WriteThread.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray6MT.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray6MT.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray7MT$WriteThread.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray7MT.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray7MT.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray7MTA$CountUsedThread.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray7MTA.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray7MTA.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray8MT$WriteThread.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray8MT.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KCountArray8MT.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/KmerCount3.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KmerCount3.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/KmerCount4.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KmerCount4.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/KmerCount5.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KmerCount5.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/KmerCount6.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KmerCount6.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/KmerCountAbstract.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/KmerCountAbstract.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount2.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount2.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/ParseBloomFilter.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/ParseBloomFilter.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/PolyFilter$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
|
|
%%JAVAJARDIR%%/bbmap/bloom/ReadCounter.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/ReadCounter_old$1.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/ReadCounter_old$CountThread.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/ReadCounter_old.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/ReadCounter_old.java
|
|
%%JAVAJARDIR%%/bbmap/bloom/TestLargeKmer.class
|
|
%%JAVAJARDIR%%/bbmap/bloom/TestLargeKmer.java
|
|
%%JAVAJARDIR%%/bbmap/cardinality/BBLog.class
|
|
%%JAVAJARDIR%%/bbmap/cardinality/BBLog.java
|
|
%%JAVAJARDIR%%/bbmap/cardinality/BBLog_simple.class
|
|
%%JAVAJARDIR%%/bbmap/cardinality/BBLog_simple.java
|
|
%%JAVAJARDIR%%/bbmap/cardinality/CardinalityTracker.class
|
|
%%JAVAJARDIR%%/bbmap/cardinality/CardinalityTracker.java
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLog.class
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLog.java
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLog16.class
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLog16.java
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLog2.class
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLog2.java
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLog8.class
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLog8.java
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLog8_simple.class
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLog8_simple.java
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLogWrapper$LogLogThread.class
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLogWrapper.class
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLogWrapper.java
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLog_old$LogLogWrapper$LogLogThread.class
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLog_old$LogLogWrapper.class
|
|
%%JAVAJARDIR%%/bbmap/cardinality/LogLog_old.class
|
|
%%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$ClumpThread.class
|
|
%%JAVAJARDIR%%/bbmap/clump/ClumpList$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/clump/ClumpList.class
|
|
%%JAVAJARDIR%%/bbmap/clump/ClumpList.java
|
|
%%JAVAJARDIR%%/bbmap/clump/ClumpTools.class
|
|
%%JAVAJARDIR%%/bbmap/clump/ClumpTools.java
|
|
%%JAVAJARDIR%%/bbmap/clump/Clumpify.class
|
|
%%JAVAJARDIR%%/bbmap/clump/Clumpify.java
|
|
%%JAVAJARDIR%%/bbmap/clump/Hasher.class
|
|
%%JAVAJARDIR%%/bbmap/clump/Hasher.java
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerComparator$HashThread.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerComparator.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerComparator.java
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerComparator2.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerComparator2.java
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerComparatorX.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerComparatorX.java
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerComparatorY.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerComparatorY.java
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerReduce$HashThread.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerReduce.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerReduce.java
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerSort$FetchThread1.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerSort$HashSplitThread.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerSort.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerSort.java
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerSort1.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerSort1.java
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerSort2.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerSort2.java
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerSort3$FetchThread3$FetchSubThread.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerSort3$FetchThread3.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerSort3.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerSort3.java
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerSplit$HashThread.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerSplit.class
|
|
%%JAVAJARDIR%%/bbmap/clump/KmerSplit.java
|
|
%%JAVAJARDIR%%/bbmap/clump/PivotSet$HashThread.class
|
|
%%JAVAJARDIR%%/bbmap/clump/PivotSet.class
|
|
%%JAVAJARDIR%%/bbmap/clump/PivotSet.java
|
|
%%JAVAJARDIR%%/bbmap/clump/README.md
|
|
%%JAVAJARDIR%%/bbmap/clump/ReadKey.class
|
|
%%JAVAJARDIR%%/bbmap/clump/ReadKey.java
|
|
%%JAVAJARDIR%%/bbmap/clump/Splitter.class
|
|
%%JAVAJARDIR%%/bbmap/clump/Splitter.java
|
|
%%JAVAJARDIR%%/bbmap/clump/StreamToOutput.class
|
|
%%JAVAJARDIR%%/bbmap/clump/StreamToOutput.java
|
|
%%JAVAJARDIR%%/bbmap/cluster/Cluster.class
|
|
%%JAVAJARDIR%%/bbmap/cluster/Cluster.java
|
|
%%JAVAJARDIR%%/bbmap/cluster/ClusterTools.class
|
|
%%JAVAJARDIR%%/bbmap/cluster/ClusterTools.java
|
|
%%JAVAJARDIR%%/bbmap/cluster/MergeReadHeaders.class
|
|
%%JAVAJARDIR%%/bbmap/cluster/MergeReadHeaders.java
|
|
%%JAVAJARDIR%%/bbmap/cluster/README.md
|
|
%%JAVAJARDIR%%/bbmap/cluster/ReadTag.class
|
|
%%JAVAJARDIR%%/bbmap/cluster/ReadTag.java
|
|
%%JAVAJARDIR%%/bbmap/cluster/ReclusterByKmer$ClusterThread.class
|
|
%%JAVAJARDIR%%/bbmap/cluster/ReclusterByKmer.class
|
|
%%JAVAJARDIR%%/bbmap/cluster/ReclusterByKmer.java
|
|
%%JAVAJARDIR%%/bbmap/consensus/BaseGraph.class
|
|
%%JAVAJARDIR%%/bbmap/consensus/BaseGraph.java
|
|
%%JAVAJARDIR%%/bbmap/consensus/BaseGraphPart.class
|
|
%%JAVAJARDIR%%/bbmap/consensus/BaseGraphPart.java
|
|
%%JAVAJARDIR%%/bbmap/consensus/BaseNode.class
|
|
%%JAVAJARDIR%%/bbmap/consensus/BaseNode.java
|
|
%%JAVAJARDIR%%/bbmap/consensus/ConsensusMaker$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/consensus/ConsensusMaker.class
|
|
%%JAVAJARDIR%%/bbmap/consensus/ConsensusMaker.java
|
|
%%JAVAJARDIR%%/bbmap/consensus/ConsensusObject.class
|
|
%%JAVAJARDIR%%/bbmap/consensus/ConsensusObject.java
|
|
%%JAVAJARDIR%%/bbmap/consensus/FixScaffoldGaps$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/consensus/FixScaffoldGaps$Scaffold.class
|
|
%%JAVAJARDIR%%/bbmap/consensus/FixScaffoldGaps.class
|
|
%%JAVAJARDIR%%/bbmap/consensus/FixScaffoldGaps.java
|
|
%%JAVAJARDIR%%/bbmap/consensus/Lilypad$Contig.class
|
|
%%JAVAJARDIR%%/bbmap/consensus/Lilypad$Edge.class
|
|
%%JAVAJARDIR%%/bbmap/consensus/Lilypad$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
|
|
%%JAVAJARDIR%%/bbmap/dna/AminoAcid.java
|
|
%%JAVAJARDIR%%/bbmap/dna/ChromArrayMaker.class
|
|
%%JAVAJARDIR%%/bbmap/dna/ChromArrayMaker.java
|
|
%%JAVAJARDIR%%/bbmap/dna/ChromToFasta$1.class
|
|
%%JAVAJARDIR%%/bbmap/dna/ChromToFasta.class
|
|
%%JAVAJARDIR%%/bbmap/dna/ChromToFasta.java
|
|
%%JAVAJARDIR%%/bbmap/dna/ChromosomeArray.class
|
|
%%JAVAJARDIR%%/bbmap/dna/ChromosomeArray.java
|
|
%%JAVAJARDIR%%/bbmap/dna/Data.class
|
|
%%JAVAJARDIR%%/bbmap/dna/Data.java
|
|
%%JAVAJARDIR%%/bbmap/dna/Exon.class
|
|
%%JAVAJARDIR%%/bbmap/dna/Exon.java
|
|
%%JAVAJARDIR%%/bbmap/dna/FastaToChromArrays2$1.class
|
|
%%JAVAJARDIR%%/bbmap/dna/FastaToChromArrays2.class
|
|
%%JAVAJARDIR%%/bbmap/dna/FastaToChromArrays2.java
|
|
%%JAVAJARDIR%%/bbmap/dna/Gene.class
|
|
%%JAVAJARDIR%%/bbmap/dna/Gene.java
|
|
%%JAVAJARDIR%%/bbmap/dna/GeneSet.class
|
|
%%JAVAJARDIR%%/bbmap/dna/GeneSet.java
|
|
%%JAVAJARDIR%%/bbmap/dna/Matrix.class
|
|
%%JAVAJARDIR%%/bbmap/dna/Matrix.java
|
|
%%JAVAJARDIR%%/bbmap/dna/Motif.class
|
|
%%JAVAJARDIR%%/bbmap/dna/Motif.java
|
|
%%JAVAJARDIR%%/bbmap/dna/MotifMulti.class
|
|
%%JAVAJARDIR%%/bbmap/dna/MotifMulti.java
|
|
%%JAVAJARDIR%%/bbmap/dna/MotifProbsN.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/dna/Scaffold.java
|
|
%%JAVAJARDIR%%/bbmap/driver/BBVersion.class
|
|
%%JAVAJARDIR%%/bbmap/driver/BBVersion.java
|
|
%%JAVAJARDIR%%/bbmap/driver/ClearRam.class
|
|
%%JAVAJARDIR%%/bbmap/driver/ClearRam.java
|
|
%%JAVAJARDIR%%/bbmap/driver/CollateSpikeIn.class
|
|
%%JAVAJARDIR%%/bbmap/driver/CollateSpikeIn.java
|
|
%%JAVAJARDIR%%/bbmap/driver/CompareReferenceGenomes.class
|
|
%%JAVAJARDIR%%/bbmap/driver/CompareReferenceGenomes.java
|
|
%%JAVAJARDIR%%/bbmap/driver/CompareSequences.class
|
|
%%JAVAJARDIR%%/bbmap/driver/CompareSequences.java
|
|
%%JAVAJARDIR%%/bbmap/driver/ConcatenateFiles.class
|
|
%%JAVAJARDIR%%/bbmap/driver/ConcatenateFiles.java
|
|
%%JAVAJARDIR%%/bbmap/driver/ConcatenateTextFiles$1.class
|
|
%%JAVAJARDIR%%/bbmap/driver/ConcatenateTextFiles$WriteThread.class
|
|
%%JAVAJARDIR%%/bbmap/driver/ConcatenateTextFiles.class
|
|
%%JAVAJARDIR%%/bbmap/driver/ConcatenateTextFiles.java
|
|
%%JAVAJARDIR%%/bbmap/driver/Concatenator.class
|
|
%%JAVAJARDIR%%/bbmap/driver/Concatenator.java
|
|
%%JAVAJARDIR%%/bbmap/driver/ConvertSamToAln.class
|
|
%%JAVAJARDIR%%/bbmap/driver/ConvertSamToAln.java
|
|
%%JAVAJARDIR%%/bbmap/driver/CorrelateIdentity.class
|
|
%%JAVAJARDIR%%/bbmap/driver/CorrelateIdentity.java
|
|
%%JAVAJARDIR%%/bbmap/driver/CountRNAs.class
|
|
%%JAVAJARDIR%%/bbmap/driver/CountRNAs.java
|
|
%%JAVAJARDIR%%/bbmap/driver/CountSharedLines.class
|
|
%%JAVAJARDIR%%/bbmap/driver/CountSharedLines.java
|
|
%%JAVAJARDIR%%/bbmap/driver/EstherFilter.class
|
|
%%JAVAJARDIR%%/bbmap/driver/EstherFilter.java
|
|
%%JAVAJARDIR%%/bbmap/driver/FilterAssemblySummary.class
|
|
%%JAVAJARDIR%%/bbmap/driver/FilterAssemblySummary.java
|
|
%%JAVAJARDIR%%/bbmap/driver/FilterLines.class
|
|
%%JAVAJARDIR%%/bbmap/driver/FilterLines.java
|
|
%%JAVAJARDIR%%/bbmap/driver/FilterReadsByName.class
|
|
%%JAVAJARDIR%%/bbmap/driver/FilterReadsByName.java
|
|
%%JAVAJARDIR%%/bbmap/driver/FindMotifs.class
|
|
%%JAVAJARDIR%%/bbmap/driver/FindMotifs.java
|
|
%%JAVAJARDIR%%/bbmap/driver/FixChr.class
|
|
%%JAVAJARDIR%%/bbmap/driver/FixChr.java
|
|
%%JAVAJARDIR%%/bbmap/driver/FixDumbFile.class
|
|
%%JAVAJARDIR%%/bbmap/driver/FixDumbFile.java
|
|
%%JAVAJARDIR%%/bbmap/driver/GenerateNoCallsFromCoverage.class
|
|
%%JAVAJARDIR%%/bbmap/driver/GenerateNoCallsFromCoverage.java
|
|
%%JAVAJARDIR%%/bbmap/driver/GetSequence.class
|
|
%%JAVAJARDIR%%/bbmap/driver/GetSequence.java
|
|
%%JAVAJARDIR%%/bbmap/driver/GetUniquePrefixes.class
|
|
%%JAVAJARDIR%%/bbmap/driver/GetUniquePrefixes.java
|
|
%%JAVAJARDIR%%/bbmap/driver/Grep.class
|
|
%%JAVAJARDIR%%/bbmap/driver/Grep.java
|
|
%%JAVAJARDIR%%/bbmap/driver/Life.class
|
|
%%JAVAJARDIR%%/bbmap/driver/Life.java
|
|
%%JAVAJARDIR%%/bbmap/driver/LineCount.class
|
|
%%JAVAJARDIR%%/bbmap/driver/LineCount.java
|
|
%%JAVAJARDIR%%/bbmap/driver/LoadReads.class
|
|
%%JAVAJARDIR%%/bbmap/driver/LoadReads.java
|
|
%%JAVAJARDIR%%/bbmap/driver/LookAtID.class
|
|
%%JAVAJARDIR%%/bbmap/driver/LookAtID.java
|
|
%%JAVAJARDIR%%/bbmap/driver/MakeTestScript.class
|
|
%%JAVAJARDIR%%/bbmap/driver/MakeTestScript.java
|
|
%%JAVAJARDIR%%/bbmap/driver/MakeTestScriptScoreOnly.class
|
|
%%JAVAJARDIR%%/bbmap/driver/MakeTestScriptScoreOnly.java
|
|
%%JAVAJARDIR%%/bbmap/driver/MeasureGene.class
|
|
%%JAVAJARDIR%%/bbmap/driver/MeasureGene.java
|
|
%%JAVAJARDIR%%/bbmap/driver/MergeBigelow.class
|
|
%%JAVAJARDIR%%/bbmap/driver/MergeBigelow.java
|
|
%%JAVAJARDIR%%/bbmap/driver/MergeCoverageOTU.class
|
|
%%JAVAJARDIR%%/bbmap/driver/MergeCoverageOTU.java
|
|
%%JAVAJARDIR%%/bbmap/driver/MergeTextFiles.class
|
|
%%JAVAJARDIR%%/bbmap/driver/MergeTextFiles.java
|
|
%%JAVAJARDIR%%/bbmap/driver/MergeTextFiles2.class
|
|
%%JAVAJARDIR%%/bbmap/driver/MergeTextFiles2.java
|
|
%%JAVAJARDIR%%/bbmap/driver/MoveFiles.class
|
|
%%JAVAJARDIR%%/bbmap/driver/MoveFiles.java
|
|
%%JAVAJARDIR%%/bbmap/driver/ParseCrossblockResults$ResultsLine.class
|
|
%%JAVAJARDIR%%/bbmap/driver/ParseCrossblockResults.class
|
|
%%JAVAJARDIR%%/bbmap/driver/ParseCrossblockResults.java
|
|
%%JAVAJARDIR%%/bbmap/driver/PlotGC.class
|
|
%%JAVAJARDIR%%/bbmap/driver/PlotGC.java
|
|
%%JAVAJARDIR%%/bbmap/driver/PrintEnv.class
|
|
%%JAVAJARDIR%%/bbmap/driver/PrintEnv.java
|
|
%%JAVAJARDIR%%/bbmap/driver/ProcessFragMerging.class
|
|
%%JAVAJARDIR%%/bbmap/driver/ProcessFragMerging.java
|
|
%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed.class
|
|
%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed.java
|
|
%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed2.class
|
|
%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed2.java
|
|
%%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.class
|
|
%%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.java
|
|
%%JAVAJARDIR%%/bbmap/driver/README.md
|
|
%%JAVAJARDIR%%/bbmap/driver/ReduceSilva.class
|
|
%%JAVAJARDIR%%/bbmap/driver/ReduceSilva.java
|
|
%%JAVAJARDIR%%/bbmap/driver/RenameAndMux$MuxThread.class
|
|
%%JAVAJARDIR%%/bbmap/driver/RenameAndMux.class
|
|
%%JAVAJARDIR%%/bbmap/driver/RenameAndMux.java
|
|
%%JAVAJARDIR%%/bbmap/driver/RenameByHeader.class
|
|
%%JAVAJARDIR%%/bbmap/driver/RenameByHeader.java
|
|
%%JAVAJARDIR%%/bbmap/driver/RenameNcbiToTid.class
|
|
%%JAVAJARDIR%%/bbmap/driver/RenameNcbiToTid.java
|
|
%%JAVAJARDIR%%/bbmap/driver/RenameRefseqFiles.class
|
|
%%JAVAJARDIR%%/bbmap/driver/RenameRefseqFiles.java
|
|
%%JAVAJARDIR%%/bbmap/driver/Sample.class
|
|
%%JAVAJARDIR%%/bbmap/driver/Sample.java
|
|
%%JAVAJARDIR%%/bbmap/driver/Search.class
|
|
%%JAVAJARDIR%%/bbmap/driver/Search.java
|
|
%%JAVAJARDIR%%/bbmap/driver/SelectReads.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SelectReads.java
|
|
%%JAVAJARDIR%%/bbmap/driver/SniffSplices.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SniffSplices.java
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeContamReport$ComparatorA.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeContamReport$ComparatorB.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeContamReport$StringLongLong.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeContamReport.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeContamReport.java
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeCoverage.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeCoverage.java
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeCrossblock.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeCrossblock.java
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeMSDIN.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeMSDIN.java
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeQuast$Entry.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeQuast$QuastSummary.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeQuast.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeQuast.java
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeSealCrosstalk$Result.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeSealCrosstalk.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeSealCrosstalk.java
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeSealStats$SealSummary.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeSealStats.class
|
|
%%JAVAJARDIR%%/bbmap/driver/SummarizeSealStats.java
|
|
%%JAVAJARDIR%%/bbmap/driver/TestCompressionSpeed.class
|
|
%%JAVAJARDIR%%/bbmap/driver/TestCompressionSpeed.java
|
|
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$1.class
|
|
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$AtomBox.class
|
|
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$CountBox.class
|
|
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$CountThread.class
|
|
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$LockBox.class
|
|
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$VolatileBox.class
|
|
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed.class
|
|
%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed.java
|
|
%%JAVAJARDIR%%/bbmap/driver/Translator.class
|
|
%%JAVAJARDIR%%/bbmap/driver/Translator.java
|
|
%%JAVAJARDIR%%/bbmap/driver/Translator2.class
|
|
%%JAVAJARDIR%%/bbmap/driver/Translator2.java
|
|
%%JAVAJARDIR%%/bbmap/driver/TransposeTextFile.class
|
|
%%JAVAJARDIR%%/bbmap/driver/TransposeTextFile.java
|
|
%%JAVAJARDIR%%/bbmap/driver/TrimSamFile.class
|
|
%%JAVAJARDIR%%/bbmap/driver/TrimSamFile.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ArrayFile.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ArrayFile.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile2$BF1Thread.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile2.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ByteFile2.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ByteStreamWriter.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ByteStreamWriter.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ChainBlock.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ChainBlock.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ChainLine.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/fileIO/CopyFiles.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/CopyFiles.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/CopyFiles2.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/CopyFiles2.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/FileFormat.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/FileFormat.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/FindFiles.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/FindFiles.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/GenericTextFile.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/GenericTextFile.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/LoadThread.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/LoadThread.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/MatrixFile.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/MatrixFile.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/OpenFile.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/OpenFile.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/PipeThread.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ReadWrite.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/ReadWrite.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/SummaryFile$1.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/SummaryFile.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/SummaryFile.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/TextFile.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/TextFile.java
|
|
%%JAVAJARDIR%%/bbmap/fileIO/TextStreamWriter.class
|
|
%%JAVAJARDIR%%/bbmap/fileIO/TextStreamWriter.java
|
|
%%JAVAJARDIR%%/bbmap/fun/Calc.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Calc.java
|
|
%%JAVAJARDIR%%/bbmap/fun/Chance.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Chance.java
|
|
%%JAVAJARDIR%%/bbmap/fun/Crunch.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Crunch.java
|
|
%%JAVAJARDIR%%/bbmap/fun/DiskBench$ReadThread.class
|
|
%%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$Edge.class
|
|
%%JAVAJARDIR%%/bbmap/fun/FindPath$Node.class
|
|
%%JAVAJARDIR%%/bbmap/fun/FindPath$Path.class
|
|
%%JAVAJARDIR%%/bbmap/fun/FindPath.class
|
|
%%JAVAJARDIR%%/bbmap/fun/FindPath.java
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo.java
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo2.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo2.java
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo3$LongList.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo3$Pair.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo3.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo3.java
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo4$Pair.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo4.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo4.java
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo5$LongList.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo5.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo5.java
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo6.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo6.java
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo7.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Foo7.java
|
|
%%JAVAJARDIR%%/bbmap/fun/Genetic$Bug.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Genetic.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Genetic.java
|
|
%%JAVAJARDIR%%/bbmap/fun/Life.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Life.java
|
|
%%JAVAJARDIR%%/bbmap/fun/MakeAdjacencyList$1.class
|
|
%%JAVAJARDIR%%/bbmap/fun/MakeAdjacencyList.class
|
|
%%JAVAJARDIR%%/bbmap/fun/MakeAdjacencyList.java
|
|
%%JAVAJARDIR%%/bbmap/fun/Merced$Person.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Merced.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Merced.java
|
|
%%JAVAJARDIR%%/bbmap/fun/PalSim.class
|
|
%%JAVAJARDIR%%/bbmap/fun/PalSim.java
|
|
%%JAVAJARDIR%%/bbmap/fun/Palindrome.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Palindrome.java
|
|
%%JAVAJARDIR%%/bbmap/fun/Palindrome2$Drome.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Palindrome2.class
|
|
%%JAVAJARDIR%%/bbmap/fun/Palindrome2.java
|
|
%%JAVAJARDIR%%/bbmap/fun/ParseDouble.class
|
|
%%JAVAJARDIR%%/bbmap/fun/ParseDouble.java
|
|
%%JAVAJARDIR%%/bbmap/fun/ProbShared.class
|
|
%%JAVAJARDIR%%/bbmap/fun/ProbShared.java
|
|
%%JAVAJARDIR%%/bbmap/fun/ProbShared2.class
|
|
%%JAVAJARDIR%%/bbmap/fun/ProbShared2.java
|
|
%%JAVAJARDIR%%/bbmap/fun/ProbShared3.class
|
|
%%JAVAJARDIR%%/bbmap/fun/ProbShared3.java
|
|
%%JAVAJARDIR%%/bbmap/fun/README.md
|
|
%%JAVAJARDIR%%/bbmap/gff/CompareGff.class
|
|
%%JAVAJARDIR%%/bbmap/gff/CompareGff.java
|
|
%%JAVAJARDIR%%/bbmap/gff/CompareGff_old.class
|
|
%%JAVAJARDIR%%/bbmap/gff/CompareGff_old.java
|
|
%%JAVAJARDIR%%/bbmap/gff/CutGff$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/gff/CutGff.class
|
|
%%JAVAJARDIR%%/bbmap/gff/CutGff.java
|
|
%%JAVAJARDIR%%/bbmap/gff/CutGff_ST.class
|
|
%%JAVAJARDIR%%/bbmap/gff/CutGff_ST.java
|
|
%%JAVAJARDIR%%/bbmap/gff/GbffFeature.class
|
|
%%JAVAJARDIR%%/bbmap/gff/GbffFeature.java
|
|
%%JAVAJARDIR%%/bbmap/gff/GbffFile.class
|
|
%%JAVAJARDIR%%/bbmap/gff/GbffFile.java
|
|
%%JAVAJARDIR%%/bbmap/gff/GbffLocus.class
|
|
%%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$1.class
|
|
%%JAVAJARDIR%%/bbmap/gff/VcfToGff.class
|
|
%%JAVAJARDIR%%/bbmap/gff/VcfToGff.java
|
|
%%JAVAJARDIR%%/bbmap/hiseq/AnalyzeFlowCell$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/AnalyzeFlowCell.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/AnalyzeFlowCell.java
|
|
%%JAVAJARDIR%%/bbmap/hiseq/BGI2Illumina.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/BGI2Illumina.java
|
|
%%JAVAJARDIR%%/bbmap/hiseq/BGIHeaderParser.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/BGIHeaderParser.java
|
|
%%JAVAJARDIR%%/bbmap/hiseq/BGIHeaderParser2.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/BGIHeaderParser2.java
|
|
%%JAVAJARDIR%%/bbmap/hiseq/CycleTracker.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/CycleTracker.java
|
|
%%JAVAJARDIR%%/bbmap/hiseq/FlowCell.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/FlowCell.java
|
|
%%JAVAJARDIR%%/bbmap/hiseq/FlowcellCoordinate.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/FlowcellCoordinate.java
|
|
%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser1.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser1.java
|
|
%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser2.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser2.java
|
|
%%JAVAJARDIR%%/bbmap/hiseq/Lane$TileIterator.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/Lane.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/Lane.java
|
|
%%JAVAJARDIR%%/bbmap/hiseq/MicroTile.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/MicroTile.java
|
|
%%JAVAJARDIR%%/bbmap/hiseq/PlotFlowCell$WorkerThread.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/PlotFlowCell.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/PlotFlowCell.java
|
|
%%JAVAJARDIR%%/bbmap/hiseq/PlotHist.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/hiseq/Tile.java
|
|
%%JAVAJARDIR%%/bbmap/hiseq/TileDump.class
|
|
%%JAVAJARDIR%%/bbmap/hiseq/TileDump.java
|
|
%%JAVAJARDIR%%/bbmap/hmm/HMMSearchLine.class
|
|
%%JAVAJARDIR%%/bbmap/hmm/HMMSearchLine.java
|
|
%%JAVAJARDIR%%/bbmap/hmm/HMMSearchReport.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJNI.java
|
|
%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJava.class
|
|
%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJava.java
|
|
%%JAVAJARDIR%%/bbmap/icecream/IceCreamFinder$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/icecream/IceCreamFinder.class
|
|
%%JAVAJARDIR%%/bbmap/icecream/IceCreamFinder.java
|
|
%%JAVAJARDIR%%/bbmap/icecream/IceCreamGrader.class
|
|
%%JAVAJARDIR%%/bbmap/icecream/IceCreamGrader.java
|
|
%%JAVAJARDIR%%/bbmap/icecream/IceCreamMaker$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/icecream/IceCreamMaker.class
|
|
%%JAVAJARDIR%%/bbmap/icecream/IceCreamMaker.java
|
|
%%JAVAJARDIR%%/bbmap/icecream/PBHeader.class
|
|
%%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$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio.class
|
|
%%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio.java
|
|
%%JAVAJARDIR%%/bbmap/icecream/ZMW.class
|
|
%%JAVAJARDIR%%/bbmap/icecream/ZMW.java
|
|
%%JAVAJARDIR%%/bbmap/icecream/ZMWStreamer.class
|
|
%%JAVAJARDIR%%/bbmap/icecream/ZMWStreamer.java
|
|
%%JAVAJARDIR%%/bbmap/jasper/KmerPosition.class
|
|
%%JAVAJARDIR%%/bbmap/jasper/KmerPosition.java
|
|
%%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.class
|
|
%%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.java
|
|
%%JAVAJARDIR%%/bbmap/jasper/README.md
|
|
%%JAVAJARDIR%%/bbmap/jgi/AddAdapters.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/AddAdapters.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/AdjustHomopolymers.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/AdjustHomopolymers.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/Assembly.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Assembly.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2$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$LoadThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/BBDuk$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/BBDuk.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/BBDuk.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/BBMask$MaskLowEntropyThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/BBMask$MaskRepeatThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/BBMask$MaskSamThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/BBMask.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/BBMask.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/BBMerge$MateThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/BBMerge.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/BBMerge.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/BBMergeOverlapper.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/BBMergeOverlapper.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/BBQC.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/BBQC.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/CalcTrueQuality$CountMatrixSet.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CalcTrueQuality$GBMatrixSet.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CalcTrueQuality$Worker.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CalcTrueQuality.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CalcTrueQuality.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/CalcUniqueness$Counter.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CalcUniqueness.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CalcUniqueness.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/CallPeaks$Peak.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CallPeaks.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CallPeaks.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/CheckStrand.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CheckStrand.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/CheckStrand2$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CheckStrand2$Seq.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CheckStrand2.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CheckStrand2.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/Consect.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Consect.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/CountDuplicates$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CountDuplicates.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CountDuplicates.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/CountDuplicatesBuffered$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CountDuplicatesBuffered.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CountDuplicatesBuffered.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/CountGC$1.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CountGC.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CountGC.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/CountUniqueness.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CountUniqueness.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/CovStatsLine.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CovStatsLine.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/CoveragePileup.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CoveragePileup.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/CoveragePileupMT$LoadThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CoveragePileupMT.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CoveragePileupMT.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/CrisprFinder$1.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CrisprFinder$Alignment.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CrisprFinder$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CrisprFinder.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CrisprFinder.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/CutPrimers.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/CutPrimers.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/DecontaminateByNormalization.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/DecontaminateByNormalization.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe$ClusterLengthComparator.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe$ClusterThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe$HashThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe$MstThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe$Overlap.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe$Unit.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe$UnitOffsetComparator.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2$ClusterLengthComparator.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2$ClusterThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2$HashThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2$MstThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2$Overlap.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2$Unit.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2$UnitOffsetComparator.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Dedupe2.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/DedupeByMapping$Quad.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/DedupeByMapping.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/DedupeByMapping.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein$ClusterLengthComparator.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein$ClusterThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein$HashThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein$MstThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein$Overlap.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein$Unit.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein$UnitOffsetComparator.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/DedupeProtein.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/DemuxByName.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/DemuxByName.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/DemuxByName2.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/DemuxByName2.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/Difference.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Difference.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/FilterByCoverage.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/FilterByCoverage.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/FilterBySequence$Code.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/FilterBySequence$LoadThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/FilterBySequence$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/FilterBySequence.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/FilterBySequence.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/FilterReadsWithSubs.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/FilterReadsWithSubs.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/FindHiCJunctions.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/FindHiCJunctions.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/FindPrimers$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/FindPrimers.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/FindPrimers.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/FindPrimers_old.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/FindPrimers_old.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/FindString.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/FindString.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/FungalRelease.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/FungalRelease.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$KapaEntry.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$Plate.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$TagData.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$Well.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/GetReads.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/GetReads.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/GradeMergedReads.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/GradeMergedReads.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/GreedyBarCodeFinder.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/GreedyBarCodeFinder.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/IdentityMatrix$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/IdentityMatrix.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/IdentityMatrix.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/Info.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Info.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/KExpand.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/KExpand.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/KeepBestCopy.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/KeepBestCopy.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerCountExact$DumpKmersThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerCountExact$MakeKhistThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerCountExact.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerCountExact.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerCountMulti$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerCountMulti.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerCountMulti.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerCoverage$1.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerCoverage$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerCoverage.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerCoverage.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerFilterSetMaker.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerFilterSetMaker.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerNormalize$1.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerNormalize$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerNormalize.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerNormalize.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerSample.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/KmerSample.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram$1.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/MakePolymers.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/MakePolymers.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/MergeBarcodes.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/MergeBarcodes.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/MergeSam.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/MergeSam.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/Orf.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Orf.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/PartitionReads$Partition.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/PartitionReads.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/PartitionReads.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/PhylipToFasta.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/PhylipToFasta.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/PickSubset$Edge.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/PickSubset$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/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
|
|
%%JAVAJARDIR%%/bbmap/jgi/RemapQuality.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/RemoveBadBarcodes.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/RemoveBadBarcodes.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/RenameReads.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/RenameReads.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/ReplaceHeaders.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/ReplaceHeaders.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/RepresentativeSet$Edge.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/RepresentativeSet$Node.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/RepresentativeSet.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/RepresentativeSet.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/SamToEst$1.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/SamToEst$EST.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/SamToEst.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/SamToEst.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/Seal$LoadThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Seal$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Seal.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Seal.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/SealRefInfo.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/SealRefInfo.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$CountComparator.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$Kmer.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$NumComparator.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/SplitNexteraLMP.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/SplitNexteraLMP.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/SplitPairsAndSingles.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/SplitPairsAndSingles.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/SplitSam4Way.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/SplitSam4Way.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/SplitSam6Way.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/SplitSam6Way.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/TestFilesystem$WriteThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/TestFormat$TestThread.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/TestFormat.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/TestFormat.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/TetramerFrequencies$Line.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/jgi/TrimContigs.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/TrimContigs.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/UnicodeToAscii.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/UnicodeToAscii.java
|
|
%%JAVAJARDIR%%/bbmap/jgi/Unzip.class
|
|
%%JAVAJARDIR%%/bbmap/jgi/Unzip.java
|
|
%%JAVAJARDIR%%/bbmap/json/JsonLiteral.class
|
|
%%JAVAJARDIR%%/bbmap/json/JsonLiteral.java
|
|
%%JAVAJARDIR%%/bbmap/json/JsonObject.class
|
|
%%JAVAJARDIR%%/bbmap/json/JsonObject.java
|
|
%%JAVAJARDIR%%/bbmap/json/JsonParser.class
|
|
%%JAVAJARDIR%%/bbmap/json/JsonParser.java
|
|
%%JAVAJARDIR%%/bbmap/json/README.md
|
|
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable$AllocThread.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/DumpThread.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/DumpThread.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/HashArray.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/HashArray.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/HashArray1D$Walker1D.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/HashArray1D.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/HashArray1D.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/HashArray2D.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/HashArray2D.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/HashArrayHybrid.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/HashArrayHybrid.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/HashArrayHybridFast.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/HashArrayHybridFast.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/HashBuffer.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/HashBuffer.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/HashForest.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/HashForest.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/HistogramMaker$FillThread.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/HistogramMaker.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/HistogramMaker.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerBuffer.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerBuffer.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerLink.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerLink.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerNode.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerNode.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerNode1D.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerNode1D.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerNode2D.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerNode2D.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerTable.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerTable.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet$LoadThread.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet$WalkerKST.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/README.md
|
|
%%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/SimpleKmerTable.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/SimpleKmerTable.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/TableLoaderLockFree$LoadThread.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/TableLoaderLockFree.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/TableLoaderLockFree.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/TableReader.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/TableReader.java
|
|
%%JAVAJARDIR%%/bbmap/kmer/Walker.class
|
|
%%JAVAJARDIR%%/bbmap/kmer/Walker.java
|
|
%%JAVAJARDIR%%/bbmap/ml/Bell.class
|
|
%%JAVAJARDIR%%/bbmap/ml/Bell.java
|
|
%%JAVAJARDIR%%/bbmap/ml/Cell.class
|
|
%%JAVAJARDIR%%/bbmap/ml/Cell.java
|
|
%%JAVAJARDIR%%/bbmap/ml/CellNet.class
|
|
%%JAVAJARDIR%%/bbmap/ml/CellNet.java
|
|
%%JAVAJARDIR%%/bbmap/ml/CellNetParser.class
|
|
%%JAVAJARDIR%%/bbmap/ml/CellNetParser.java
|
|
%%JAVAJARDIR%%/bbmap/ml/CellNetReverseComparator.class
|
|
%%JAVAJARDIR%%/bbmap/ml/CellNetReverseComparator.java
|
|
%%JAVAJARDIR%%/bbmap/ml/DataLoader$Triple.class
|
|
%%JAVAJARDIR%%/bbmap/ml/DataLoader.class
|
|
%%JAVAJARDIR%%/bbmap/ml/DataLoader.java
|
|
%%JAVAJARDIR%%/bbmap/ml/ExtendedMSig.class
|
|
%%JAVAJARDIR%%/bbmap/ml/ExtendedMSig.java
|
|
%%JAVAJARDIR%%/bbmap/ml/ExtendedSigmoid.class
|
|
%%JAVAJARDIR%%/bbmap/ml/ExtendedSigmoid.java
|
|
%%JAVAJARDIR%%/bbmap/ml/Function.class
|
|
%%JAVAJARDIR%%/bbmap/ml/Function.java
|
|
%%JAVAJARDIR%%/bbmap/ml/Functions.class
|
|
%%JAVAJARDIR%%/bbmap/ml/Functions.java
|
|
%%JAVAJARDIR%%/bbmap/ml/JobData.class
|
|
%%JAVAJARDIR%%/bbmap/ml/JobData.java
|
|
%%JAVAJARDIR%%/bbmap/ml/JobResults.class
|
|
%%JAVAJARDIR%%/bbmap/ml/JobResults.java
|
|
%%JAVAJARDIR%%/bbmap/ml/MSig.class
|
|
%%JAVAJARDIR%%/bbmap/ml/MSig.java
|
|
%%JAVAJARDIR%%/bbmap/ml/Matrix.class
|
|
%%JAVAJARDIR%%/bbmap/ml/Matrix.java
|
|
%%JAVAJARDIR%%/bbmap/ml/NetFilter$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/ml/NetFilter.class
|
|
%%JAVAJARDIR%%/bbmap/ml/NetFilter.java
|
|
%%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders$Header.class
|
|
%%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders.class
|
|
%%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders.java
|
|
%%JAVAJARDIR%%/bbmap/ml/Profiler.class
|
|
%%JAVAJARDIR%%/bbmap/ml/Profiler.java
|
|
%%JAVAJARDIR%%/bbmap/ml/README.md
|
|
%%JAVAJARDIR%%/bbmap/ml/RSLog.class
|
|
%%JAVAJARDIR%%/bbmap/ml/RSLog.java
|
|
%%JAVAJARDIR%%/bbmap/ml/ReduceColumns.class
|
|
%%JAVAJARDIR%%/bbmap/ml/ReduceColumns.java
|
|
%%JAVAJARDIR%%/bbmap/ml/Sample.class
|
|
%%JAVAJARDIR%%/bbmap/ml/Sample.java
|
|
%%JAVAJARDIR%%/bbmap/ml/SampleErrorComparator.class
|
|
%%JAVAJARDIR%%/bbmap/ml/SampleErrorComparator.java
|
|
%%JAVAJARDIR%%/bbmap/ml/SampleSet.class
|
|
%%JAVAJARDIR%%/bbmap/ml/SampleSet.java
|
|
%%JAVAJARDIR%%/bbmap/ml/SampleValueComparator.class
|
|
%%JAVAJARDIR%%/bbmap/ml/SampleValueComparator.java
|
|
%%JAVAJARDIR%%/bbmap/ml/ScannerThread$LaunchThread.class
|
|
%%JAVAJARDIR%%/bbmap/ml/ScannerThread.class
|
|
%%JAVAJARDIR%%/bbmap/ml/ScannerThread.java
|
|
%%JAVAJARDIR%%/bbmap/ml/ScoreSequence.class
|
|
%%JAVAJARDIR%%/bbmap/ml/ScoreSequence.java
|
|
%%JAVAJARDIR%%/bbmap/ml/Seed.class
|
|
%%JAVAJARDIR%%/bbmap/ml/Seed.java
|
|
%%JAVAJARDIR%%/bbmap/ml/SequenceToVector$1.class
|
|
%%JAVAJARDIR%%/bbmap/ml/SequenceToVector.class
|
|
%%JAVAJARDIR%%/bbmap/ml/SequenceToVector.java
|
|
%%JAVAJARDIR%%/bbmap/ml/Sigmoid.class
|
|
%%JAVAJARDIR%%/bbmap/ml/Sigmoid.java
|
|
%%JAVAJARDIR%%/bbmap/ml/Source.class
|
|
%%JAVAJARDIR%%/bbmap/ml/Source.java
|
|
%%JAVAJARDIR%%/bbmap/ml/Status.class
|
|
%%JAVAJARDIR%%/bbmap/ml/Status.java
|
|
%%JAVAJARDIR%%/bbmap/ml/Subset.class
|
|
%%JAVAJARDIR%%/bbmap/ml/Subset.java
|
|
%%JAVAJARDIR%%/bbmap/ml/Swish.class
|
|
%%JAVAJARDIR%%/bbmap/ml/Swish.java
|
|
%%JAVAJARDIR%%/bbmap/ml/Tanh.class
|
|
%%JAVAJARDIR%%/bbmap/ml/Tanh.java
|
|
%%JAVAJARDIR%%/bbmap/ml/Trainer.class
|
|
%%JAVAJARDIR%%/bbmap/ml/Trainer.java
|
|
%%JAVAJARDIR%%/bbmap/ml/TrainerThread$LaunchThread.class
|
|
%%JAVAJARDIR%%/bbmap/ml/TrainerThread.class
|
|
%%JAVAJARDIR%%/bbmap/ml/TrainerThread.java
|
|
%%JAVAJARDIR%%/bbmap/ml/WorkerThread.class
|
|
%%JAVAJARDIR%%/bbmap/ml/WorkerThread.java
|
|
%%JAVAJARDIR%%/bbmap/pacbio/CalcCoverageFromSites$1.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/CalcCoverageFromSites.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/CalcCoverageFromSites.java
|
|
%%JAVAJARDIR%%/bbmap/pacbio/GenerateMultiChrom.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/GenerateMultiChrom.java
|
|
%%JAVAJARDIR%%/bbmap/pacbio/MakePacBioScript.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/MakePacBioScript.java
|
|
%%JAVAJARDIR%%/bbmap/pacbio/MergeFastaContigs$1.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/MergeFastaContigs.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/MergeFastaContigs.java
|
|
%%JAVAJARDIR%%/bbmap/pacbio/MergeReadsAndGenome$1.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/MergeReadsAndGenome.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/MergeReadsAndGenome.java
|
|
%%JAVAJARDIR%%/bbmap/pacbio/PartitionFastaFile.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/PartitionFastaFile.java
|
|
%%JAVAJARDIR%%/bbmap/pacbio/PartitionReads$1.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/PartitionReads.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/PartitionReads.java
|
|
%%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized$1.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized$Buffer.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2.java
|
|
%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters3$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters3.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters3.java
|
|
%%JAVAJARDIR%%/bbmap/pacbio/SiteR.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/SiteR.java
|
|
%%JAVAJARDIR%%/bbmap/pacbio/SortSites$1.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/SortSites.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/SortSites.java
|
|
%%JAVAJARDIR%%/bbmap/pacbio/SplitOffPerfectContigs$1.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/SplitOffPerfectContigs.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/SplitOffPerfectContigs.java
|
|
%%JAVAJARDIR%%/bbmap/pacbio/StackSites$1.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/StackSites$Glob.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/StackSites.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/StackSites.java
|
|
%%JAVAJARDIR%%/bbmap/pacbio/StackSites2$1.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/StackSites2$Glob.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/StackSites2.class
|
|
%%JAVAJARDIR%%/bbmap/pacbio/StackSites2.java
|
|
%%JAVAJARDIR%%/bbmap/prok/AnalyzeGenes$FileThread.class
|
|
%%JAVAJARDIR%%/bbmap/prok/AnalyzeGenes.class
|
|
%%JAVAJARDIR%%/bbmap/prok/AnalyzeGenes.java
|
|
%%JAVAJARDIR%%/bbmap/prok/CallGenes$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/prok/CallGenes.class
|
|
%%JAVAJARDIR%%/bbmap/prok/CallGenes.java
|
|
%%JAVAJARDIR%%/bbmap/prok/FetchProks$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/prok/FetchProks$Stats.class
|
|
%%JAVAJARDIR%%/bbmap/prok/FetchProks.class
|
|
%%JAVAJARDIR%%/bbmap/prok/FetchProks.java
|
|
%%JAVAJARDIR%%/bbmap/prok/FilterSilva.class
|
|
%%JAVAJARDIR%%/bbmap/prok/FilterSilva.java
|
|
%%JAVAJARDIR%%/bbmap/prok/FrameStats.class
|
|
%%JAVAJARDIR%%/bbmap/prok/FrameStats.java
|
|
%%JAVAJARDIR%%/bbmap/prok/GeneCaller.class
|
|
%%JAVAJARDIR%%/bbmap/prok/GeneCaller.java
|
|
%%JAVAJARDIR%%/bbmap/prok/GeneModel.class
|
|
%%JAVAJARDIR%%/bbmap/prok/GeneModel.java
|
|
%%JAVAJARDIR%%/bbmap/prok/GeneModelParser.class
|
|
%%JAVAJARDIR%%/bbmap/prok/GeneModelParser.java
|
|
%%JAVAJARDIR%%/bbmap/prok/MergeRibo$ListComparator.class
|
|
%%JAVAJARDIR%%/bbmap/prok/MergeRibo$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/prok/MergeRibo$Ribo.class
|
|
%%JAVAJARDIR%%/bbmap/prok/MergeRibo.class
|
|
%%JAVAJARDIR%%/bbmap/prok/MergeRibo.java
|
|
%%JAVAJARDIR%%/bbmap/prok/MergeRibo_Fast$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/prok/MergeRibo_Fast$Ribo.class
|
|
%%JAVAJARDIR%%/bbmap/prok/MergeRibo_Fast.class
|
|
%%JAVAJARDIR%%/bbmap/prok/MergeRibo_Fast.java
|
|
%%JAVAJARDIR%%/bbmap/prok/Orf.class
|
|
%%JAVAJARDIR%%/bbmap/prok/Orf.java
|
|
%%JAVAJARDIR%%/bbmap/prok/PFeature$FeatureComparatorScore.class
|
|
%%JAVAJARDIR%%/bbmap/prok/PFeature.class
|
|
%%JAVAJARDIR%%/bbmap/prok/PFeature.java
|
|
%%JAVAJARDIR%%/bbmap/prok/PGMTools$1.class
|
|
%%JAVAJARDIR%%/bbmap/prok/PGMTools.class
|
|
%%JAVAJARDIR%%/bbmap/prok/PGMTools.java
|
|
%%JAVAJARDIR%%/bbmap/prok/ProkObject.class
|
|
%%JAVAJARDIR%%/bbmap/prok/ProkObject.java
|
|
%%JAVAJARDIR%%/bbmap/prok/README.md
|
|
%%JAVAJARDIR%%/bbmap/prok/RiboMaker$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/prok/RiboMaker.class
|
|
%%JAVAJARDIR%%/bbmap/prok/RiboMaker.java
|
|
%%JAVAJARDIR%%/bbmap/prok/ScafData.class
|
|
%%JAVAJARDIR%%/bbmap/prok/ScafData.java
|
|
%%JAVAJARDIR%%/bbmap/prok/ScoreTracker.class
|
|
%%JAVAJARDIR%%/bbmap/prok/ScoreTracker.java
|
|
%%JAVAJARDIR%%/bbmap/prok/SplitRibo$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/prok/SplitRibo.class
|
|
%%JAVAJARDIR%%/bbmap/prok/SplitRibo.java
|
|
%%JAVAJARDIR%%/bbmap/prok/StatsContainer.class
|
|
%%JAVAJARDIR%%/bbmap/prok/StatsContainer.java
|
|
%%JAVAJARDIR%%/bbmap/repeat/Palindrome.class
|
|
%%JAVAJARDIR%%/bbmap/repeat/Palindrome.java
|
|
%%JAVAJARDIR%%/bbmap/repeat/PalindromeFinder.class
|
|
%%JAVAJARDIR%%/bbmap/repeat/PalindromeFinder.java
|
|
%%JAVAJARDIR%%/bbmap/repeat/Repeat$PosComparator.class
|
|
%%JAVAJARDIR%%/bbmap/repeat/Repeat$PosComparator2.class
|
|
%%JAVAJARDIR%%/bbmap/repeat/Repeat.class
|
|
%%JAVAJARDIR%%/bbmap/repeat/Repeat.java
|
|
%%JAVAJARDIR%%/bbmap/repeat/RepeatFinder$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/repeat/RepeatFinder.class
|
|
%%JAVAJARDIR%%/bbmap/repeat/RepeatFinder.java
|
|
%%JAVAJARDIR%%/bbmap/repeat/RepeatSet.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParser.java
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParser1.class
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParser1.java
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParser2.class
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParser2.java
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParser4.class
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParser4.java
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParserS.class
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParserS.java
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParserS1.class
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParserS1.java
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParserS2.class
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParserS2.java
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParserS3.class
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParserS3.java
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParserS4.class
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParserS4.java
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParserS4Reverse.class
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParserS4Reverse.java
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParserSimple.class
|
|
%%JAVAJARDIR%%/bbmap/shared/LineParserSimple.java
|
|
%%JAVAJARDIR%%/bbmap/shared/MetadataWriter.class
|
|
%%JAVAJARDIR%%/bbmap/shared/MetadataWriter.java
|
|
%%JAVAJARDIR%%/bbmap/shared/Parse.class
|
|
%%JAVAJARDIR%%/bbmap/shared/Parse.java
|
|
%%JAVAJARDIR%%/bbmap/shared/Parser.class
|
|
%%JAVAJARDIR%%/bbmap/shared/Parser.java
|
|
%%JAVAJARDIR%%/bbmap/shared/PreParser.class
|
|
%%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$1.class
|
|
%%JAVAJARDIR%%/bbmap/shared/Tools.class
|
|
%%JAVAJARDIR%%/bbmap/shared/Tools.java
|
|
%%JAVAJARDIR%%/bbmap/shared/TrimRead.class
|
|
%%JAVAJARDIR%%/bbmap/shared/TrimRead.java
|
|
%%JAVAJARDIR%%/bbmap/shared/Vector.class
|
|
%%JAVAJARDIR%%/bbmap/shared/Vector.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/AddSSU$SketchHeader.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/AddSSU.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/AddSSU.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/AlignmentJob.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/AlignmentJob.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/AlignmentThreadPool$AlignmentThread.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/AlignmentThreadPool.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/AlignmentThreadPool.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/AnalyzeSketchResults$SSUThread.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/AnalyzeSketchResults.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/AnalyzeSketchResults.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/Blacklist.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/Blacklist.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker2$KeyPair.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker2$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker2.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker2.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/CompareBuffer.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/CompareBuffer.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/CompareSSU$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/CompareSSU.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/CompareSSU.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/CompareSketch$CompareThread.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/CompareSketch.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/CompareSketch.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/Comparison$Depth2Comparator.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/Comparison$DepthComparator.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/Comparison$HitsComparator.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/Comparison$KIDComparator.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/Comparison$SSUComparator.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/Comparison$ScoreComparator.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/Comparison$VolumeComparator.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/Comparison$WKIDComparator.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/Comparison.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/Comparison.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/DisplayParams.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/DisplayParams.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/InvertKey.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/InvertKey.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/KmerLimit$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/KmerLimit.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/KmerLimit.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/KmerLimit2$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/KmerLimit2.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/KmerLimit2.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/MergeSketch.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/MergeSketch.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/README.md
|
|
%%JAVAJARDIR%%/bbmap/sketch/Record.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/Record.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/RecordSet.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/RecordSet.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/ResultLineParser.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/ResultLineParser.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/SSUMap.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SSUMap.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/SendSketch.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SendSketch.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/Sketch.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/Sketch.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchHeap.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchHeap.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchIdComparator.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchIdComparator.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchIndex$IndexThread.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchIndex.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchIndex.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchMaker$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchMaker$WriteThread.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchMaker.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchMaker.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchMakerMini.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchMakerMini.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchObject.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchObject.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchResults.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchResults.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchSearcher$CompareThread.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchSearcher.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchSearcher.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchTool$LoadThread.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchTool$LoadThread2.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchTool$SketchThread.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchTool.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SketchTool.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/SubSketch.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SubSketch.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/SummarizeSketchStats$SketchResultsLine.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SummarizeSketchStats$SketchResultsSummary.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SummarizeSketchStats.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/SummarizeSketchStats.java
|
|
%%JAVAJARDIR%%/bbmap/sketch/Whitelist.class
|
|
%%JAVAJARDIR%%/bbmap/sketch/Whitelist.java
|
|
%%JAVAJARDIR%%/bbmap/sort/ContigLengthComparator.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorClump.java
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorCrispr.class
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorCrispr.java
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorFlowcell.class
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorFlowcell.java
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorID.class
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorID.java
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorList.class
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorList.java
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorMapping.class
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorMapping.java
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorName.class
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorName.java
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorPosition.class
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorPosition.java
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorRandom.class
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorRandom.java
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTaxa.class
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTaxa.java
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological.class
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological.java
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological5Bit.class
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological5Bit.java
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadErrorComparator.class
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadErrorComparator.java
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadLengthComparator.class
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadLengthComparator.java
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadQualityComparator.class
|
|
%%JAVAJARDIR%%/bbmap/sort/ReadQualityComparator.java
|
|
%%JAVAJARDIR%%/bbmap/sort/Shuffle$ShuffleThread.class
|
|
%%JAVAJARDIR%%/bbmap/sort/Shuffle.class
|
|
%%JAVAJARDIR%%/bbmap/sort/Shuffle.java
|
|
%%JAVAJARDIR%%/bbmap/sort/Shuffle2$WriteThread.class
|
|
%%JAVAJARDIR%%/bbmap/sort/Shuffle2.class
|
|
%%JAVAJARDIR%%/bbmap/sort/Shuffle2.java
|
|
%%JAVAJARDIR%%/bbmap/sort/SortByName$WriteThread.class
|
|
%%JAVAJARDIR%%/bbmap/sort/SortByName.class
|
|
%%JAVAJARDIR%%/bbmap/sort/SortByName.java
|
|
%%JAVAJARDIR%%/bbmap/sort/SortReadsByID$1.class
|
|
%%JAVAJARDIR%%/bbmap/sort/SortReadsByID$Block.class
|
|
%%JAVAJARDIR%%/bbmap/sort/SortReadsByID.class
|
|
%%JAVAJARDIR%%/bbmap/sort/SortReadsByID.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ArrayListSet$Pack.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ArrayListSet.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ArrayListSet.java
|
|
%%JAVAJARDIR%%/bbmap/stream/BufferedMultiCros.class
|
|
%%JAVAJARDIR%%/bbmap/stream/BufferedMultiCros.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentCollectionReadInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentCollectionReadInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentDepot.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentDepot.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadInputStream$1.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadInputStream$ReadThread.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadOutputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadOutputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentLegacyReadInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentLegacyReadInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadInputStreamD.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadInputStreamD.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadListDepot.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadListDepot.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStreamD$ListenThread.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStreamD.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStreamD.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadStreamInterface.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadStreamInterface.java
|
|
%%JAVAJARDIR%%/bbmap/stream/CrisContainer.class
|
|
%%JAVAJARDIR%%/bbmap/stream/CrisContainer.java
|
|
%%JAVAJARDIR%%/bbmap/stream/CrisWrapper.class
|
|
%%JAVAJARDIR%%/bbmap/stream/CrisWrapper.java
|
|
%%JAVAJARDIR%%/bbmap/stream/CustomHeader.class
|
|
%%JAVAJARDIR%%/bbmap/stream/CustomHeader.java
|
|
%%JAVAJARDIR%%/bbmap/stream/DualCris.class
|
|
%%JAVAJARDIR%%/bbmap/stream/DualCris.java
|
|
%%JAVAJARDIR%%/bbmap/stream/EmblReadInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/EmblReadInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/FASTQ.class
|
|
%%JAVAJARDIR%%/bbmap/stream/FASTQ.java
|
|
%%JAVAJARDIR%%/bbmap/stream/FastaQualReadInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/FastaQualReadInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/FastaReadInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/FastaReadInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/FastaShredInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/FastaShredInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/FastqReadInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/FastqReadInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/GbkReadInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/GbkReadInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/HeaderInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/HeaderInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/MDWalker.class
|
|
%%JAVAJARDIR%%/bbmap/stream/MDWalker.java
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros.class
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros.java
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros2$Buffer.class
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros2.class
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros2.java
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros3$Buffer.class
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros3.class
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros3.java
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros4$Buffer.class
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros4$RetireThread.class
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros4$Token.class
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros4.class
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros4.java
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros5$Buffer.class
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros5.class
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros5.java
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros6$Buffer.class
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros6$TimestampComparator.class
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros6.class
|
|
%%JAVAJARDIR%%/bbmap/stream/MultiCros6.java
|
|
%%JAVAJARDIR%%/bbmap/stream/NullOutputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/NullOutputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/OnelineReadInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/OnelineReadInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/RTextInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/RTextInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/RandomReadInputStream3.class
|
|
%%JAVAJARDIR%%/bbmap/stream/RandomReadInputStream3.java
|
|
%%JAVAJARDIR%%/bbmap/stream/Read.class
|
|
%%JAVAJARDIR%%/bbmap/stream/Read.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ReadInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ReadInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ReadStreamByteWriter.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ReadStreamByteWriter.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ReadStreamWriter$Job.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ReadStreamWriter.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ReadStreamWriter.java
|
|
%%JAVAJARDIR%%/bbmap/stream/SamHeader.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SamHeader.java
|
|
%%JAVAJARDIR%%/bbmap/stream/SamLine.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SamLine.java
|
|
%%JAVAJARDIR%%/bbmap/stream/SamLineStreamer$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SamLineStreamer.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SamLineStreamer.java
|
|
%%JAVAJARDIR%%/bbmap/stream/SamReadInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SamReadInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/SamReadStreamer$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SamReadStreamer.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SamReadStreamer.java
|
|
%%JAVAJARDIR%%/bbmap/stream/SamStreamer.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SamStreamer.java
|
|
%%JAVAJARDIR%%/bbmap/stream/SamStreamerMF.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SamStreamerMF.java
|
|
%%JAVAJARDIR%%/bbmap/stream/SamStreamerWrapper.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SamStreamerWrapper.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ScaffoldCoordinates.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ScaffoldCoordinates.java
|
|
%%JAVAJARDIR%%/bbmap/stream/ScarfReadInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/ScarfReadInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/SequentialReadInputStream.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SequentialReadInputStream.java
|
|
%%JAVAJARDIR%%/bbmap/stream/SiteScore$PositionComparator.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SiteScore.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SiteScore.java
|
|
%%JAVAJARDIR%%/bbmap/stream/SiteScoreR$IDComparator.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SiteScoreR$NormalizedComparator.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SiteScoreR$PositionComparator.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SiteScoreR.class
|
|
%%JAVAJARDIR%%/bbmap/stream/SiteScoreR.java
|
|
%%JAVAJARDIR%%/bbmap/structures/AbstractBitSet.class
|
|
%%JAVAJARDIR%%/bbmap/structures/AbstractBitSet.java
|
|
%%JAVAJARDIR%%/bbmap/structures/AbstractIntHashMap.class
|
|
%%JAVAJARDIR%%/bbmap/structures/AbstractIntHashMap.java
|
|
%%JAVAJARDIR%%/bbmap/structures/AtomicBitSet.class
|
|
%%JAVAJARDIR%%/bbmap/structures/AtomicBitSet.java
|
|
%%JAVAJARDIR%%/bbmap/structures/AtomicStringNum.class
|
|
%%JAVAJARDIR%%/bbmap/structures/AtomicStringNum.java
|
|
%%JAVAJARDIR%%/bbmap/structures/ByteBuilder.class
|
|
%%JAVAJARDIR%%/bbmap/structures/ByteBuilder.java
|
|
%%JAVAJARDIR%%/bbmap/structures/CRange.class
|
|
%%JAVAJARDIR%%/bbmap/structures/CRange.java
|
|
%%JAVAJARDIR%%/bbmap/structures/CoverageArray.class
|
|
%%JAVAJARDIR%%/bbmap/structures/CoverageArray.java
|
|
%%JAVAJARDIR%%/bbmap/structures/CoverageArray2.class
|
|
%%JAVAJARDIR%%/bbmap/structures/CoverageArray2.java
|
|
%%JAVAJARDIR%%/bbmap/structures/CoverageArray2A.class
|
|
%%JAVAJARDIR%%/bbmap/structures/CoverageArray2A.java
|
|
%%JAVAJARDIR%%/bbmap/structures/CoverageArray3.class
|
|
%%JAVAJARDIR%%/bbmap/structures/CoverageArray3.java
|
|
%%JAVAJARDIR%%/bbmap/structures/CoverageArray3A.class
|
|
%%JAVAJARDIR%%/bbmap/structures/CoverageArray3A.java
|
|
%%JAVAJARDIR%%/bbmap/structures/Crispr.class
|
|
%%JAVAJARDIR%%/bbmap/structures/Crispr.java
|
|
%%JAVAJARDIR%%/bbmap/structures/DoubleList.class
|
|
%%JAVAJARDIR%%/bbmap/structures/DoubleList.java
|
|
%%JAVAJARDIR%%/bbmap/structures/Feature.class
|
|
%%JAVAJARDIR%%/bbmap/structures/Feature.java
|
|
%%JAVAJARDIR%%/bbmap/structures/FloatList.class
|
|
%%JAVAJARDIR%%/bbmap/structures/FloatList.java
|
|
%%JAVAJARDIR%%/bbmap/structures/Heap$HeapIterator.class
|
|
%%JAVAJARDIR%%/bbmap/structures/Heap.class
|
|
%%JAVAJARDIR%%/bbmap/structures/Heap.java
|
|
%%JAVAJARDIR%%/bbmap/structures/HeapLoc$HeapIterator.class
|
|
%%JAVAJARDIR%%/bbmap/structures/HeapLoc.class
|
|
%%JAVAJARDIR%%/bbmap/structures/HeapLoc.java
|
|
%%JAVAJARDIR%%/bbmap/structures/IntHashMap.class
|
|
%%JAVAJARDIR%%/bbmap/structures/IntHashMap.java
|
|
%%JAVAJARDIR%%/bbmap/structures/IntHashMapBinary.class
|
|
%%JAVAJARDIR%%/bbmap/structures/IntHashMapBinary.java
|
|
%%JAVAJARDIR%%/bbmap/structures/IntHashSet.class
|
|
%%JAVAJARDIR%%/bbmap/structures/IntHashSet.java
|
|
%%JAVAJARDIR%%/bbmap/structures/IntHashSetList.class
|
|
%%JAVAJARDIR%%/bbmap/structures/IntHashSetList.java
|
|
%%JAVAJARDIR%%/bbmap/structures/IntList.class
|
|
%%JAVAJARDIR%%/bbmap/structures/IntList.java
|
|
%%JAVAJARDIR%%/bbmap/structures/IntList2.class
|
|
%%JAVAJARDIR%%/bbmap/structures/IntList2.java
|
|
%%JAVAJARDIR%%/bbmap/structures/IntList3.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/structures/IntMap.java
|
|
%%JAVAJARDIR%%/bbmap/structures/ListNum.class
|
|
%%JAVAJARDIR%%/bbmap/structures/ListNum.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongArrayListHashMap.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongArrayListHashMap.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongHashMap.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongHashMap.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongHashSet.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongHashSet.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongHeap.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongHeap.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongHeapMap.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongHeapMap.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongHeapSet.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongHeapSet.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongHeapSetInterface.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongHeapSetInterface.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongList.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongList.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongList2.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongList2.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongList3.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongList3.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongListSet$LongListSetIterator.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongListSet.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongListSet.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongLongHashMap.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongLongHashMap.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongLongHashMapHybrid.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongLongHashMapHybrid.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongLongListHashMap.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongLongListHashMap.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongM.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongM.java
|
|
%%JAVAJARDIR%%/bbmap/structures/LongPair.class
|
|
%%JAVAJARDIR%%/bbmap/structures/LongPair.java
|
|
%%JAVAJARDIR%%/bbmap/structures/MultiBitSet.class
|
|
%%JAVAJARDIR%%/bbmap/structures/MultiBitSet.java
|
|
%%JAVAJARDIR%%/bbmap/structures/Point.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/structures/SeqCountM.java
|
|
%%JAVAJARDIR%%/bbmap/structures/SeqMap$1.class
|
|
%%JAVAJARDIR%%/bbmap/structures/SeqMap$2.class
|
|
%%JAVAJARDIR%%/bbmap/structures/SeqMap$3.class
|
|
%%JAVAJARDIR%%/bbmap/structures/SeqMap.class
|
|
%%JAVAJARDIR%%/bbmap/structures/SeqMap.java
|
|
%%JAVAJARDIR%%/bbmap/structures/SeqPos.class
|
|
%%JAVAJARDIR%%/bbmap/structures/SeqPos.java
|
|
%%JAVAJARDIR%%/bbmap/structures/SeqPosM.class
|
|
%%JAVAJARDIR%%/bbmap/structures/SeqPosM.java
|
|
%%JAVAJARDIR%%/bbmap/structures/SetLoc.class
|
|
%%JAVAJARDIR%%/bbmap/structures/SetLoc.java
|
|
%%JAVAJARDIR%%/bbmap/structures/StandardDeviator$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/structures/StandardDeviator.class
|
|
%%JAVAJARDIR%%/bbmap/structures/StandardDeviator.java
|
|
%%JAVAJARDIR%%/bbmap/structures/StringCount.class
|
|
%%JAVAJARDIR%%/bbmap/structures/StringCount.java
|
|
%%JAVAJARDIR%%/bbmap/structures/StringNum.class
|
|
%%JAVAJARDIR%%/bbmap/structures/StringNum.java
|
|
%%JAVAJARDIR%%/bbmap/structures/StringPair.class
|
|
%%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$HashThread.class
|
|
%%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid.class
|
|
%%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid.java
|
|
%%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid_old$HashThread.class
|
|
%%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid_old.class
|
|
%%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid_old.java
|
|
%%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/tax/AnalyzeAccession.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/tax/FilterByTaxa.java
|
|
%%JAVAJARDIR%%/bbmap/tax/FindAncestor.class
|
|
%%JAVAJARDIR%%/bbmap/tax/FindAncestor.java
|
|
%%JAVAJARDIR%%/bbmap/tax/GiToTaxid.class
|
|
%%JAVAJARDIR%%/bbmap/tax/GiToTaxid.java
|
|
%%JAVAJARDIR%%/bbmap/tax/GiToTaxidInt.class
|
|
%%JAVAJARDIR%%/bbmap/tax/GiToTaxidInt.java
|
|
%%JAVAJARDIR%%/bbmap/tax/IDNode.class
|
|
%%JAVAJARDIR%%/bbmap/tax/IDNode.java
|
|
%%JAVAJARDIR%%/bbmap/tax/IDTree.class
|
|
%%JAVAJARDIR%%/bbmap/tax/IDTree.java
|
|
%%JAVAJARDIR%%/bbmap/tax/ImgRecord.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/tax/RenameIMG.java
|
|
%%JAVAJARDIR%%/bbmap/tax/ShrinkAccession.class
|
|
%%JAVAJARDIR%%/bbmap/tax/ShrinkAccession.java
|
|
%%JAVAJARDIR%%/bbmap/tax/SplitByTaxa.class
|
|
%%JAVAJARDIR%%/bbmap/tax/SplitByTaxa.java
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxApp$1.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxApp.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxApp.java
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxClient.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxClient.java
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxFilter$1.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxFilter.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxFilter.java
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxNode$CountComparator.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxNode.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxNode.java
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxServer$CompareThread.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxServer$HelpHandler.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxServer$IconHandler.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxServer$KillHandler.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxServer$SketchHandler$SketchInstance.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxServer$SketchHandler.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxServer$StatsHandler.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxServer$TaxHandler.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxServer.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxServer.java
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxSize.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxSize.java
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxTree.class
|
|
%%JAVAJARDIR%%/bbmap/tax/TaxTree.java
|
|
%%JAVAJARDIR%%/bbmap/template/A_Sample.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_Sample.java
|
|
%%JAVAJARDIR%%/bbmap/template/A_Sample2.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_Sample2.java
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleBasic.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleBasic.java
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleBasic2.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleBasic2.java
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleByteFile.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleByteFile.java
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleByteFileMT$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleByteFileMT.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleByteFileMT.java
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleD.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleD.java
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleMT$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleMT.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleMT.java
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleMultipleInput.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleMultipleInput.java
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleSamStreamer$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleSamStreamer.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleSamStreamer.java
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleSummary.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_SampleSummary.java
|
|
%%JAVAJARDIR%%/bbmap/template/A_Sample_Generator$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_Sample_Generator.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_Sample_Generator.java
|
|
%%JAVAJARDIR%%/bbmap/template/A_Sample_Unpaired.class
|
|
%%JAVAJARDIR%%/bbmap/template/A_Sample_Unpaired.java
|
|
%%JAVAJARDIR%%/bbmap/template/Accumulator.class
|
|
%%JAVAJARDIR%%/bbmap/template/Accumulator.java
|
|
%%JAVAJARDIR%%/bbmap/template/BBTool_ST.class
|
|
%%JAVAJARDIR%%/bbmap/template/BBTool_ST.java
|
|
%%JAVAJARDIR%%/bbmap/template/DoWorker.class
|
|
%%JAVAJARDIR%%/bbmap/template/DoWorker.java
|
|
%%JAVAJARDIR%%/bbmap/template/README.md
|
|
%%JAVAJARDIR%%/bbmap/template/ThreadPoolJob.class
|
|
%%JAVAJARDIR%%/bbmap/template/ThreadPoolJob.java
|
|
%%JAVAJARDIR%%/bbmap/template/ThreadWaiter.class
|
|
%%JAVAJARDIR%%/bbmap/template/ThreadWaiter.java
|
|
%%JAVAJARDIR%%/bbmap/tracker/AdapterTracker.class
|
|
%%JAVAJARDIR%%/bbmap/tracker/AdapterTracker.java
|
|
%%JAVAJARDIR%%/bbmap/tracker/CrisprTracker.class
|
|
%%JAVAJARDIR%%/bbmap/tracker/CrisprTracker.java
|
|
%%JAVAJARDIR%%/bbmap/tracker/EntropyTracker.class
|
|
%%JAVAJARDIR%%/bbmap/tracker/EntropyTracker.java
|
|
%%JAVAJARDIR%%/bbmap/tracker/PalindromeTracker.class
|
|
%%JAVAJARDIR%%/bbmap/tracker/PalindromeTracker.java
|
|
%%JAVAJARDIR%%/bbmap/tracker/PolymerTracker.class
|
|
%%JAVAJARDIR%%/bbmap/tracker/PolymerTracker.java
|
|
%%JAVAJARDIR%%/bbmap/tracker/QualityTracker.class
|
|
%%JAVAJARDIR%%/bbmap/tracker/QualityTracker.java
|
|
%%JAVAJARDIR%%/bbmap/tracker/ReadStats.class
|
|
%%JAVAJARDIR%%/bbmap/tracker/ReadStats.java
|
|
%%JAVAJARDIR%%/bbmap/tracker/SealStats$SealStatsLine.class
|
|
%%JAVAJARDIR%%/bbmap/tracker/SealStats.class
|
|
%%JAVAJARDIR%%/bbmap/tracker/SealStats.java
|
|
%%JAVAJARDIR%%/bbmap/ukmer/AbstractKmerTableU$AllocThread.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/AbstractKmerTableU.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/AbstractKmerTableU.java
|
|
%%JAVAJARDIR%%/bbmap/ukmer/DumpThreadU.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/DumpThreadU.java
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayU.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayU.java
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayU1D$WalkerU1D.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayU1D.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayU1D.java
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayU2D.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayU2D.java
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayUHybrid.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HashArrayUHybrid.java
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HashBufferU.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HashBufferU.java
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HashForestU.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HashForestU.java
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HistogramMakerU$FillThread.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HistogramMakerU.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/HistogramMakerU.java
|
|
%%JAVAJARDIR%%/bbmap/ukmer/Kmer.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/Kmer.java
|
|
%%JAVAJARDIR%%/bbmap/ukmer/KmerBufferU.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/KmerBufferU.java
|
|
%%JAVAJARDIR%%/bbmap/ukmer/KmerNodeU.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/KmerNodeU.java
|
|
%%JAVAJARDIR%%/bbmap/ukmer/KmerNodeU1D.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/KmerNodeU1D.java
|
|
%%JAVAJARDIR%%/bbmap/ukmer/KmerNodeU2D.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/KmerNodeU2D.java
|
|
%%JAVAJARDIR%%/bbmap/ukmer/KmerTableSetU$LoadThread.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/KmerTableSetU$WalkerKSTU.class
|
|
%%JAVAJARDIR%%/bbmap/ukmer/KmerTableSetU.class
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/var/ApplyVarsToReference.class
|
|
%%JAVAJARDIR%%/bbmap/var/ApplyVarsToReference.java
|
|
%%JAVAJARDIR%%/bbmap/var/GenerateConsensusVariations$1.class
|
|
%%JAVAJARDIR%%/bbmap/var/GenerateConsensusVariations.class
|
|
%%JAVAJARDIR%%/bbmap/var/GenerateConsensusVariations.java
|
|
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets.class
|
|
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets.java
|
|
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets2$1.class
|
|
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets2$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets2.class
|
|
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets2.java
|
|
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets3$1.class
|
|
%%JAVAJARDIR%%/bbmap/var/GenerateVarlets3$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
|
|
%%JAVAJARDIR%%/bbmap/var/StackVariations.java
|
|
%%JAVAJARDIR%%/bbmap/var/StackVariations2$1.class
|
|
%%JAVAJARDIR%%/bbmap/var/StackVariations2$SVThread.class
|
|
%%JAVAJARDIR%%/bbmap/var/StackVariations2.class
|
|
%%JAVAJARDIR%%/bbmap/var/StackVariations2.java
|
|
%%JAVAJARDIR%%/bbmap/var/VarLine.class
|
|
%%JAVAJARDIR%%/bbmap/var/VarLine.java
|
|
%%JAVAJARDIR%%/bbmap/var/Variation.class
|
|
%%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$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/var2/CallVariants.class
|
|
%%JAVAJARDIR%%/bbmap/var2/CallVariants.java
|
|
%%JAVAJARDIR%%/bbmap/var2/CallVariants2$Sample$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/var2/CallVariants2$Sample.class
|
|
%%JAVAJARDIR%%/bbmap/var2/CallVariants2.class
|
|
%%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$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/var2/FilterSam.class
|
|
%%JAVAJARDIR%%/bbmap/var2/FilterSam.java
|
|
%%JAVAJARDIR%%/bbmap/var2/FilterVCF$ProcessThread.class
|
|
%%JAVAJARDIR%%/bbmap/var2/FilterVCF.class
|
|
%%JAVAJARDIR%%/bbmap/var2/FilterVCF.java
|
|
%%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
|
|
%%JAVAJARDIR%%/bbmap/var2/Realigner.class
|
|
%%JAVAJARDIR%%/bbmap/var2/Realigner.java
|
|
%%JAVAJARDIR%%/bbmap/var2/SamFilter.class
|
|
%%JAVAJARDIR%%/bbmap/var2/SamFilter.java
|
|
%%JAVAJARDIR%%/bbmap/var2/ScafMap.class
|
|
%%JAVAJARDIR%%/bbmap/var2/ScafMap.java
|
|
%%JAVAJARDIR%%/bbmap/var2/Scaffold.class
|
|
%%JAVAJARDIR%%/bbmap/var2/Scaffold.java
|
|
%%JAVAJARDIR%%/bbmap/var2/SoftClipper.class
|
|
%%JAVAJARDIR%%/bbmap/var2/SoftClipper.java
|
|
%%JAVAJARDIR%%/bbmap/var2/VCFFile$1.class
|
|
%%JAVAJARDIR%%/bbmap/var2/VCFFile.class
|
|
%%JAVAJARDIR%%/bbmap/var2/VCFFile.java
|
|
%%JAVAJARDIR%%/bbmap/var2/VCFLine.class
|
|
%%JAVAJARDIR%%/bbmap/var2/VCFLine.java
|
|
%%JAVAJARDIR%%/bbmap/var2/Var.class
|
|
%%JAVAJARDIR%%/bbmap/var2/Var.java
|
|
%%JAVAJARDIR%%/bbmap/var2/VarFilter.class
|
|
%%JAVAJARDIR%%/bbmap/var2/VarFilter.java
|
|
%%JAVAJARDIR%%/bbmap/var2/VarHelper.class
|
|
%%JAVAJARDIR%%/bbmap/var2/VarHelper.java
|
|
%%JAVAJARDIR%%/bbmap/var2/VarKey.class
|
|
%%JAVAJARDIR%%/bbmap/var2/VarKey.java
|
|
%%JAVAJARDIR%%/bbmap/var2/VarMap$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
|