diff --git a/biology/bbmap/Makefile b/biology/bbmap/Makefile index ab74e416478a..0e30158fa4b0 100644 --- a/biology/bbmap/Makefile +++ b/biology/bbmap/Makefile @@ -1,51 +1,52 @@ PORTNAME= bbmap -DISTVERSION= 39.34 -PORTREVISION= 2 +DISTVERSIONPREFIX= v +DISTVERSION= 40.02 CATEGORIES= biology java -MASTER_SITES= SF/bbmap/ -DISTNAME= BBMap_${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= BBMap short read aligner, and other bioinformatic tools WWW= https://jgi.doe.gov/data-and-tools/bbtools/ \ https://sourceforge.net/projects/bbmap/ \ https://bitbucket.org/berkeleylab/jgi-bbtools/src/master/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt RUN_DEPENDS= bash:shells/bash \ pbzip2:archivers/pbzip2 \ pigz:archivers/pigz USES= java shebangfix +USE_GITHUB= yes +GH_ACCOUNT= bbushnell +GH_PROJECT= BBTools SHEBANG_FILES= ${WRKSRC}/*.sh NO_ARCH= yes NO_BUILD= yes -WRKSRC= ${WRKDIR}/${PORTNAME} - LIBEXEC_DIR= ${PREFIX}/libexec/bbmap pre-configure: ${REINPLACE_CMD} -e 's|"$$DIR""current/"|${JAVAJARDIR}/bbmap|g' \ ${WRKSRC}/*.sh ${REINPLACE_CMD} \ -e 's|"$$DIR""/calcmem.sh"|${LIBEXEC_DIR}/bbmap/calcmem.sh|g' \ ${WRKSRC}/*.sh # FIXME: Find out which scripts are meant to be part of the CLI do-install: @${MKDIR} ${STAGEDIR}${LIBEXEC_DIR} @${MKDIR} ${STAGEDIR}${JAVAJARDIR}/bbmap ${INSTALL_SCRIPT} ${WRKSRC}/*.sh ${STAGEDIR}${LIBEXEC_DIR} cd ${WRKSRC}/current && ${COPYTREE_SHARE} . \ ${STAGEDIR}${JAVAJARDIR}/bbmap -.for f in bbduk.sh bbnorm.sh dedupe.sh bbmap.sh bloomfilter.sh reformat.sh \ - bbmerge.sh tadpole.sh +.for f in bbmap.sh bbduk.sh bbmerge.sh bbnorm.sh tadpole.sh clumpify.sh \ + callvariants.sh bbsplit.sh sendsketch.sh comparesketch.sh \ + dedupe.sh bbmap.sh bloomfilter.sh reformat.sh \ + bbmerge.sh tadpole.sh bbversion.sh ${RLN} ${STAGEDIR}${LIBEXEC_DIR}/${f} ${STAGEDIR}${PREFIX}/bin .endfor .include diff --git a/biology/bbmap/distinfo b/biology/bbmap/distinfo index c65e1b09d3ef..a93398a9d9ad 100644 --- a/biology/bbmap/distinfo +++ b/biology/bbmap/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1755776772 -SHA256 (BBMap_39.34.tar.gz) = c9c096c6ce3cc87da5607b731532bb9ac0aaebea2bd8fbf0a56e235968c4fbf4 -SIZE (BBMap_39.34.tar.gz) = 13743574 +TIMESTAMP = 1788195134 +SHA256 (bbushnell-BBTools-v40.02_GH0.tar.gz) = 4faec10a452ea7974c778c3c207a7885e43e639a89b9a360b6d16bfb9b61a6cd +SIZE (bbushnell-BBTools-v40.02_GH0.tar.gz) = 30250324 diff --git a/biology/bbmap/files/patch-calcmem.sh b/biology/bbmap/files/patch-calcmem.sh index 77e676990387..922559f4a4b3 100644 --- a/biology/bbmap/files/patch-calcmem.sh +++ b/biology/bbmap/files/patch-calcmem.sh @@ -1,29 +1,29 @@ ---- calcmem.sh.orig 2024-12-10 19:13:48 UTC +--- calcmem.sh.orig 2026-08-31 16:31:16 UTC +++ calcmem.sh -@@ -78,26 +78,6 @@ function setEnvironment(){ +@@ -144,26 +144,6 @@ setEnvironment(){ if [[ "$SHIFTER_RUNTIME" = "1" ]]; then #Ignore NERSC_HOST shifter=1 - elif [ -z "$EC2_HOME" ]; then - #Let's assume this is the AWS taxonomy server... - PATH=/test1/binaries/bgzip:$PATH - PATH=/test1/binaries/lbzip2/bin:$PATH - PATH=/test1/binaries/sambamba:$PATH - #PATH=/test1/binaries/java/jdk-11.0.2/bin:$PATH - PATH=/test1/binaries/pigz2/pigz-2.4:$PATH - elif [ -z "$NERSC_HOST" ]; then - #Not NERSC; do nothing - : - elif [ -z "$NERSC_HOST" ]; then - #Not NERSC; do nothing - : - else - PATH=/global/cfs/cdirs/bbtools/bgzip:$PATH - PATH=/global/cfs/cdirs/bbtools/lbzip2/bin:$PATH -- PATH=/global/cfs/cdirs/bbtools/samtools116/samtools-1.16.1:$PATH +- PATH=/global/cfs/cdirs/bbtools/samtools116/samtools-1.16.1:$PATH - #PATH=/global/projectb/sandbox/gaag/bbtools/sambamba:$PATH - PATH=/global/cfs/cdirs/bbtools/java/jdk-17/bin:$PATH - PATH=/global/cfs/cdirs/bbtools/pigz2/pigz-2.4:$PATH fi } diff --git a/biology/bbmap/pkg-plist b/biology/bbmap/pkg-plist index 6dc7649290c2..0ad398396c3a 100644 --- a/biology/bbmap/pkg-plist +++ b/biology/bbmap/pkg-plist @@ -1,2723 +1,3866 @@ bin/bbduk.sh bin/bbmap.sh bin/bbmerge.sh bin/bbnorm.sh +bin/bbsplit.sh +bin/bbversion.sh bin/bloomfilter.sh +bin/callvariants.sh +bin/clumpify.sh +bin/comparesketch.sh bin/dedupe.sh bin/reformat.sh +bin/sendsketch.sh bin/tadpole.sh -libexec/bbmap/Xcalcmem.sh libexec/bbmap/a_sample_mt.sh libexec/bbmap/addadapters.sh libexec/bbmap/addssu.sh +libexec/bbmap/addx.sh libexec/bbmap/adjusthomopolymers.sh +libexec/bbmap/alignerbenchmark.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/balancevectors.sh +libexec/bbmap/bamlinestreamer.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/bbdukOld.sh +libexec/bbmap/bbdukS.sh libexec/bbmap/bbest.sh libexec/bbmap/bbfakereads.sh libexec/bbmap/bbmap.sh +libexec/bbmap/bbmap5.sh +libexec/bbmap/bbmapacc.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/bedset.sh libexec/bbmap/bloomfilter.sh libexec/bbmap/bloomfilterparser.sh libexec/bbmap/calcmem.sh libexec/bbmap/calctruequality.sh +libexec/bbmap/calibrate.sh libexec/bbmap/callgenes.sh libexec/bbmap/callpeaks.sh libexec/bbmap/callvariants.sh libexec/bbmap/callvariants2.sh libexec/bbmap/cat.sh +libexec/bbmap/cbcl2text.sh libexec/bbmap/cg2illumina.sh libexec/bbmap/checkstrand.sh libexec/bbmap/cladeloader.sh +libexec/bbmap/cladeserver.sh +libexec/bbmap/cloudplot.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/covmaker.sh libexec/bbmap/crossblock.sh libexec/bbmap/crosscontaminate.sh libexec/bbmap/crosscutaligner.sh libexec/bbmap/cutgff.sh libexec/bbmap/cutprimers.sh +libexec/bbmap/ddlblacklist.sh +libexec/bbmap/ddlcalibrate.sh +libexec/bbmap/ddlcompare.sh +libexec/bbmap/ddlmerger.sh +libexec/bbmap/ddlwriter.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/dlctieraccuracy.sh libexec/bbmap/driftingaligner.sh libexec/bbmap/driftingplusaligner.sh libexec/bbmap/estherfilter.sh libexec/bbmap/explodetree.sh +libexec/bbmap/fastqscan.sh libexec/bbmap/fetchproks.sh +libexec/bbmap/filescan.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/findssu.sh +libexec/bbmap/fix_script_paths.sh libexec/bbmap/fixgaps.sh +libexec/bbmap/fll2simulate.sh libexec/bbmap/fungalrelease.sh libexec/bbmap/fuse.sh +libexec/bbmap/fusebytaxa.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/gradevcf.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/invertvcf.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/kmercountshort.sh libexec/bbmap/kmercoverage.sh libexec/bbmap/kmerfilterset.sh +libexec/bbmap/kmerhashdump.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/lowcomplexcalibrate.sh libexec/bbmap/makechimeras.sh libexec/bbmap/makecontaminatedgenomes.sh libexec/bbmap/makepolymers.sh libexec/bbmap/makequickbinvector.sh +libexec/bbmap/mantissacompare.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/mergesam2.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/netconvert.sh libexec/bbmap/netfilter.sh libexec/bbmap/novademux.sh +libexec/bbmap/parallelogram.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/profile.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/rankingvectorizer.sh libexec/bbmap/readlength.sh -libexec/bbmap/readqc.sh +libexec/bbmap/reassemble.sh libexec/bbmap/reducecolumns.sh libexec/bbmap/reducesilva.sh libexec/bbmap/reformat.sh +libexec/bbmap/reformat2.sh +libexec/bbmap/reformat3.sh libexec/bbmap/reformatpb.sh +libexec/bbmap/regressiontrainer.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/renamecami.sh libexec/bbmap/renameimg.sh libexec/bbmap/renameref.sh libexec/bbmap/repair.sh libexec/bbmap/replaceheaders.sh libexec/bbmap/representative.sh +libexec/bbmap/restorebases.sh libexec/bbmap/rqcfilter.sh libexec/bbmap/rqcfilter2.sh +libexec/bbmap/rqcfilter3.sh libexec/bbmap/runhmm.sh +libexec/bbmap/samstreamer.sh libexec/bbmap/samtoroc.sh +libexec/bbmap/scalarintervals.sh +libexec/bbmap/scalars.sh libexec/bbmap/scoresequence.sh +libexec/bbmap/scrabblealigner.sh libexec/bbmap/seal.sh +libexec/bbmap/sendclade.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/smithwaterman.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/ssuserver.sh libexec/bbmap/stats.sh libexec/bbmap/stats3.sh libexec/bbmap/statswrapper.sh +libexec/bbmap/stream.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/testalignersbatch.sh +libexec/bbmap/testalignerslength.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/trainLCHist.sh libexec/bbmap/translate6frames.sh libexec/bbmap/trimcontigs.sh +libexec/bbmap/ttllsimulate.sh libexec/bbmap/unicode2ascii.sh libexec/bbmap/unzip.sh libexec/bbmap/vcf2gff.sh +libexec/bbmap/vectorutils.sh libexec/bbmap/visualizealignment.sh libexec/bbmap/wavefrontaligner.sh +libexec/bbmap/wavefrontalignerviz.sh libexec/bbmap/webcheck.sh libexec/bbmap/wobblealigner.sh libexec/bbmap/wobbleplusaligner.sh +libexec/bbmap/xdrophaligner.sh +libexec/bbmap/zz_rename_package.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/SideChannel4.class +%%JAVAJARDIR%%/bbmap/aligner/SideChannel4.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/Reassemble$GenomeRecord.class +%%JAVAJARDIR%%/bbmap/assemble/Reassemble.class +%%JAVAJARDIR%%/bbmap/assemble/Reassemble.java %%JAVAJARDIR%%/bbmap/assemble/Rollback.class %%JAVAJARDIR%%/bbmap/assemble/Rollback.java %%JAVAJARDIR%%/bbmap/assemble/ShaveObject.class %%JAVAJARDIR%%/bbmap/assemble/ShaveObject.java %%JAVAJARDIR%%/bbmap/assemble/Shaver.class %%JAVAJARDIR%%/bbmap/assemble/Shaver.java %%JAVAJARDIR%%/bbmap/assemble/Shaver1$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/bbduk/Allocator$AllocThread.class +%%JAVAJARDIR%%/bbmap/bbduk/Allocator.class +%%JAVAJARDIR%%/bbmap/bbduk/Allocator.java +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk2$LoadThread.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk2$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk2.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk2.java +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk3$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk3.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk3.java +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk4$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk4.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk4.java +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk5$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk5.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk5.java +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk6$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk6.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDuk6.java +%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndex.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndex.java +%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexAbstract.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexAbstract.java +%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexAndLoader$LoadThread.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexAndLoader.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexAndLoader.java +%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexMask.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexMask.java +%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexMask2.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexMask2.java +%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexMod.class +%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndexMod.java +%%JAVAJARDIR%%/bbmap/bbduk/BBDukIndex_clean$LoadThread.class 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%%JAVAJARDIR%%/bbmap/bin/AbstractRefiner$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/ClusterWriter.class +%%JAVAJARDIR%%/bbmap/bin/ClusterWriter.java +%%JAVAJARDIR%%/bbmap/bin/ClusterWriter2$WriteThread.class +%%JAVAJARDIR%%/bbmap/bin/ClusterWriter2.class +%%JAVAJARDIR%%/bbmap/bin/ClusterWriter2.java %%JAVAJARDIR%%/bbmap/bin/ConservationModel.class %%JAVAJARDIR%%/bbmap/bin/ConservationModel.java %%JAVAJARDIR%%/bbmap/bin/Contig$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/CovMaker.class +%%JAVAJARDIR%%/bbmap/bin/CovMaker.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$CCLine.class +%%JAVAJARDIR%%/bbmap/bin/GradeBins$PTAccumulator.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/RenameCAMI.class +%%JAVAJARDIR%%/bbmap/bin/RenameCAMI.java +%%JAVAJARDIR%%/bbmap/bin/SamLoader3$ParallelWorker.class +%%JAVAJARDIR%%/bbmap/bin/SamLoader3$QueueWorker.class +%%JAVAJARDIR%%/bbmap/bin/SamLoader3$Worker.class +%%JAVAJARDIR%%/bbmap/bin/SamLoader3.class +%%JAVAJARDIR%%/bbmap/bin/SamLoader3.java %%JAVAJARDIR%%/bbmap/bin/ScoreComparator.class %%JAVAJARDIR%%/bbmap/bin/ScoreComparator.java %%JAVAJARDIR%%/bbmap/bin/SimilarityMeasures.class %%JAVAJARDIR%%/bbmap/bin/SimilarityMeasures.java %%JAVAJARDIR%%/bbmap/bin/SketchRecord.class %%JAVAJARDIR%%/bbmap/bin/SketchRecord.java %%JAVAJARDIR%%/bbmap/bin/Sketchable.class %%JAVAJARDIR%%/bbmap/bin/Sketchable.java %%JAVAJARDIR%%/bbmap/bin/SpectraCounter$LoadThread.class %%JAVAJARDIR%%/bbmap/bin/SpectraCounter.class %%JAVAJARDIR%%/bbmap/bin/SpectraCounter.java +%%JAVAJARDIR%%/bbmap/bin/Strictness.class +%%JAVAJARDIR%%/bbmap/bin/Strictness.java +%%JAVAJARDIR%%/bbmap/bin/binmap/BinMap.class +%%JAVAJARDIR%%/bbmap/bin/binmap/BinMap.java +%%JAVAJARDIR%%/bbmap/bin/binmap/BinMap2$1.class +%%JAVAJARDIR%%/bbmap/bin/binmap/BinMap2.class +%%JAVAJARDIR%%/bbmap/bin/binmap/BinMap2.java +%%JAVAJARDIR%%/bbmap/bin/binmap/BinMapSlice.class +%%JAVAJARDIR%%/bbmap/bin/binmap/BinMapSlice.java +%%JAVAJARDIR%%/bbmap/bin/binmap/Key.class +%%JAVAJARDIR%%/bbmap/bin/binmap/Key.java +%%JAVAJARDIR%%/bbmap/bin/binmap/Key0.class +%%JAVAJARDIR%%/bbmap/bin/binmap/Key0.java +%%JAVAJARDIR%%/bbmap/bin/binmap/KeyG.class +%%JAVAJARDIR%%/bbmap/bin/binmap/KeyG.java +%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGC.class +%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGC.java +%%JAVAJARDIR%%/bbmap/bin/binmap/KeyGD.class 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%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrectorWrapper$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/AbstractCardStats.class +%%JAVAJARDIR%%/bbmap/cardinality/AbstractCardStats.java +%%JAVAJARDIR%%/bbmap/cardinality/ApacheHLL4Wrapper.class +%%JAVAJARDIR%%/bbmap/cardinality/ApacheHLL4Wrapper.java +%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticCompressedDynamicLogLog4.class +%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticCompressedDynamicLogLog4.java +%%JAVAJARDIR%%/bbmap/cardinality/ArithmeticCompressedDynamicLogLog5.class 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%%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/FilterReadsByNameOld.class +%%JAVAJARDIR%%/bbmap/driver/FilterReadsByNameOld.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/ByteFile1F.class +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1F.java +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1Fc.class +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1Fc.java +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1old.class +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1old.java %%JAVAJARDIR%%/bbmap/fileIO/ByteFile2$BF1Thread.class %%JAVAJARDIR%%/bbmap/fileIO/ByteFile2.class %%JAVAJARDIR%%/bbmap/fileIO/ByteFile2.java +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile3$BufferJob.class +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile3$ProcessThread.class +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile3.class +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile3.java +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile4$BufferJob.class +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile4$ProcessThread.class +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile4.class +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile4.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/Concatenate2.class +%%JAVAJARDIR%%/bbmap/fileIO/Concatenate2.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$1.class %%JAVAJARDIR%%/bbmap/fileIO/SummaryFile.class %%JAVAJARDIR%%/bbmap/fileIO/SummaryFile.java %%JAVAJARDIR%%/bbmap/fileIO/TextFile.class %%JAVAJARDIR%%/bbmap/fileIO/TextFile.java %%JAVAJARDIR%%/bbmap/fileIO/TextStreamWriter.class %%JAVAJARDIR%%/bbmap/fileIO/TextStreamWriter.java +%%JAVAJARDIR%%/bbmap/fun/BenchIntAppend2.class +%%JAVAJARDIR%%/bbmap/fun/BenchIntAppend2.java +%%JAVAJARDIR%%/bbmap/fun/BenchLongAppend.class +%%JAVAJARDIR%%/bbmap/fun/BenchLongAppend.java +%%JAVAJARDIR%%/bbmap/fun/BenchStringAppend.class +%%JAVAJARDIR%%/bbmap/fun/BenchStringAppend.java 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%%JAVAJARDIR%%/bbmap/fun/DiskSpaceAnalyzer$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$Path.class %%JAVAJARDIR%%/bbmap/fun/FindPath.class %%JAVAJARDIR%%/bbmap/fun/FindPath.java +%%JAVAJARDIR%%/bbmap/fun/FindPrimes.class +%%JAVAJARDIR%%/bbmap/fun/FindPrimes.java %%JAVAJARDIR%%/bbmap/fun/Foo.class %%JAVAJARDIR%%/bbmap/fun/Foo.java %%JAVAJARDIR%%/bbmap/fun/Foo2.class %%JAVAJARDIR%%/bbmap/fun/Foo2.java %%JAVAJARDIR%%/bbmap/fun/Foo3$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$ProcessThread.class %%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio.class %%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio.java %%JAVAJARDIR%%/bbmap/icecream/ZMW.class %%JAVAJARDIR%%/bbmap/icecream/ZMW.java %%JAVAJARDIR%%/bbmap/icecream/ZMWStreamer.class %%JAVAJARDIR%%/bbmap/icecream/ZMWStreamer.java +%%JAVAJARDIR%%/bbmap/idaligner/AlignerBenchmark$SynHeader.class +%%JAVAJARDIR%%/bbmap/idaligner/AlignerBenchmark.class +%%JAVAJARDIR%%/bbmap/idaligner/AlignerBenchmark.java +%%JAVAJARDIR%%/bbmap/idaligner/AlignmentStats.class +%%JAVAJARDIR%%/bbmap/idaligner/AlignmentStats.java +%%JAVAJARDIR%%/bbmap/idaligner/BandedAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/BandedAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/BandedAlignerConcise.class +%%JAVAJARDIR%%/bbmap/idaligner/BandedAlignerConcise.java +%%JAVAJARDIR%%/bbmap/idaligner/BandedAlignerInt.class +%%JAVAJARDIR%%/bbmap/idaligner/BandedAlignerInt.java +%%JAVAJARDIR%%/bbmap/idaligner/BandedAlignerM.class +%%JAVAJARDIR%%/bbmap/idaligner/BandedAlignerM.java +%%JAVAJARDIR%%/bbmap/idaligner/BandedByteAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/BandedByteAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAligner2.class +%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAligner2.java +%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAligner3.class +%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAligner3.java +%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAlignerInt.class +%%JAVAJARDIR%%/bbmap/idaligner/BandedPlusAlignerInt.java +%%JAVAJARDIR%%/bbmap/idaligner/CrossCutAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/CrossCutAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/DiagonalAligner$ExtzResult.class +%%JAVAJARDIR%%/bbmap/idaligner/DiagonalAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/DiagonalAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/DriftingAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/DriftingAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/DriftingAlignerConcise.class +%%JAVAJARDIR%%/bbmap/idaligner/DriftingAlignerConcise.java +%%JAVAJARDIR%%/bbmap/idaligner/DriftingAlignerM.class +%%JAVAJARDIR%%/bbmap/idaligner/DriftingAlignerM.java +%%JAVAJARDIR%%/bbmap/idaligner/DriftingPlusAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/DriftingPlusAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/DriftingPlusAligner2.class +%%JAVAJARDIR%%/bbmap/idaligner/DriftingPlusAligner2.java +%%JAVAJARDIR%%/bbmap/idaligner/DriftingPlusAligner3.class +%%JAVAJARDIR%%/bbmap/idaligner/DriftingPlusAligner3.java +%%JAVAJARDIR%%/bbmap/idaligner/Factory.class +%%JAVAJARDIR%%/bbmap/idaligner/Factory.java +%%JAVAJARDIR%%/bbmap/idaligner/GlocalAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/GlocalAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/GlocalAlignerConcise.class +%%JAVAJARDIR%%/bbmap/idaligner/GlocalAlignerConcise.java +%%JAVAJARDIR%%/bbmap/idaligner/GlocalAlignerInt.class +%%JAVAJARDIR%%/bbmap/idaligner/GlocalAlignerInt.java +%%JAVAJARDIR%%/bbmap/idaligner/GlocalAlignerOld.class +%%JAVAJARDIR%%/bbmap/idaligner/GlocalAlignerOld.java +%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner2.class +%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner2.java +%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner3.class +%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner3.java +%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner4.class +%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner4.java +%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner5.class +%%JAVAJARDIR%%/bbmap/idaligner/GlocalPlusAligner5.java +%%JAVAJARDIR%%/bbmap/idaligner/IDAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/IDAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/IDAlignerStatics.class +%%JAVAJARDIR%%/bbmap/idaligner/IDAlignerStatics.java +%%JAVAJARDIR%%/bbmap/idaligner/IntListAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/IntListAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/Parallelogram.class +%%JAVAJARDIR%%/bbmap/idaligner/Parallelogram.java +%%JAVAJARDIR%%/bbmap/idaligner/QuabbleAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/QuabbleAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/QuantumAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/QuantumAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerConcise.class +%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerConcise.java +%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerConcise2.class +%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerConcise2.java +%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerM.class +%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerM.java +%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerQC.class +%%JAVAJARDIR%%/bbmap/idaligner/QuantumAlignerQC.java +%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner2.class +%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner2.java +%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner3.class +%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner3.java +%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner4.class +%%JAVAJARDIR%%/bbmap/idaligner/QuantumPlusAligner4.java +%%JAVAJARDIR%%/bbmap/idaligner/RelativeAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/RelativeAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/ScrabbleAffine.class +%%JAVAJARDIR%%/bbmap/idaligner/ScrabbleAffine.java +%%JAVAJARDIR%%/bbmap/idaligner/ScrabbleAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/ScrabbleAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/ScrabbleAligner2.class +%%JAVAJARDIR%%/bbmap/idaligner/ScrabbleAligner2.java +%%JAVAJARDIR%%/bbmap/idaligner/SmithWaterman.class +%%JAVAJARDIR%%/bbmap/idaligner/SmithWaterman.java +%%JAVAJARDIR%%/bbmap/idaligner/Test$Runner.class +%%JAVAJARDIR%%/bbmap/idaligner/Test.class +%%JAVAJARDIR%%/bbmap/idaligner/Test.java +%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerBatch.class +%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerBatch.java +%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerLength.class +%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerLength.java +%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerSuite$Job.class +%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerSuite$Worker.class +%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerSuite.class +%%JAVAJARDIR%%/bbmap/idaligner/TestAlignerSuite.java +%%JAVAJARDIR%%/bbmap/idaligner/Tracer.class +%%JAVAJARDIR%%/bbmap/idaligner/Tracer.java +%%JAVAJARDIR%%/bbmap/idaligner/TracerAffine.class +%%JAVAJARDIR%%/bbmap/idaligner/TracerAffine.java +%%JAVAJARDIR%%/bbmap/idaligner/VisualizationConverter.class +%%JAVAJARDIR%%/bbmap/idaligner/VisualizationConverter.java +%%JAVAJARDIR%%/bbmap/idaligner/Visualizer.class +%%JAVAJARDIR%%/bbmap/idaligner/Visualizer.java +%%JAVAJARDIR%%/bbmap/idaligner/WaveFrontAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/WaveFrontAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/WaveFrontAligner2.class +%%JAVAJARDIR%%/bbmap/idaligner/WaveFrontAligner2.java +%%JAVAJARDIR%%/bbmap/idaligner/WaveFrontAlignerViz.class +%%JAVAJARDIR%%/bbmap/idaligner/WaveFrontAlignerViz.java +%%JAVAJARDIR%%/bbmap/idaligner/WobbleAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/WobbleAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/WobbleAlignerConcise.class +%%JAVAJARDIR%%/bbmap/idaligner/WobbleAlignerConcise.java +%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner.java +%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner2.class +%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner2.java +%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner3.class +%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner3.java +%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner4.class +%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner4.java +%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner5.class +%%JAVAJARDIR%%/bbmap/idaligner/WobblePlusAligner5.java +%%JAVAJARDIR%%/bbmap/idaligner/XDropHAligner.class +%%JAVAJARDIR%%/bbmap/idaligner/XDropHAligner.java +%%JAVAJARDIR%%/bbmap/ifa/ClippingTest.class +%%JAVAJARDIR%%/bbmap/ifa/ClippingTest.java +%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner$ProcessThread.class +%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner.class +%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner.java +%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner2$ProcessThread.class +%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner2.class +%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner2.java +%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner3$ProcessThread.class +%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner3.class +%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner3.java +%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner4$ProcessThread.class +%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner4.class +%%JAVAJARDIR%%/bbmap/ifa/IndelFreeAligner4.java +%%JAVAJARDIR%%/bbmap/ifa/IntIndex.class +%%JAVAJARDIR%%/bbmap/ifa/IntIndex.java +%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculator.class +%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculator.java +%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculator2.class +%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculator2.java +%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculator3.class +%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculator3.java +%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculatorOld.class +%%JAVAJARDIR%%/bbmap/ifa/MinHitsCalculatorOld.java +%%JAVAJARDIR%%/bbmap/ifa/PackedIndex.class +%%JAVAJARDIR%%/bbmap/ifa/PackedIndex.java +%%JAVAJARDIR%%/bbmap/ifa/PackedIndex4.class +%%JAVAJARDIR%%/bbmap/ifa/PackedIndex4.java +%%JAVAJARDIR%%/bbmap/ifa/Query.class +%%JAVAJARDIR%%/bbmap/ifa/Query.java +%%JAVAJARDIR%%/bbmap/illumina/Cbcl2Text.class +%%JAVAJARDIR%%/bbmap/illumina/Cbcl2Text.java +%%JAVAJARDIR%%/bbmap/illumina/CbclDecoder.class +%%JAVAJARDIR%%/bbmap/illumina/CbclDecoder.java +%%JAVAJARDIR%%/bbmap/illumina/CbclHeader.class +%%JAVAJARDIR%%/bbmap/illumina/CbclHeader.java +%%JAVAJARDIR%%/bbmap/illumina/CbclInspector.class +%%JAVAJARDIR%%/bbmap/illumina/CbclInspector.java +%%JAVAJARDIR%%/bbmap/illumina/ClusterData.class +%%JAVAJARDIR%%/bbmap/illumina/ClusterData.java +%%JAVAJARDIR%%/bbmap/illumina/FilterReader.class +%%JAVAJARDIR%%/bbmap/illumina/FilterReader.java +%%JAVAJARDIR%%/bbmap/illumina/LocsReader.class +%%JAVAJARDIR%%/bbmap/illumina/LocsReader.java +%%JAVAJARDIR%%/bbmap/illumina/RunInfoParser.class +%%JAVAJARDIR%%/bbmap/illumina/RunInfoParser.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$ProcessThread.class %%JAVAJARDIR%%/bbmap/jgi/KmerCountMulti.class %%JAVAJARDIR%%/bbmap/jgi/KmerCountMulti.java +%%JAVAJARDIR%%/bbmap/jgi/KmerCountShort$ProcessThread.class +%%JAVAJARDIR%%/bbmap/jgi/KmerCountShort.class +%%JAVAJARDIR%%/bbmap/jgi/KmerCountShort.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/KmerHashDump.class +%%JAVAJARDIR%%/bbmap/jgi/KmerHashDump.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$1.class %%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.class %%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.java %%JAVAJARDIR%%/bbmap/jgi/MakePolymers.class %%JAVAJARDIR%%/bbmap/jgi/MakePolymers.java %%JAVAJARDIR%%/bbmap/jgi/MergeBarcodes.class %%JAVAJARDIR%%/bbmap/jgi/MergeBarcodes.java %%JAVAJARDIR%%/bbmap/jgi/MergeSam.class %%JAVAJARDIR%%/bbmap/jgi/MergeSam.java +%%JAVAJARDIR%%/bbmap/jgi/MergeSam2.class +%%JAVAJARDIR%%/bbmap/jgi/MergeSam2.java %%JAVAJARDIR%%/bbmap/jgi/Orf.class %%JAVAJARDIR%%/bbmap/jgi/Orf.java -%%JAVAJARDIR%%/bbmap/jgi/PartitionReads$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/RQCFilter3.class +%%JAVAJARDIR%%/bbmap/jgi/RQCFilter3.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/Reformat2$ProcessThread.class +%%JAVAJARDIR%%/bbmap/jgi/Reformat2.class +%%JAVAJARDIR%%/bbmap/jgi/Reformat2.java %%JAVAJARDIR%%/bbmap/jgi/ReformatReads.class %%JAVAJARDIR%%/bbmap/jgi/ReformatReads.java +%%JAVAJARDIR%%/bbmap/jgi/ReformatReadsOld.class +%%JAVAJARDIR%%/bbmap/jgi/ReformatReadsOld.java +%%JAVAJARDIR%%/bbmap/jgi/ReformatStreamer$ProcessThread.class +%%JAVAJARDIR%%/bbmap/jgi/ReformatStreamer.class +%%JAVAJARDIR%%/bbmap/jgi/ReformatStreamer.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$AllocThread.class %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.class %%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.java +%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet$CountGCThread.class %%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/KmerTableInterface.class +%%JAVAJARDIR%%/bbmap/kmer/KmerTableInterface.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/map/AbstractBitSet.class +%%JAVAJARDIR%%/bbmap/map/AbstractBitSet.java +%%JAVAJARDIR%%/bbmap/map/AbstractIntHashMap.class +%%JAVAJARDIR%%/bbmap/map/AbstractIntHashMap.java +%%JAVAJARDIR%%/bbmap/map/AtomicBitSet.class +%%JAVAJARDIR%%/bbmap/map/AtomicBitSet.java +%%JAVAJARDIR%%/bbmap/map/IntHashMap.class +%%JAVAJARDIR%%/bbmap/map/IntHashMap.java +%%JAVAJARDIR%%/bbmap/map/IntHashMap2.class +%%JAVAJARDIR%%/bbmap/map/IntHashMap2.java +%%JAVAJARDIR%%/bbmap/map/IntHashMap3.class +%%JAVAJARDIR%%/bbmap/map/IntHashMap3.java +%%JAVAJARDIR%%/bbmap/map/IntHashMapBinary.class +%%JAVAJARDIR%%/bbmap/map/IntHashMapBinary.java +%%JAVAJARDIR%%/bbmap/map/IntHashMapInterface.class +%%JAVAJARDIR%%/bbmap/map/IntHashMapInterface.java +%%JAVAJARDIR%%/bbmap/map/IntHashSet.class 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%%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/parse/LineParser.class +%%JAVAJARDIR%%/bbmap/parse/LineParser.java +%%JAVAJARDIR%%/bbmap/parse/LineParser1.class +%%JAVAJARDIR%%/bbmap/parse/LineParser1.java +%%JAVAJARDIR%%/bbmap/parse/LineParser2.class +%%JAVAJARDIR%%/bbmap/parse/LineParser2.java +%%JAVAJARDIR%%/bbmap/parse/LineParser4.class +%%JAVAJARDIR%%/bbmap/parse/LineParser4.java 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%%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$ProcessThread.class %%JAVAJARDIR%%/bbmap/prok/SplitRibo.class %%JAVAJARDIR%%/bbmap/prok/SplitRibo.java %%JAVAJARDIR%%/bbmap/prok/StatsContainer.class %%JAVAJARDIR%%/bbmap/prok/StatsContainer.java +%%JAVAJARDIR%%/bbmap/rand/FastRandom.class +%%JAVAJARDIR%%/bbmap/rand/FastRandom.java +%%JAVAJARDIR%%/bbmap/rand/FastRandomAES.class +%%JAVAJARDIR%%/bbmap/rand/FastRandomAES.java +%%JAVAJARDIR%%/bbmap/rand/FastRandomSIMD.class +%%JAVAJARDIR%%/bbmap/rand/FastRandomSIMD.java +%%JAVAJARDIR%%/bbmap/rand/FastRandomXoshiro.class +%%JAVAJARDIR%%/bbmap/rand/FastRandomXoshiro.java +%%JAVAJARDIR%%/bbmap/rand/JavaRandom.class 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%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker2.java %%JAVAJARDIR%%/bbmap/sketch/CompareBuffer.class %%JAVAJARDIR%%/bbmap/sketch/CompareBuffer.java %%JAVAJARDIR%%/bbmap/sketch/CompareSSU$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$Pack.class %%JAVAJARDIR%%/bbmap/stream/ArrayListSet.class %%JAVAJARDIR%%/bbmap/stream/ArrayListSet.java +%%JAVAJARDIR%%/bbmap/stream/BamStreamer$ProcessThread.class +%%JAVAJARDIR%%/bbmap/stream/BamStreamer.class +%%JAVAJARDIR%%/bbmap/stream/BamStreamer.java +%%JAVAJARDIR%%/bbmap/stream/BamWriter$ProcessThread.class +%%JAVAJARDIR%%/bbmap/stream/BamWriter$SamWriterInputJob.class +%%JAVAJARDIR%%/bbmap/stream/BamWriter$SamWriterOutputJob.class +%%JAVAJARDIR%%/bbmap/stream/BamWriter.class +%%JAVAJARDIR%%/bbmap/stream/BamWriter.java +%%JAVAJARDIR%%/bbmap/stream/BedReadFilter.class +%%JAVAJARDIR%%/bbmap/stream/BedReadFilter.java %%JAVAJARDIR%%/bbmap/stream/BufferedMultiCros.class %%JAVAJARDIR%%/bbmap/stream/BufferedMultiCros.java +%%JAVAJARDIR%%/bbmap/stream/CigarNormalizer.class +%%JAVAJARDIR%%/bbmap/stream/CigarNormalizer.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$ListenThread.class %%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStreamD.class %%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStreamD.java %%JAVAJARDIR%%/bbmap/stream/ConcurrentReadStreamInterface.class %%JAVAJARDIR%%/bbmap/stream/ConcurrentReadStreamInterface.java %%JAVAJARDIR%%/bbmap/stream/CrisContainer.class %%JAVAJARDIR%%/bbmap/stream/CrisContainer.java %%JAVAJARDIR%%/bbmap/stream/CrisWrapper.class %%JAVAJARDIR%%/bbmap/stream/CrisWrapper.java %%JAVAJARDIR%%/bbmap/stream/CustomHeader.class %%JAVAJARDIR%%/bbmap/stream/CustomHeader.java %%JAVAJARDIR%%/bbmap/stream/DualCris.class %%JAVAJARDIR%%/bbmap/stream/DualCris.java %%JAVAJARDIR%%/bbmap/stream/EmblReadInputStream.class %%JAVAJARDIR%%/bbmap/stream/EmblReadInputStream.java %%JAVAJARDIR%%/bbmap/stream/FASTQ.class %%JAVAJARDIR%%/bbmap/stream/FASTQ.java %%JAVAJARDIR%%/bbmap/stream/FastaQualReadInputStream.class %%JAVAJARDIR%%/bbmap/stream/FastaQualReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/FastaQualStreamer$ProcessThread.class +%%JAVAJARDIR%%/bbmap/stream/FastaQualStreamer.class +%%JAVAJARDIR%%/bbmap/stream/FastaQualStreamer.java +%%JAVAJARDIR%%/bbmap/stream/FastaQualStreamerZT.class +%%JAVAJARDIR%%/bbmap/stream/FastaQualStreamerZT.java +%%JAVAJARDIR%%/bbmap/stream/FastaQualWriterST$WriterRunnable.class 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+%%JAVAJARDIR%%/bbmap/stream/GfaReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/GfaStreamerST$ProcessThread.class +%%JAVAJARDIR%%/bbmap/stream/GfaStreamerST.class +%%JAVAJARDIR%%/bbmap/stream/GfaStreamerST.java +%%JAVAJARDIR%%/bbmap/stream/HasID.class +%%JAVAJARDIR%%/bbmap/stream/HasID.java %%JAVAJARDIR%%/bbmap/stream/HeaderInputStream.class %%JAVAJARDIR%%/bbmap/stream/HeaderInputStream.java +%%JAVAJARDIR%%/bbmap/stream/JobQueue$HasIDComparator.class +%%JAVAJARDIR%%/bbmap/stream/JobQueue.class +%%JAVAJARDIR%%/bbmap/stream/JobQueue.java %%JAVAJARDIR%%/bbmap/stream/MDWalker.class %%JAVAJARDIR%%/bbmap/stream/MDWalker.java +%%JAVAJARDIR%%/bbmap/stream/MDWalker2.class +%%JAVAJARDIR%%/bbmap/stream/MDWalker2.java %%JAVAJARDIR%%/bbmap/stream/MultiCros.class %%JAVAJARDIR%%/bbmap/stream/MultiCros.java %%JAVAJARDIR%%/bbmap/stream/MultiCros2$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$TimestampComparator.class %%JAVAJARDIR%%/bbmap/stream/MultiCros6.class %%JAVAJARDIR%%/bbmap/stream/MultiCros6.java %%JAVAJARDIR%%/bbmap/stream/NullOutputStream.class %%JAVAJARDIR%%/bbmap/stream/NullOutputStream.java %%JAVAJARDIR%%/bbmap/stream/OnelineReadInputStream.class %%JAVAJARDIR%%/bbmap/stream/OnelineReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/OrderedQueueSystem.class 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%%JAVAJARDIR%%/bbmap/stream/ReadStreamWriter$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/SamHeaderWriter$WriterThread.class +%%JAVAJARDIR%%/bbmap/stream/SamHeaderWriter.class +%%JAVAJARDIR%%/bbmap/stream/SamHeaderWriter.java %%JAVAJARDIR%%/bbmap/stream/SamLine.class %%JAVAJARDIR%%/bbmap/stream/SamLine.java -%%JAVAJARDIR%%/bbmap/stream/SamLineStreamer$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$ProcessThread.class -%%JAVAJARDIR%%/bbmap/stream/SamReadStreamer.class -%%JAVAJARDIR%%/bbmap/stream/SamReadStreamer.java +%%JAVAJARDIR%%/bbmap/stream/SamStreamer$ProcessThread.class %%JAVAJARDIR%%/bbmap/stream/SamStreamer.class %%JAVAJARDIR%%/bbmap/stream/SamStreamer.java %%JAVAJARDIR%%/bbmap/stream/SamStreamerMF.class %%JAVAJARDIR%%/bbmap/stream/SamStreamerMF.java +%%JAVAJARDIR%%/bbmap/stream/SamStreamerST$ProcessThread.class +%%JAVAJARDIR%%/bbmap/stream/SamStreamerST.class +%%JAVAJARDIR%%/bbmap/stream/SamStreamerST.java %%JAVAJARDIR%%/bbmap/stream/SamStreamerWrapper.class %%JAVAJARDIR%%/bbmap/stream/SamStreamerWrapper.java +%%JAVAJARDIR%%/bbmap/stream/SamWriter$ProcessThread.class +%%JAVAJARDIR%%/bbmap/stream/SamWriter$SamWriterInputJob.class +%%JAVAJARDIR%%/bbmap/stream/SamWriter$SamWriterOutputJob.class +%%JAVAJARDIR%%/bbmap/stream/SamWriter.class +%%JAVAJARDIR%%/bbmap/stream/SamWriter.java +%%JAVAJARDIR%%/bbmap/stream/SamWriterST.class +%%JAVAJARDIR%%/bbmap/stream/SamWriterST.java +%%JAVAJARDIR%%/bbmap/stream/SamWriterST2$WriterRunnable.class +%%JAVAJARDIR%%/bbmap/stream/SamWriterST2.class +%%JAVAJARDIR%%/bbmap/stream/SamWriterST2.java %%JAVAJARDIR%%/bbmap/stream/ScaffoldCoordinates.class %%JAVAJARDIR%%/bbmap/stream/ScaffoldCoordinates.java +%%JAVAJARDIR%%/bbmap/stream/ScaffoldRenamer.class +%%JAVAJARDIR%%/bbmap/stream/ScaffoldRenamer.java %%JAVAJARDIR%%/bbmap/stream/ScarfReadInputStream.class %%JAVAJARDIR%%/bbmap/stream/ScarfReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/ScarfStreamer$ProcessThread.class +%%JAVAJARDIR%%/bbmap/stream/ScarfStreamer.class +%%JAVAJARDIR%%/bbmap/stream/ScarfStreamer.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/stream/Streamer.class +%%JAVAJARDIR%%/bbmap/stream/Streamer.java +%%JAVAJARDIR%%/bbmap/stream/StreamerFactory.class +%%JAVAJARDIR%%/bbmap/stream/StreamerFactory.java +%%JAVAJARDIR%%/bbmap/stream/StreamerWrapper.class +%%JAVAJARDIR%%/bbmap/stream/StreamerWrapper.java +%%JAVAJARDIR%%/bbmap/stream/TestMDWalker.class +%%JAVAJARDIR%%/bbmap/stream/TestMDWalker.java +%%JAVAJARDIR%%/bbmap/stream/Writer.class +%%JAVAJARDIR%%/bbmap/stream/Writer.java +%%JAVAJARDIR%%/bbmap/stream/WriterFactory.class +%%JAVAJARDIR%%/bbmap/stream/WriterFactory.java +%%JAVAJARDIR%%/bbmap/stream/bam/BamIndexWriter$BinData.class +%%JAVAJARDIR%%/bbmap/stream/bam/BamIndexWriter$ReferenceIndex.class +%%JAVAJARDIR%%/bbmap/stream/bam/BamIndexWriter.class +%%JAVAJARDIR%%/bbmap/stream/bam/BamIndexWriter.java +%%JAVAJARDIR%%/bbmap/stream/bam/BamInputStream.class +%%JAVAJARDIR%%/bbmap/stream/bam/BamInputStream.java +%%JAVAJARDIR%%/bbmap/stream/bam/BamOutputStream.class +%%JAVAJARDIR%%/bbmap/stream/bam/BamOutputStream.java +%%JAVAJARDIR%%/bbmap/stream/bam/BamReadInputStream.class +%%JAVAJARDIR%%/bbmap/stream/bam/BamReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/bam/BamReadInputStreamST.class +%%JAVAJARDIR%%/bbmap/stream/bam/BamReadInputStreamST.java +%%JAVAJARDIR%%/bbmap/stream/bam/BamReader.class +%%JAVAJARDIR%%/bbmap/stream/bam/BamReader.java +%%JAVAJARDIR%%/bbmap/stream/bam/BamToSamConverter.class +%%JAVAJARDIR%%/bbmap/stream/bam/BamToSamConverter.java +%%JAVAJARDIR%%/bbmap/stream/bam/BamWriterHelper.class +%%JAVAJARDIR%%/bbmap/stream/bam/BamWriterHelper.java +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputJob.class +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputJob.java +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStream$PrefixedInputStream.class 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+%%JAVAJARDIR%%/bbmap/stream/bam/BgzfInputStreamMT3.java +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfJob.class +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfJob.java +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStream.class +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStream.java +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStreamMT$1.class +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStreamMT$2.class +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStreamMT.class +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStreamMT.java +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStreamMT2$ProcessThread.class +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStreamMT2.class +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfOutputStreamMT2.java +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfSettings.class +%%JAVAJARDIR%%/bbmap/stream/bam/BgzfSettings.java +%%JAVAJARDIR%%/bbmap/stream/bam/DebugBgzfRead.class +%%JAVAJARDIR%%/bbmap/stream/bam/DebugBgzfRead.java +%%JAVAJARDIR%%/bbmap/stream/bam/DebugBgzfWrite.class +%%JAVAJARDIR%%/bbmap/stream/bam/DebugBgzfWrite.java +%%JAVAJARDIR%%/bbmap/stream/bam/SamToBamConverter.class +%%JAVAJARDIR%%/bbmap/stream/bam/SamToBamConverter.java +%%JAVAJARDIR%%/bbmap/stream/bam/TestBamIndexWriter.class +%%JAVAJARDIR%%/bbmap/stream/bam/TestBamIndexWriter.java +%%JAVAJARDIR%%/bbmap/stream/bam/TestBamReader.class +%%JAVAJARDIR%%/bbmap/stream/bam/TestBamReader.java +%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfA80k.class +%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfA80k.java +%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfMultithreaded.class +%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfMultithreaded.java +%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfSimple.class +%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfSimple.java +%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfSystematic.class +%%JAVAJARDIR%%/bbmap/stream/bam/TestBgzfSystematic.java +%%JAVAJARDIR%%/bbmap/stream/bam/TestEarlyClose.class +%%JAVAJARDIR%%/bbmap/stream/bam/TestEarlyClose.java +%%JAVAJARDIR%%/bbmap/stream/bam/TestSeqReverse.class +%%JAVAJARDIR%%/bbmap/stream/bam/TestSeqReverse.java +%%JAVAJARDIR%%/bbmap/stream/bam/TestSimpleBgzfRead.class +%%JAVAJARDIR%%/bbmap/stream/bam/TestSimpleBgzfRead.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/BinaryByteWrapperLE.class +%%JAVAJARDIR%%/bbmap/structures/BinaryByteWrapperLE.java %%JAVAJARDIR%%/bbmap/structures/ByteBuilder.class %%JAVAJARDIR%%/bbmap/structures/ByteBuilder.java +%%JAVAJARDIR%%/bbmap/structures/BytePrefixDispatcher.class +%%JAVAJARDIR%%/bbmap/structures/BytePrefixDispatcher.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/IntRingBuffer.class +%%JAVAJARDIR%%/bbmap/structures/IntRingBuffer.java +%%JAVAJARDIR%%/bbmap/structures/IntRingBufferCond.class +%%JAVAJARDIR%%/bbmap/structures/IntRingBufferCond.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/structures/XNum.class +%%JAVAJARDIR%%/bbmap/structures/XNum.java %%JAVAJARDIR%%/bbmap/synth/CoverageModel.class %%JAVAJARDIR%%/bbmap/synth/CoverageModel.java %%JAVAJARDIR%%/bbmap/synth/CrossContaminate$Vessel.class %%JAVAJARDIR%%/bbmap/synth/CrossContaminate.class %%JAVAJARDIR%%/bbmap/synth/CrossContaminate.java %%JAVAJARDIR%%/bbmap/synth/FakeReads.class %%JAVAJARDIR%%/bbmap/synth/FakeReads.java +%%JAVAJARDIR%%/bbmap/synth/FuseByTaxa.class +%%JAVAJARDIR%%/bbmap/synth/FuseByTaxa.java %%JAVAJARDIR%%/bbmap/synth/FuseSequence.class %%JAVAJARDIR%%/bbmap/synth/FuseSequence.java %%JAVAJARDIR%%/bbmap/synth/GCBias.class %%JAVAJARDIR%%/bbmap/synth/GCBias.java %%JAVAJARDIR%%/bbmap/synth/MakeChimeras.class %%JAVAJARDIR%%/bbmap/synth/MakeChimeras.java %%JAVAJARDIR%%/bbmap/synth/MakeContaminatedGenomes.class %%JAVAJARDIR%%/bbmap/synth/MakeContaminatedGenomes.java %%JAVAJARDIR%%/bbmap/synth/MutateGenome$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_SampleStreamer.class +%%JAVAJARDIR%%/bbmap/template/A_SampleStreamer.java +%%JAVAJARDIR%%/bbmap/template/A_SampleStreamerMT$ProcessThread.class +%%JAVAJARDIR%%/bbmap/template/A_SampleStreamerMT.class +%%JAVAJARDIR%%/bbmap/template/A_SampleStreamerMT.java %%JAVAJARDIR%%/bbmap/template/A_SampleSummary.class %%JAVAJARDIR%%/bbmap/template/A_SampleSummary.java %%JAVAJARDIR%%/bbmap/template/A_Sample_Generator$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/KmerTracker.class +%%JAVAJARDIR%%/bbmap/tracker/KmerTracker.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/BalanceVectors.class +%%JAVAJARDIR%%/bbmap/var2/BalanceVectors.java +%%JAVAJARDIR%%/bbmap/var2/BedMask$1.class +%%JAVAJARDIR%%/bbmap/var2/BedMask.class +%%JAVAJARDIR%%/bbmap/var2/BedMask.java +%%JAVAJARDIR%%/bbmap/var2/BedSet$1.class 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%%JAVAJARDIR%%/bbmap/var2/FilterVCF.class %%JAVAJARDIR%%/bbmap/var2/FilterVCF.java +%%JAVAJARDIR%%/bbmap/var2/GradeVCF$ProcessThread.class +%%JAVAJARDIR%%/bbmap/var2/GradeVCF.class +%%JAVAJARDIR%%/bbmap/var2/GradeVCF.java +%%JAVAJARDIR%%/bbmap/var2/InvertVCF.class +%%JAVAJARDIR%%/bbmap/var2/InvertVCF.java +%%JAVAJARDIR%%/bbmap/var2/LabelVCF.class +%%JAVAJARDIR%%/bbmap/var2/LabelVCF.java %%JAVAJARDIR%%/bbmap/var2/MergeSamples$MergeThread.class %%JAVAJARDIR%%/bbmap/var2/MergeSamples.class %%JAVAJARDIR%%/bbmap/var2/MergeSamples.java +%%JAVAJARDIR%%/bbmap/var2/NNChooser$NetEntry.class +%%JAVAJARDIR%%/bbmap/var2/NNChooser.class +%%JAVAJARDIR%%/bbmap/var2/NNChooser.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/RestoreBases$1.class +%%JAVAJARDIR%%/bbmap/var2/RestoreBases.class +%%JAVAJARDIR%%/bbmap/var2/RestoreBases.java %%JAVAJARDIR%%/bbmap/var2/SamFilter.class %%JAVAJARDIR%%/bbmap/var2/SamFilter.java %%JAVAJARDIR%%/bbmap/var2/ScafMap.class %%JAVAJARDIR%%/bbmap/var2/ScafMap.java +%%JAVAJARDIR%%/bbmap/var2/ScafMapNameTest.class +%%JAVAJARDIR%%/bbmap/var2/ScafMapNameTest.java %%JAVAJARDIR%%/bbmap/var2/Scaffold.class %%JAVAJARDIR%%/bbmap/var2/Scaffold.java %%JAVAJARDIR%%/bbmap/var2/SoftClipper.class %%JAVAJARDIR%%/bbmap/var2/SoftClipper.java +%%JAVAJARDIR%%/bbmap/var2/TransferLabels.class +%%JAVAJARDIR%%/bbmap/var2/TransferLabels.java %%JAVAJARDIR%%/bbmap/var2/VCFFile$1.class %%JAVAJARDIR%%/bbmap/var2/VCFFile.class %%JAVAJARDIR%%/bbmap/var2/VCFFile.java %%JAVAJARDIR%%/bbmap/var2/VCFLine.class %%JAVAJARDIR%%/bbmap/var2/VCFLine.java %%JAVAJARDIR%%/bbmap/var2/Var.class %%JAVAJARDIR%%/bbmap/var2/Var.java %%JAVAJARDIR%%/bbmap/var2/VarFilter.class %%JAVAJARDIR%%/bbmap/var2/VarFilter.java %%JAVAJARDIR%%/bbmap/var2/VarHelper.class %%JAVAJARDIR%%/bbmap/var2/VarHelper.java %%JAVAJARDIR%%/bbmap/var2/VarKey.class %%JAVAJARDIR%%/bbmap/var2/VarKey.java +%%JAVAJARDIR%%/bbmap/var2/VarM.class +%%JAVAJARDIR%%/bbmap/var2/VarM.java %%JAVAJARDIR%%/bbmap/var2/VarMap$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/VcfToTrainingVectors.class +%%JAVAJARDIR%%/bbmap/var2/VcfToTrainingVectors.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 +%%JAVAJARDIR%%/bbmap/var2/VectorUMP45.class +%%JAVAJARDIR%%/bbmap/var2/VectorUMP45.java +%%JAVAJARDIR%%/bbmap/var2/VectorsFromLabeledVCF.class +%%JAVAJARDIR%%/bbmap/var2/VectorsFromLabeledVCF.java