diff options
author | Jason W. Bacon <jwb@FreeBSD.org> | 2021-04-18 16:21:29 +0000 |
---|---|---|
committer | Jason W. Bacon <jwb@FreeBSD.org> | 2021-04-18 16:21:29 +0000 |
commit | 15458dfbacb842d71a41dcfdb6be83301ef0b7b6 (patch) | |
tree | cf23b97bd36873e1edf0d933625bdea79678ce2e | |
parent | 48ddc73c5822130dd3f00361ec6998eec0a29e6d (diff) | |
download | ports-15458dfbacb842d71a41dcfdb6be83301ef0b7b6.tar.gz ports-15458dfbacb842d71a41dcfdb6be83301ef0b7b6.zip |
biology/bbmap: BBMap short read aligner, and other bioinformatic tools
This package includes BBMap, a short read aligner, as well as various other
bioinformatic tools. It is written in pure Java, can run on any platform, and
has no dependencies other than Java being installed (compiled for Java 6 and
higher). All tools are efficient and multithreaded.
-rw-r--r-- | biology/Makefile | 1 | ||||
-rw-r--r-- | biology/bbmap/Makefile | 45 | ||||
-rw-r--r-- | biology/bbmap/distinfo | 3 | ||||
-rw-r--r-- | biology/bbmap/files/patch-calcmem.sh | 33 | ||||
-rw-r--r-- | biology/bbmap/pkg-descr | 6 | ||||
-rw-r--r-- | biology/bbmap/pkg-plist | 1976 |
6 files changed, 2064 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 956405f7e693..40af21229bfa 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -6,6 +6,7 @@ SUBDIR += avida SUBDIR += babel SUBDIR += bamtools + SUBDIR += bbmap SUBDIR += bcftools SUBDIR += bedtools SUBDIR += bioawk diff --git a/biology/bbmap/Makefile b/biology/bbmap/Makefile new file mode 100644 index 000000000000..9f20eab70e8c --- /dev/null +++ b/biology/bbmap/Makefile @@ -0,0 +1,45 @@ +PORTNAME= bbmap +DISTVERSION= 38.90 +CATEGORIES= biology java +MASTER_SITES= SF/bbmap/ +DISTNAME= BBMap_${PORTVERSION} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= BBMap short read aligner, and other bioinformatic tools + +LICENSE= BSD3CLAUSE +LICENSE_FILE= ${WRKSRC}/license.txt + +RUN_DEPENDS= bash:shells/bash \ + pigz:archivers/pigz \ + pbzip2:archivers/pbzip2 + +USES= shebangfix +USE_JAVA= yes + +SHEBANG_FILES= ${WRKSRC}/*.sh + +WRKSRC= ${WRKDIR}/${PORTNAME} +NO_BUILD= yes +NO_ARCH= yes + +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' \ + ${WRKSRC}/*.sh + +do-install: + @${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 + ${RLN} ${STAGEDIR}${LIBEXEC_DIR}/${f} ${STAGEDIR}${PREFIX}/bin +.endfor + +.include <bsd.port.mk> diff --git a/biology/bbmap/distinfo b/biology/bbmap/distinfo new file mode 100644 index 000000000000..2dcabac6c8b8 --- /dev/null +++ b/biology/bbmap/distinfo @@ -0,0 +1,3 @@ +TIMESTAMP = 1618324169 +SHA256 (BBMap_38.90.tar.gz) = a366531c566da5e7246ccf707b6770a92246c1cfe29fd30dc2d800c0d82269f1 +SIZE (BBMap_38.90.tar.gz) = 10516866 diff --git a/biology/bbmap/files/patch-calcmem.sh b/biology/bbmap/files/patch-calcmem.sh new file mode 100644 index 000000000000..db002636a860 --- /dev/null +++ b/biology/bbmap/files/patch-calcmem.sh @@ -0,0 +1,33 @@ +--- calcmem.sh.orig 2021-04-13 14:05:28 UTC ++++ calcmem.sh +@@ -72,30 +72,6 @@ function setEnvironment(){ + if [[ $SHIFTER_RUNTIME == 1 ]]; then + #Ignore NERSC_HOST + shifter=1 +- elif [ -v "$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 +- : +- else +- PATH=/global/projectb/sandbox/gaag/bbtools/bgzip:$PATH +- PATH=/global/projectb/sandbox/gaag/bbtools/lbzip2/bin:$PATH +- PATH=/global/projectb/sandbox/gaag/bbtools/sambamba:$PATH +- PATH=/global/projectb/sandbox/gaag/bbtools/java/jdk-11.0.2/bin:$PATH +- PATH=/global/projectb/sandbox/gaag/bbtools/pigz2/pigz-2.4:$PATH +- +- if [[ $NERSC_HOST == cori ]]; then +- +- #module unload PrgEnv-intel +- #module load PrgEnv-gnu/7.1 +- PATH=/global/projectb/sandbox/gaag/bbtools/samtools_cori/bin:$PATH +- : +- fi + fi + } + diff --git a/biology/bbmap/pkg-descr b/biology/bbmap/pkg-descr new file mode 100644 index 000000000000..dabb59d91cb8 --- /dev/null +++ b/biology/bbmap/pkg-descr @@ -0,0 +1,6 @@ +This package includes BBMap, a short read aligner, as well as various other +bioinformatic tools. It is written in pure Java, can run on any platform, and +has no dependencies other than Java being installed (compiled for Java 6 and +higher). All tools are efficient and multithreaded. + +WWW: https://jgi.doe.gov/data-and-tools/bbtools/ diff --git a/biology/bbmap/pkg-plist b/biology/bbmap/pkg-plist new file mode 100644 index 000000000000..195fa6f86ab3 --- /dev/null +++ b/biology/bbmap/pkg-plist @@ -0,0 +1,1976 @@ +bin/bbduk.sh +bin/bbmap.sh +bin/bbnorm.sh +bin/bloomfilter.sh +bin/dedupe.sh +bin/reformat.sh +libexec/bbmap/a_sample_mt.sh +libexec/bbmap/addadapters.sh +libexec/bbmap/addssu.sh +libexec/bbmap/adjusthomopolymers.sh +libexec/bbmap/alltoall.sh +libexec/bbmap/analyzeaccession.sh +libexec/bbmap/analyzegenes.sh +libexec/bbmap/analyzesketchresults.sh +libexec/bbmap/applyvariants.sh +libexec/bbmap/bbcms.sh +libexec/bbmap/bbcountunique.sh +libexec/bbmap/bbduk.sh +libexec/bbmap/bbest.sh +libexec/bbmap/bbfakereads.sh +libexec/bbmap/bbmap.sh +libexec/bbmap/bbmapskimmer.sh +libexec/bbmap/bbmask.sh +libexec/bbmap/bbmerge-auto.sh +libexec/bbmap/bbmerge.sh +libexec/bbmap/bbnorm.sh +libexec/bbmap/bbrealign.sh +libexec/bbmap/bbrename.sh +libexec/bbmap/bbsketch.sh +libexec/bbmap/bbsplit.sh +libexec/bbmap/bbsplitpairs.sh +libexec/bbmap/bbstats.sh +libexec/bbmap/bbversion.sh +libexec/bbmap/bbwrap.sh +libexec/bbmap/bloomfilter.sh +libexec/bbmap/calcmem.sh +libexec/bbmap/calctruequality.sh +libexec/bbmap/callgenes.sh +libexec/bbmap/callpeaks.sh +libexec/bbmap/callvariants.sh +libexec/bbmap/callvariants2.sh +libexec/bbmap/clumpify.sh +libexec/bbmap/commonkmers.sh +libexec/bbmap/comparegff.sh +libexec/bbmap/comparesketch.sh +libexec/bbmap/comparessu.sh +libexec/bbmap/comparevcf.sh +libexec/bbmap/consect.sh +libexec/bbmap/consensus.sh +libexec/bbmap/countbarcodes.sh +libexec/bbmap/countgc.sh +libexec/bbmap/countsharedlines.sh +libexec/bbmap/crossblock.sh +libexec/bbmap/crosscontaminate.sh +libexec/bbmap/cutgff.sh +libexec/bbmap/cutprimers.sh +libexec/bbmap/decontaminate.sh +libexec/bbmap/dedupe.sh +libexec/bbmap/dedupe2.sh +libexec/bbmap/dedupebymapping.sh +libexec/bbmap/demuxbyname.sh +libexec/bbmap/diskbench.sh +libexec/bbmap/estherfilter.sh +libexec/bbmap/explodetree.sh +libexec/bbmap/fetchproks.sh +libexec/bbmap/filterassemblysummary.sh +libexec/bbmap/filterbarcodes.sh +libexec/bbmap/filterbycoverage.sh +libexec/bbmap/filterbyname.sh +libexec/bbmap/filterbysequence.sh +libexec/bbmap/filterbytaxa.sh +libexec/bbmap/filterbytile.sh +libexec/bbmap/filterlines.sh +libexec/bbmap/filterqc.sh +libexec/bbmap/filtersam.sh +libexec/bbmap/filtersilva.sh +libexec/bbmap/filtersubs.sh +libexec/bbmap/filtervcf.sh +libexec/bbmap/fixgaps.sh +libexec/bbmap/fungalrelease.sh +libexec/bbmap/fuse.sh +libexec/bbmap/gbff2gff.sh +libexec/bbmap/getreads.sh +libexec/bbmap/gi2ancestors.sh +libexec/bbmap/gi2taxid.sh +libexec/bbmap/gitable.sh +libexec/bbmap/grademerge.sh +libexec/bbmap/gradesam.sh +libexec/bbmap/icecreamfinder.sh +libexec/bbmap/icecreamgrader.sh +libexec/bbmap/icecreammaker.sh +libexec/bbmap/idmatrix.sh +libexec/bbmap/idtree.sh +libexec/bbmap/invertkey.sh +libexec/bbmap/kapastats.sh +libexec/bbmap/kcompress.sh +libexec/bbmap/keepbestcopy.sh +libexec/bbmap/khist.sh +libexec/bbmap/kmercountexact.sh +libexec/bbmap/kmercountmulti.sh +libexec/bbmap/kmercoverage.sh +libexec/bbmap/kmerfilterset.sh +libexec/bbmap/kmerlimit.sh +libexec/bbmap/kmerlimit2.sh +libexec/bbmap/kmerposition.sh +libexec/bbmap/kmutate.sh +libexec/bbmap/lilypad.sh +libexec/bbmap/loadreads.sh +libexec/bbmap/loglog.sh +libexec/bbmap/makechimeras.sh +libexec/bbmap/makecontaminatedgenomes.sh +libexec/bbmap/makepolymers.sh +libexec/bbmap/mapPacBio.sh +libexec/bbmap/matrixtocolumns.sh +libexec/bbmap/mergeOTUs.sh +libexec/bbmap/mergebarcodes.sh +libexec/bbmap/mergepgm.sh +libexec/bbmap/mergeribo.sh +libexec/bbmap/mergesam.sh +libexec/bbmap/mergesketch.sh +libexec/bbmap/mergesorted.sh +libexec/bbmap/msa.sh +libexec/bbmap/mutate.sh +libexec/bbmap/muxbyname.sh +libexec/bbmap/partition.sh +libexec/bbmap/phylip2fasta.sh +libexec/bbmap/pileup.sh +libexec/bbmap/plotflowcell.sh +libexec/bbmap/plotgc.sh +libexec/bbmap/postfilter.sh +libexec/bbmap/printtime.sh +libexec/bbmap/processfrag.sh +libexec/bbmap/processhi-c.sh +libexec/bbmap/processspeed.sh +libexec/bbmap/randomgenome.sh +libexec/bbmap/randomreads.sh +libexec/bbmap/readlength.sh +libexec/bbmap/readqc.sh +libexec/bbmap/reducesilva.sh +libexec/bbmap/reformat.sh +libexec/bbmap/reformatpb.sh +libexec/bbmap/removebadbarcodes.sh +libexec/bbmap/removecatdogmousehuman.sh +libexec/bbmap/removehuman.sh +libexec/bbmap/removehuman2.sh +libexec/bbmap/removemicrobes.sh +libexec/bbmap/removesmartbell.sh +libexec/bbmap/rename.sh +libexec/bbmap/renameimg.sh +libexec/bbmap/repair.sh +libexec/bbmap/replaceheaders.sh +libexec/bbmap/representative.sh +libexec/bbmap/rqcfilter.sh +libexec/bbmap/rqcfilter2.sh +libexec/bbmap/runhmm.sh +libexec/bbmap/samtoroc.sh +libexec/bbmap/seal.sh +libexec/bbmap/sendsketch.sh +libexec/bbmap/shred.sh +libexec/bbmap/shrinkaccession.sh +libexec/bbmap/shuffle.sh +libexec/bbmap/shuffle2.sh +libexec/bbmap/sketch.sh +libexec/bbmap/sketchblacklist.sh +libexec/bbmap/sketchblacklist2.sh +libexec/bbmap/sortbyname.sh +libexec/bbmap/splitbytaxa.sh +libexec/bbmap/splitnextera.sh +libexec/bbmap/splitribo.sh +libexec/bbmap/splitsam.sh +libexec/bbmap/splitsam4way.sh +libexec/bbmap/splitsam6way.sh +libexec/bbmap/stats.sh +libexec/bbmap/statswrapper.sh +libexec/bbmap/streamsam.sh +libexec/bbmap/subsketch.sh +libexec/bbmap/summarizecontam.sh +libexec/bbmap/summarizecoverage.sh +libexec/bbmap/summarizecrossblock.sh +libexec/bbmap/summarizemerge.sh +libexec/bbmap/summarizequast.sh +libexec/bbmap/summarizescafstats.sh +libexec/bbmap/summarizeseal.sh +libexec/bbmap/summarizesketch.sh +libexec/bbmap/synthmda.sh +libexec/bbmap/tadpipe.sh +libexec/bbmap/tadpole.sh +libexec/bbmap/tadwrapper.sh +libexec/bbmap/taxonomy.sh +libexec/bbmap/taxserver.sh +libexec/bbmap/taxsize.sh +libexec/bbmap/taxtree.sh +libexec/bbmap/testfilesystem.sh +libexec/bbmap/testformat.sh +libexec/bbmap/testformat2.sh +libexec/bbmap/tetramerfreq.sh +libexec/bbmap/textfile.sh +libexec/bbmap/translate6frames.sh +libexec/bbmap/unicode2ascii.sh +libexec/bbmap/unzip.sh +libexec/bbmap/vcf2gff.sh +libexec/bbmap/webcheck.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/RandomReads3$1.class +%%JAVAJARDIR%%/bbmap/align2/RandomReads3.class +%%JAVAJARDIR%%/bbmap/align2/RandomReads3.java +%%JAVAJARDIR%%/bbmap/align2/RefToIndex.class +%%JAVAJARDIR%%/bbmap/align2/RefToIndex.java +%%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput.class +%%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput.java +%%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput2.class +%%JAVAJARDIR%%/bbmap/align2/ReformatBatchOutput2.java +%%JAVAJARDIR%%/bbmap/align2/Solver.class +%%JAVAJARDIR%%/bbmap/align2/Solver.java +%%JAVAJARDIR%%/bbmap/align2/SplitMappedReads.class +%%JAVAJARDIR%%/bbmap/align2/SplitMappedReads.java +%%JAVAJARDIR%%/bbmap/align2/TranslateColorspaceRead.class +%%JAVAJARDIR%%/bbmap/align2/TranslateColorspaceRead.java +%%JAVAJARDIR%%/bbmap/aligner/Aligner.class +%%JAVAJARDIR%%/bbmap/aligner/Aligner.java +%%JAVAJARDIR%%/bbmap/aligner/Alignment.class +%%JAVAJARDIR%%/bbmap/aligner/Alignment.java +%%JAVAJARDIR%%/bbmap/aligner/AlignmentResult.class +%%JAVAJARDIR%%/bbmap/aligner/AlignmentResult.java +%%JAVAJARDIR%%/bbmap/aligner/AllToAll$ProcessThread.class +%%JAVAJARDIR%%/bbmap/aligner/AllToAll.class +%%JAVAJARDIR%%/bbmap/aligner/AllToAll.java +%%JAVAJARDIR%%/bbmap/aligner/FlatAligner.class +%%JAVAJARDIR%%/bbmap/aligner/FlatAligner.java +%%JAVAJARDIR%%/bbmap/aligner/FlatAligner2.class +%%JAVAJARDIR%%/bbmap/aligner/FlatAligner2.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/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/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$BuildThread.class +%%JAVAJARDIR%%/bbmap/assemble/KmerCompressor.class +%%JAVAJARDIR%%/bbmap/assemble/KmerCompressor.java +%%JAVAJARDIR%%/bbmap/assemble/Postfilter.class +%%JAVAJARDIR%%/bbmap/assemble/Postfilter.java +%%JAVAJARDIR%%/bbmap/assemble/Rollback.class +%%JAVAJARDIR%%/bbmap/assemble/Rollback.java +%%JAVAJARDIR%%/bbmap/assemble/ShaveObject.class +%%JAVAJARDIR%%/bbmap/assemble/ShaveObject.java +%%JAVAJARDIR%%/bbmap/assemble/Shaver.class +%%JAVAJARDIR%%/bbmap/assemble/Shaver.java +%%JAVAJARDIR%%/bbmap/assemble/Shaver1$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/bloom/BloomFilter.class +%%JAVAJARDIR%%/bbmap/bloom/BloomFilter.java +%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrector.class +%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrector.java +%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrectorWrapper$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrectorWrapper.class +%%JAVAJARDIR%%/bbmap/bloom/BloomFilterCorrectorWrapper.java +%%JAVAJARDIR%%/bbmap/bloom/BloomFilterWrapper$ProcessThread.class +%%JAVAJARDIR%%/bbmap/bloom/BloomFilterWrapper.class +%%JAVAJARDIR%%/bbmap/bloom/BloomFilterWrapper.java +%%JAVAJARDIR%%/bbmap/bloom/ErrorCorrect$1.class +%%JAVAJARDIR%%/bbmap/bloom/ErrorCorrect.class +%%JAVAJARDIR%%/bbmap/bloom/ErrorCorrect.java +%%JAVAJARDIR%%/bbmap/bloom/KCountArray$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/KmerCount6MT$CountThread.class +%%JAVAJARDIR%%/bbmap/bloom/KmerCount6MT.class +%%JAVAJARDIR%%/bbmap/bloom/KmerCount6MT.java +%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MT$CountThread.class +%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MT.class +%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MT.java +%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MTA$1.class +%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MTA$CountThread.class +%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MTA$CountThread2.class +%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MTA.class +%%JAVAJARDIR%%/bbmap/bloom/KmerCount7MTA.java +%%JAVAJARDIR%%/bbmap/bloom/KmerCountAbstract.class +%%JAVAJARDIR%%/bbmap/bloom/KmerCountAbstract.java +%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount.class +%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount.java +%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount2.class +%%JAVAJARDIR%%/bbmap/bloom/LargeKmerCount2.java +%%JAVAJARDIR%%/bbmap/bloom/TestLargeKmer.class +%%JAVAJARDIR%%/bbmap/bloom/TestLargeKmer.java +%%JAVAJARDIR%%/bbmap/cardinality/BBLog.class +%%JAVAJARDIR%%/bbmap/cardinality/BBLog.java +%%JAVAJARDIR%%/bbmap/cardinality/BBLog_simple.class +%%JAVAJARDIR%%/bbmap/cardinality/BBLog_simple.java +%%JAVAJARDIR%%/bbmap/cardinality/CardinalityTracker.class +%%JAVAJARDIR%%/bbmap/cardinality/CardinalityTracker.java +%%JAVAJARDIR%%/bbmap/cardinality/LogLog.class +%%JAVAJARDIR%%/bbmap/cardinality/LogLog.java +%%JAVAJARDIR%%/bbmap/cardinality/LogLog16.class +%%JAVAJARDIR%%/bbmap/cardinality/LogLog16.java +%%JAVAJARDIR%%/bbmap/cardinality/LogLog2.class +%%JAVAJARDIR%%/bbmap/cardinality/LogLog2.java +%%JAVAJARDIR%%/bbmap/cardinality/LogLog8.class +%%JAVAJARDIR%%/bbmap/cardinality/LogLog8.java +%%JAVAJARDIR%%/bbmap/cardinality/LogLog8_simple.class +%%JAVAJARDIR%%/bbmap/cardinality/LogLog8_simple.java +%%JAVAJARDIR%%/bbmap/cardinality/LogLogWrapper$LogLogThread.class +%%JAVAJARDIR%%/bbmap/cardinality/LogLogWrapper.class +%%JAVAJARDIR%%/bbmap/cardinality/LogLogWrapper.java +%%JAVAJARDIR%%/bbmap/cardinality/LogLog_old$LogLogWrapper$LogLogThread.class +%%JAVAJARDIR%%/bbmap/cardinality/LogLog_old$LogLogWrapper.class +%%JAVAJARDIR%%/bbmap/cardinality/LogLog_old.class +%%JAVAJARDIR%%/bbmap/cardinality/LogLog_old.java +%%JAVAJARDIR%%/bbmap/cardinality/MultiLogLog.class +%%JAVAJARDIR%%/bbmap/cardinality/MultiLogLog.java +%%JAVAJARDIR%%/bbmap/clump/Clump.class +%%JAVAJARDIR%%/bbmap/clump/Clump.java +%%JAVAJARDIR%%/bbmap/clump/ClumpList$ClumpThread.class +%%JAVAJARDIR%%/bbmap/clump/ClumpList$ProcessThread.class +%%JAVAJARDIR%%/bbmap/clump/ClumpList.class +%%JAVAJARDIR%%/bbmap/clump/ClumpList.java +%%JAVAJARDIR%%/bbmap/clump/ClumpTools.class +%%JAVAJARDIR%%/bbmap/clump/ClumpTools.java +%%JAVAJARDIR%%/bbmap/clump/Clumpify.class +%%JAVAJARDIR%%/bbmap/clump/Clumpify.java +%%JAVAJARDIR%%/bbmap/clump/KmerComparator$HashThread.class +%%JAVAJARDIR%%/bbmap/clump/KmerComparator.class +%%JAVAJARDIR%%/bbmap/clump/KmerComparator.java +%%JAVAJARDIR%%/bbmap/clump/KmerComparator2.class +%%JAVAJARDIR%%/bbmap/clump/KmerComparator2.java +%%JAVAJARDIR%%/bbmap/clump/KmerComparatorX.class +%%JAVAJARDIR%%/bbmap/clump/KmerComparatorX.java +%%JAVAJARDIR%%/bbmap/clump/KmerComparatorY.class +%%JAVAJARDIR%%/bbmap/clump/KmerComparatorY.java +%%JAVAJARDIR%%/bbmap/clump/KmerReduce$HashThread.class +%%JAVAJARDIR%%/bbmap/clump/KmerReduce.class +%%JAVAJARDIR%%/bbmap/clump/KmerReduce.java +%%JAVAJARDIR%%/bbmap/clump/KmerSort$FetchThread1.class +%%JAVAJARDIR%%/bbmap/clump/KmerSort$HashSplitThread.class +%%JAVAJARDIR%%/bbmap/clump/KmerSort.class +%%JAVAJARDIR%%/bbmap/clump/KmerSort.java +%%JAVAJARDIR%%/bbmap/clump/KmerSort1.class +%%JAVAJARDIR%%/bbmap/clump/KmerSort1.java +%%JAVAJARDIR%%/bbmap/clump/KmerSort2.class +%%JAVAJARDIR%%/bbmap/clump/KmerSort2.java +%%JAVAJARDIR%%/bbmap/clump/KmerSort3$FetchThread3$FetchSubThread.class +%%JAVAJARDIR%%/bbmap/clump/KmerSort3$FetchThread3.class +%%JAVAJARDIR%%/bbmap/clump/KmerSort3.class +%%JAVAJARDIR%%/bbmap/clump/KmerSort3.java +%%JAVAJARDIR%%/bbmap/clump/KmerSplit$HashThread.class +%%JAVAJARDIR%%/bbmap/clump/KmerSplit.class +%%JAVAJARDIR%%/bbmap/clump/KmerSplit.java +%%JAVAJARDIR%%/bbmap/clump/PivotSet$HashThread.class +%%JAVAJARDIR%%/bbmap/clump/PivotSet.class +%%JAVAJARDIR%%/bbmap/clump/PivotSet.java +%%JAVAJARDIR%%/bbmap/clump/ReadKey.class +%%JAVAJARDIR%%/bbmap/clump/ReadKey.java +%%JAVAJARDIR%%/bbmap/clump/Splitter.class +%%JAVAJARDIR%%/bbmap/clump/Splitter.java +%%JAVAJARDIR%%/bbmap/clump/StreamToOutput.class +%%JAVAJARDIR%%/bbmap/clump/StreamToOutput.java +%%JAVAJARDIR%%/bbmap/cluster/Cluster.class +%%JAVAJARDIR%%/bbmap/cluster/Cluster.java +%%JAVAJARDIR%%/bbmap/cluster/ClusterTools.class +%%JAVAJARDIR%%/bbmap/cluster/ClusterTools.java +%%JAVAJARDIR%%/bbmap/cluster/MergeReadHeaders.class +%%JAVAJARDIR%%/bbmap/cluster/MergeReadHeaders.java +%%JAVAJARDIR%%/bbmap/cluster/ReadTag.class +%%JAVAJARDIR%%/bbmap/cluster/ReadTag.java +%%JAVAJARDIR%%/bbmap/cluster/ReclusterByKmer$ClusterThread.class +%%JAVAJARDIR%%/bbmap/cluster/ReclusterByKmer.class +%%JAVAJARDIR%%/bbmap/cluster/ReclusterByKmer.java +%%JAVAJARDIR%%/bbmap/consensus/BaseGraph.class +%%JAVAJARDIR%%/bbmap/consensus/BaseGraph.java +%%JAVAJARDIR%%/bbmap/consensus/BaseGraphPart.class +%%JAVAJARDIR%%/bbmap/consensus/BaseGraphPart.java +%%JAVAJARDIR%%/bbmap/consensus/BaseNode.class +%%JAVAJARDIR%%/bbmap/consensus/BaseNode.java +%%JAVAJARDIR%%/bbmap/consensus/ConsensusMaker$ProcessThread.class +%%JAVAJARDIR%%/bbmap/consensus/ConsensusMaker.class +%%JAVAJARDIR%%/bbmap/consensus/ConsensusMaker.java +%%JAVAJARDIR%%/bbmap/consensus/ConsensusObject.class +%%JAVAJARDIR%%/bbmap/consensus/ConsensusObject.java +%%JAVAJARDIR%%/bbmap/consensus/FixScaffoldGaps$ProcessThread.class +%%JAVAJARDIR%%/bbmap/consensus/FixScaffoldGaps$Scaffold.class +%%JAVAJARDIR%%/bbmap/consensus/FixScaffoldGaps.class +%%JAVAJARDIR%%/bbmap/consensus/FixScaffoldGaps.java +%%JAVAJARDIR%%/bbmap/consensus/Lilypad$Contig.class +%%JAVAJARDIR%%/bbmap/consensus/Lilypad$Edge.class +%%JAVAJARDIR%%/bbmap/consensus/Lilypad$ProcessThread.class +%%JAVAJARDIR%%/bbmap/consensus/Lilypad.class +%%JAVAJARDIR%%/bbmap/consensus/Lilypad.java +%%JAVAJARDIR%%/bbmap/covid/SummarizeCoverage.class +%%JAVAJARDIR%%/bbmap/covid/SummarizeCoverage.java +%%JAVAJARDIR%%/bbmap/dna/AminoAcid.class +%%JAVAJARDIR%%/bbmap/dna/AminoAcid.java +%%JAVAJARDIR%%/bbmap/dna/ChromArrayMaker.class +%%JAVAJARDIR%%/bbmap/dna/ChromArrayMaker.java +%%JAVAJARDIR%%/bbmap/dna/ChromToFasta$1.class +%%JAVAJARDIR%%/bbmap/dna/ChromToFasta.class +%%JAVAJARDIR%%/bbmap/dna/ChromToFasta.java +%%JAVAJARDIR%%/bbmap/dna/ChromosomeArray.class +%%JAVAJARDIR%%/bbmap/dna/ChromosomeArray.java +%%JAVAJARDIR%%/bbmap/dna/Data.class +%%JAVAJARDIR%%/bbmap/dna/Data.java +%%JAVAJARDIR%%/bbmap/dna/Exon.class +%%JAVAJARDIR%%/bbmap/dna/Exon.java +%%JAVAJARDIR%%/bbmap/dna/FastaToChromArrays2$1.class +%%JAVAJARDIR%%/bbmap/dna/FastaToChromArrays2.class +%%JAVAJARDIR%%/bbmap/dna/FastaToChromArrays2.java +%%JAVAJARDIR%%/bbmap/dna/Gene.class +%%JAVAJARDIR%%/bbmap/dna/Gene.java +%%JAVAJARDIR%%/bbmap/dna/GeneSet.class +%%JAVAJARDIR%%/bbmap/dna/GeneSet.java +%%JAVAJARDIR%%/bbmap/dna/Matrix.class +%%JAVAJARDIR%%/bbmap/dna/Matrix.java +%%JAVAJARDIR%%/bbmap/dna/Motif.class +%%JAVAJARDIR%%/bbmap/dna/Motif.java +%%JAVAJARDIR%%/bbmap/dna/MotifMulti.class +%%JAVAJARDIR%%/bbmap/dna/MotifMulti.java +%%JAVAJARDIR%%/bbmap/dna/MotifProbsN.class +%%JAVAJARDIR%%/bbmap/dna/MotifProbsN.java +%%JAVAJARDIR%%/bbmap/dna/MotifSimple.class +%%JAVAJARDIR%%/bbmap/dna/MotifSimple.java +%%JAVAJARDIR%%/bbmap/dna/ScafLoc.class +%%JAVAJARDIR%%/bbmap/dna/ScafLoc.java +%%JAVAJARDIR%%/bbmap/dna/Scaffold.class +%%JAVAJARDIR%%/bbmap/dna/Scaffold.java +%%JAVAJARDIR%%/bbmap/driver/BBVersion.class +%%JAVAJARDIR%%/bbmap/driver/BBVersion.java +%%JAVAJARDIR%%/bbmap/driver/ClearRam.class +%%JAVAJARDIR%%/bbmap/driver/ClearRam.java +%%JAVAJARDIR%%/bbmap/driver/CollateSpikeIn.class +%%JAVAJARDIR%%/bbmap/driver/CollateSpikeIn.java +%%JAVAJARDIR%%/bbmap/driver/CompareReferenceGenomes.class +%%JAVAJARDIR%%/bbmap/driver/CompareReferenceGenomes.java +%%JAVAJARDIR%%/bbmap/driver/CompareSequences.class +%%JAVAJARDIR%%/bbmap/driver/CompareSequences.java +%%JAVAJARDIR%%/bbmap/driver/ConcatenateFiles.class +%%JAVAJARDIR%%/bbmap/driver/ConcatenateFiles.java +%%JAVAJARDIR%%/bbmap/driver/ConcatenateTextFiles$1.class +%%JAVAJARDIR%%/bbmap/driver/ConcatenateTextFiles$WriteThread.class +%%JAVAJARDIR%%/bbmap/driver/ConcatenateTextFiles.class +%%JAVAJARDIR%%/bbmap/driver/ConcatenateTextFiles.java +%%JAVAJARDIR%%/bbmap/driver/Concatenator.class +%%JAVAJARDIR%%/bbmap/driver/Concatenator.java +%%JAVAJARDIR%%/bbmap/driver/ConvertSamToAln.class +%%JAVAJARDIR%%/bbmap/driver/ConvertSamToAln.java +%%JAVAJARDIR%%/bbmap/driver/CorrelateIdentity.class +%%JAVAJARDIR%%/bbmap/driver/CorrelateIdentity.java +%%JAVAJARDIR%%/bbmap/driver/CountRNAs.class +%%JAVAJARDIR%%/bbmap/driver/CountRNAs.java +%%JAVAJARDIR%%/bbmap/driver/CountSharedLines.class +%%JAVAJARDIR%%/bbmap/driver/CountSharedLines.java +%%JAVAJARDIR%%/bbmap/driver/EstherFilter.class +%%JAVAJARDIR%%/bbmap/driver/EstherFilter.java +%%JAVAJARDIR%%/bbmap/driver/FilterAssemblySummary.class +%%JAVAJARDIR%%/bbmap/driver/FilterAssemblySummary.java +%%JAVAJARDIR%%/bbmap/driver/FilterLines.class +%%JAVAJARDIR%%/bbmap/driver/FilterLines.java +%%JAVAJARDIR%%/bbmap/driver/FilterReadsByName.class +%%JAVAJARDIR%%/bbmap/driver/FilterReadsByName.java +%%JAVAJARDIR%%/bbmap/driver/FindMotifs.class +%%JAVAJARDIR%%/bbmap/driver/FindMotifs.java +%%JAVAJARDIR%%/bbmap/driver/FixChr.class +%%JAVAJARDIR%%/bbmap/driver/FixChr.java +%%JAVAJARDIR%%/bbmap/driver/FixDumbFile.class +%%JAVAJARDIR%%/bbmap/driver/FixDumbFile.java +%%JAVAJARDIR%%/bbmap/driver/GenerateNoCallsFromCoverage.class +%%JAVAJARDIR%%/bbmap/driver/GenerateNoCallsFromCoverage.java +%%JAVAJARDIR%%/bbmap/driver/GetSequence.class +%%JAVAJARDIR%%/bbmap/driver/GetSequence.java +%%JAVAJARDIR%%/bbmap/driver/GetUniquePrefixes.class +%%JAVAJARDIR%%/bbmap/driver/GetUniquePrefixes.java +%%JAVAJARDIR%%/bbmap/driver/Grep.class +%%JAVAJARDIR%%/bbmap/driver/Grep.java +%%JAVAJARDIR%%/bbmap/driver/Life.class +%%JAVAJARDIR%%/bbmap/driver/Life.java +%%JAVAJARDIR%%/bbmap/driver/LineCount.class +%%JAVAJARDIR%%/bbmap/driver/LineCount.java +%%JAVAJARDIR%%/bbmap/driver/LoadReads.class +%%JAVAJARDIR%%/bbmap/driver/LoadReads.java +%%JAVAJARDIR%%/bbmap/driver/LookAtID.class +%%JAVAJARDIR%%/bbmap/driver/LookAtID.java +%%JAVAJARDIR%%/bbmap/driver/MakeTestScript.class +%%JAVAJARDIR%%/bbmap/driver/MakeTestScript.java +%%JAVAJARDIR%%/bbmap/driver/MakeTestScriptScoreOnly.class +%%JAVAJARDIR%%/bbmap/driver/MakeTestScriptScoreOnly.java +%%JAVAJARDIR%%/bbmap/driver/MeasureGene.class +%%JAVAJARDIR%%/bbmap/driver/MeasureGene.java +%%JAVAJARDIR%%/bbmap/driver/MergeBigelow.class +%%JAVAJARDIR%%/bbmap/driver/MergeBigelow.java +%%JAVAJARDIR%%/bbmap/driver/MergeCoverageOTU.class +%%JAVAJARDIR%%/bbmap/driver/MergeCoverageOTU.java +%%JAVAJARDIR%%/bbmap/driver/MergeTextFiles.class +%%JAVAJARDIR%%/bbmap/driver/MergeTextFiles.java +%%JAVAJARDIR%%/bbmap/driver/MergeTextFiles2.class +%%JAVAJARDIR%%/bbmap/driver/MergeTextFiles2.java +%%JAVAJARDIR%%/bbmap/driver/MoveFiles.class +%%JAVAJARDIR%%/bbmap/driver/MoveFiles.java +%%JAVAJARDIR%%/bbmap/driver/ParseCrossblockResults$ResultsLine.class +%%JAVAJARDIR%%/bbmap/driver/ParseCrossblockResults.class +%%JAVAJARDIR%%/bbmap/driver/ParseCrossblockResults.java +%%JAVAJARDIR%%/bbmap/driver/PlotGC.class +%%JAVAJARDIR%%/bbmap/driver/PlotGC.java +%%JAVAJARDIR%%/bbmap/driver/PrintEnv.class +%%JAVAJARDIR%%/bbmap/driver/PrintEnv.java +%%JAVAJARDIR%%/bbmap/driver/ProcessFragMerging.class +%%JAVAJARDIR%%/bbmap/driver/ProcessFragMerging.java +%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed.class +%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed.java +%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed2.class +%%JAVAJARDIR%%/bbmap/driver/ProcessSpeed2.java +%%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.class +%%JAVAJARDIR%%/bbmap/driver/ProcessWebcheck.java +%%JAVAJARDIR%%/bbmap/driver/ReduceSilva.class +%%JAVAJARDIR%%/bbmap/driver/ReduceSilva.java +%%JAVAJARDIR%%/bbmap/driver/RenameAndMux$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$QuastSummary.class +%%JAVAJARDIR%%/bbmap/driver/SummarizeQuast.class +%%JAVAJARDIR%%/bbmap/driver/SummarizeQuast.java +%%JAVAJARDIR%%/bbmap/driver/SummarizeSealStats$SealSummary.class +%%JAVAJARDIR%%/bbmap/driver/SummarizeSealStats.class +%%JAVAJARDIR%%/bbmap/driver/SummarizeSealStats.java +%%JAVAJARDIR%%/bbmap/driver/TestCompressionSpeed.class +%%JAVAJARDIR%%/bbmap/driver/TestCompressionSpeed.java +%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$1.class +%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$AtomBox.class +%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$CountBox.class +%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$CountThread.class +%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$LockBox.class +%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed$VolatileBox.class +%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed.class +%%JAVAJARDIR%%/bbmap/driver/TestLockSpeed.java +%%JAVAJARDIR%%/bbmap/driver/Translator.class +%%JAVAJARDIR%%/bbmap/driver/Translator.java +%%JAVAJARDIR%%/bbmap/driver/Translator2.class +%%JAVAJARDIR%%/bbmap/driver/Translator2.java +%%JAVAJARDIR%%/bbmap/driver/TransposeTextFile.class +%%JAVAJARDIR%%/bbmap/driver/TransposeTextFile.java +%%JAVAJARDIR%%/bbmap/driver/TrimSamFile.class +%%JAVAJARDIR%%/bbmap/driver/TrimSamFile.java +%%JAVAJARDIR%%/bbmap/fileIO/ArrayFile.class +%%JAVAJARDIR%%/bbmap/fileIO/ArrayFile.java +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile.class +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile.java +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1.class +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile1.java +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile2$BF1Thread.class +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile2.class +%%JAVAJARDIR%%/bbmap/fileIO/ByteFile2.java +%%JAVAJARDIR%%/bbmap/fileIO/ByteStreamWriter.class +%%JAVAJARDIR%%/bbmap/fileIO/ByteStreamWriter.java +%%JAVAJARDIR%%/bbmap/fileIO/ChainBlock.class +%%JAVAJARDIR%%/bbmap/fileIO/ChainBlock.java +%%JAVAJARDIR%%/bbmap/fileIO/ChainLine.class +%%JAVAJARDIR%%/bbmap/fileIO/ChainLine.java +%%JAVAJARDIR%%/bbmap/fileIO/CompressFiles.class +%%JAVAJARDIR%%/bbmap/fileIO/CompressFiles.java +%%JAVAJARDIR%%/bbmap/fileIO/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/ReadWrite$1.class +%%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$WriteObjectThread.class +%%JAVAJARDIR%%/bbmap/fileIO/ReadWrite$WriteStringThread.class +%%JAVAJARDIR%%/bbmap/fileIO/ReadWrite.class +%%JAVAJARDIR%%/bbmap/fileIO/ReadWrite.java +%%JAVAJARDIR%%/bbmap/fileIO/SummaryFile$1.class +%%JAVAJARDIR%%/bbmap/fileIO/SummaryFile.class +%%JAVAJARDIR%%/bbmap/fileIO/SummaryFile.java +%%JAVAJARDIR%%/bbmap/fileIO/TextFile.class +%%JAVAJARDIR%%/bbmap/fileIO/TextFile.java +%%JAVAJARDIR%%/bbmap/fileIO/TextStreamWriter.class +%%JAVAJARDIR%%/bbmap/fileIO/TextStreamWriter.java +%%JAVAJARDIR%%/bbmap/fun/Calc.class +%%JAVAJARDIR%%/bbmap/fun/Calc.java +%%JAVAJARDIR%%/bbmap/fun/Chance.class +%%JAVAJARDIR%%/bbmap/fun/Chance.java +%%JAVAJARDIR%%/bbmap/fun/DiskBench$ReadThread.class +%%JAVAJARDIR%%/bbmap/fun/DiskBench$WriteThread.class +%%JAVAJARDIR%%/bbmap/fun/DiskBench.class +%%JAVAJARDIR%%/bbmap/fun/DiskBench.java +%%JAVAJARDIR%%/bbmap/fun/FindPath$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/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$1.class +%%JAVAJARDIR%%/bbmap/fun/MakeAdjacencyList.class +%%JAVAJARDIR%%/bbmap/fun/MakeAdjacencyList.java +%%JAVAJARDIR%%/bbmap/fun/Palindrome.class +%%JAVAJARDIR%%/bbmap/fun/Palindrome.java +%%JAVAJARDIR%%/bbmap/fun/ProbShared.class +%%JAVAJARDIR%%/bbmap/fun/ProbShared.java +%%JAVAJARDIR%%/bbmap/fun/ProbShared2.class +%%JAVAJARDIR%%/bbmap/fun/ProbShared2.java +%%JAVAJARDIR%%/bbmap/fun/ProbShared3.class +%%JAVAJARDIR%%/bbmap/fun/ProbShared3.java +%%JAVAJARDIR%%/bbmap/gff/CompareGff.class +%%JAVAJARDIR%%/bbmap/gff/CompareGff.java +%%JAVAJARDIR%%/bbmap/gff/CompareGff_old.class +%%JAVAJARDIR%%/bbmap/gff/CompareGff_old.java +%%JAVAJARDIR%%/bbmap/gff/CutGff$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/VcfToGff$1.class +%%JAVAJARDIR%%/bbmap/gff/VcfToGff.class +%%JAVAJARDIR%%/bbmap/gff/VcfToGff.java +%%JAVAJARDIR%%/bbmap/hiseq/AnalyzeFlowCell.class +%%JAVAJARDIR%%/bbmap/hiseq/AnalyzeFlowCell.java +%%JAVAJARDIR%%/bbmap/hiseq/CycleTracker.class +%%JAVAJARDIR%%/bbmap/hiseq/CycleTracker.java +%%JAVAJARDIR%%/bbmap/hiseq/FlowCell.class +%%JAVAJARDIR%%/bbmap/hiseq/FlowCell.java +%%JAVAJARDIR%%/bbmap/hiseq/FlowcellCoordinate.class +%%JAVAJARDIR%%/bbmap/hiseq/FlowcellCoordinate.java +%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser.class +%%JAVAJARDIR%%/bbmap/hiseq/IlluminaHeaderParser.java +%%JAVAJARDIR%%/bbmap/hiseq/Lane.class +%%JAVAJARDIR%%/bbmap/hiseq/Lane.java +%%JAVAJARDIR%%/bbmap/hiseq/MicroTile.class +%%JAVAJARDIR%%/bbmap/hiseq/MicroTile.java +%%JAVAJARDIR%%/bbmap/hiseq/PlotFlowCell.class +%%JAVAJARDIR%%/bbmap/hiseq/PlotFlowCell.java +%%JAVAJARDIR%%/bbmap/hiseq/Tile.class +%%JAVAJARDIR%%/bbmap/hiseq/Tile.java +%%JAVAJARDIR%%/bbmap/hmm/HMMSearchLine.class +%%JAVAJARDIR%%/bbmap/hmm/HMMSearchLine.java +%%JAVAJARDIR%%/bbmap/hmm/HMMSearchReport.class +%%JAVAJARDIR%%/bbmap/hmm/HMMSearchReport.java +%%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.class +%%JAVAJARDIR%%/bbmap/hmm/ProteinSummary.java +%%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.class +%%JAVAJARDIR%%/bbmap/icecream/IceCreamAligner.java +%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJNI.class +%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJNI.java +%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJava.class +%%JAVAJARDIR%%/bbmap/icecream/IceCreamAlignerJava.java +%%JAVAJARDIR%%/bbmap/icecream/IceCreamFinder$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$ProcessThread.class +%%JAVAJARDIR%%/bbmap/icecream/IceCreamMaker.class +%%JAVAJARDIR%%/bbmap/icecream/IceCreamMaker.java +%%JAVAJARDIR%%/bbmap/icecream/PBHeader.class +%%JAVAJARDIR%%/bbmap/icecream/PBHeader.java +%%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.class +%%JAVAJARDIR%%/bbmap/icecream/PolymerTrimmer.java +%%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.class +%%JAVAJARDIR%%/bbmap/icecream/ReadBuilder.java +%%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio$ProcessThread.class +%%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio.class +%%JAVAJARDIR%%/bbmap/icecream/ReformatPacBio.java +%%JAVAJARDIR%%/bbmap/icecream/ZMW.class +%%JAVAJARDIR%%/bbmap/icecream/ZMW.java +%%JAVAJARDIR%%/bbmap/icecream/ZMWStreamer.class +%%JAVAJARDIR%%/bbmap/icecream/ZMWStreamer.java +%%JAVAJARDIR%%/bbmap/jasper/Comparison.class +%%JAVAJARDIR%%/bbmap/jasper/Comparison.java +%%JAVAJARDIR%%/bbmap/jasper/DenseSimilarityMatrix.class +%%JAVAJARDIR%%/bbmap/jasper/DenseSimilarityMatrix.java +%%JAVAJARDIR%%/bbmap/jasper/DenseTree.class +%%JAVAJARDIR%%/bbmap/jasper/DenseTree.java +%%JAVAJARDIR%%/bbmap/jasper/DenseTreeValidate.class +%%JAVAJARDIR%%/bbmap/jasper/DenseTreeValidate.java +%%JAVAJARDIR%%/bbmap/jasper/KmerPosition.class +%%JAVAJARDIR%%/bbmap/jasper/KmerPosition.java +%%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.class +%%JAVAJARDIR%%/bbmap/jasper/KmerPosition3.java +%%JAVAJARDIR%%/bbmap/jasper/NCBIComparison.class +%%JAVAJARDIR%%/bbmap/jasper/NCBIComparison.java +%%JAVAJARDIR%%/bbmap/jasper/NCBISparseSimilarityMatrix.class +%%JAVAJARDIR%%/bbmap/jasper/NCBISparseSimilarityMatrix.java +%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTree.class +%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTree.java +%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTreeValidate.class +%%JAVAJARDIR%%/bbmap/jasper/NCBISparseTreeValidate.java +%%JAVAJARDIR%%/bbmap/jasper/NCBITreeNode.class +%%JAVAJARDIR%%/bbmap/jasper/NCBITreeNode.java +%%JAVAJARDIR%%/bbmap/jasper/Organism.class +%%JAVAJARDIR%%/bbmap/jasper/Organism.java +%%JAVAJARDIR%%/bbmap/jasper/SimilarityMatrix.class +%%JAVAJARDIR%%/bbmap/jasper/SimilarityMatrix.java +%%JAVAJARDIR%%/bbmap/jasper/SparseSimilarityMatrix.class +%%JAVAJARDIR%%/bbmap/jasper/SparseSimilarityMatrix.java +%%JAVAJARDIR%%/bbmap/jasper/SparseTree.class +%%JAVAJARDIR%%/bbmap/jasper/SparseTree.java +%%JAVAJARDIR%%/bbmap/jasper/SparseTreeValidate.class +%%JAVAJARDIR%%/bbmap/jasper/SparseTreeValidate.java +%%JAVAJARDIR%%/bbmap/jasper/TaxCompare.class +%%JAVAJARDIR%%/bbmap/jasper/TaxCompare.java +%%JAVAJARDIR%%/bbmap/jasper/TreeNode.class +%%JAVAJARDIR%%/bbmap/jasper/TreeNode.java +%%JAVAJARDIR%%/bbmap/jgi/AddAdapters.class +%%JAVAJARDIR%%/bbmap/jgi/AddAdapters.java +%%JAVAJARDIR%%/bbmap/jgi/AdjustHomopolymers.class +%%JAVAJARDIR%%/bbmap/jgi/AdjustHomopolymers.java +%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2$Triple.class +%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2.class +%%JAVAJARDIR%%/bbmap/jgi/AssemblyStats2.java +%%JAVAJARDIR%%/bbmap/jgi/AssemblyStatsWrapper.class +%%JAVAJARDIR%%/bbmap/jgi/AssemblyStatsWrapper.java +%%JAVAJARDIR%%/bbmap/jgi/BBDuk$LoadThread.class +%%JAVAJARDIR%%/bbmap/jgi/BBDuk$ProcessThread.class +%%JAVAJARDIR%%/bbmap/jgi/BBDuk.class +%%JAVAJARDIR%%/bbmap/jgi/BBDuk.java +%%JAVAJARDIR%%/bbmap/jgi/BBDuk2$LoadThread.class +%%JAVAJARDIR%%/bbmap/jgi/BBDuk2$ProcessThread.class +%%JAVAJARDIR%%/bbmap/jgi/BBDuk2.class +%%JAVAJARDIR%%/bbmap/jgi/BBDuk2.java +%%JAVAJARDIR%%/bbmap/jgi/BBMask$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/Consect.class +%%JAVAJARDIR%%/bbmap/jgi/Consect.java +%%JAVAJARDIR%%/bbmap/jgi/CorrelateBarcodes.class +%%JAVAJARDIR%%/bbmap/jgi/CorrelateBarcodes.java +%%JAVAJARDIR%%/bbmap/jgi/CountBarcodes.class +%%JAVAJARDIR%%/bbmap/jgi/CountBarcodes.java +%%JAVAJARDIR%%/bbmap/jgi/CountGC$1.class +%%JAVAJARDIR%%/bbmap/jgi/CountGC.class +%%JAVAJARDIR%%/bbmap/jgi/CountGC.java +%%JAVAJARDIR%%/bbmap/jgi/CountUniqueness.class +%%JAVAJARDIR%%/bbmap/jgi/CountUniqueness.java +%%JAVAJARDIR%%/bbmap/jgi/CovStatsLine.class +%%JAVAJARDIR%%/bbmap/jgi/CovStatsLine.java +%%JAVAJARDIR%%/bbmap/jgi/CoveragePileup.class +%%JAVAJARDIR%%/bbmap/jgi/CoveragePileup.java +%%JAVAJARDIR%%/bbmap/jgi/CrossContaminate$Vessel.class +%%JAVAJARDIR%%/bbmap/jgi/CrossContaminate.class +%%JAVAJARDIR%%/bbmap/jgi/CrossContaminate.java +%%JAVAJARDIR%%/bbmap/jgi/CutPrimers.class +%%JAVAJARDIR%%/bbmap/jgi/CutPrimers.java +%%JAVAJARDIR%%/bbmap/jgi/DecontaminateByNormalization.class +%%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/FakeReads.class +%%JAVAJARDIR%%/bbmap/jgi/FakeReads.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/FuseSequence.class +%%JAVAJARDIR%%/bbmap/jgi/FuseSequence.java +%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$KapaEntry.class +%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$Plate.class +%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$TagData.class +%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats$Well.class +%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats.class +%%JAVAJARDIR%%/bbmap/jgi/GatherKapaStats.java +%%JAVAJARDIR%%/bbmap/jgi/GetReads.class +%%JAVAJARDIR%%/bbmap/jgi/GetReads.java +%%JAVAJARDIR%%/bbmap/jgi/GradeMergedReads.class +%%JAVAJARDIR%%/bbmap/jgi/GradeMergedReads.java +%%JAVAJARDIR%%/bbmap/jgi/GreedyBarCodeFinder.class +%%JAVAJARDIR%%/bbmap/jgi/GreedyBarCodeFinder.java +%%JAVAJARDIR%%/bbmap/jgi/IdentityMatrix$ProcessThread.class +%%JAVAJARDIR%%/bbmap/jgi/IdentityMatrix.class +%%JAVAJARDIR%%/bbmap/jgi/IdentityMatrix.java +%%JAVAJARDIR%%/bbmap/jgi/Info.class +%%JAVAJARDIR%%/bbmap/jgi/Info.java +%%JAVAJARDIR%%/bbmap/jgi/KExpand.class +%%JAVAJARDIR%%/bbmap/jgi/KExpand.java +%%JAVAJARDIR%%/bbmap/jgi/KeepBestCopy.class +%%JAVAJARDIR%%/bbmap/jgi/KeepBestCopy.java +%%JAVAJARDIR%%/bbmap/jgi/KmerCountExact$DumpKmersThread.class +%%JAVAJARDIR%%/bbmap/jgi/KmerCountExact$MakeKhistThread.class +%%JAVAJARDIR%%/bbmap/jgi/KmerCountExact.class +%%JAVAJARDIR%%/bbmap/jgi/KmerCountExact.java +%%JAVAJARDIR%%/bbmap/jgi/KmerCountMulti$ProcessThread.class +%%JAVAJARDIR%%/bbmap/jgi/KmerCountMulti.class +%%JAVAJARDIR%%/bbmap/jgi/KmerCountMulti.java +%%JAVAJARDIR%%/bbmap/jgi/KmerCoverage$1.class +%%JAVAJARDIR%%/bbmap/jgi/KmerCoverage$ProcessThread.class +%%JAVAJARDIR%%/bbmap/jgi/KmerCoverage.class +%%JAVAJARDIR%%/bbmap/jgi/KmerCoverage.java +%%JAVAJARDIR%%/bbmap/jgi/KmerFilterSetMaker.class +%%JAVAJARDIR%%/bbmap/jgi/KmerFilterSetMaker.java +%%JAVAJARDIR%%/bbmap/jgi/KmerNormalize$1.class +%%JAVAJARDIR%%/bbmap/jgi/KmerNormalize$ProcessThread.class +%%JAVAJARDIR%%/bbmap/jgi/KmerNormalize.class +%%JAVAJARDIR%%/bbmap/jgi/KmerNormalize.java +%%JAVAJARDIR%%/bbmap/jgi/KmerSample.class +%%JAVAJARDIR%%/bbmap/jgi/KmerSample.java +%%JAVAJARDIR%%/bbmap/jgi/MakeChimeras.class +%%JAVAJARDIR%%/bbmap/jgi/MakeChimeras.java +%%JAVAJARDIR%%/bbmap/jgi/MakeContaminatedGenomes.class +%%JAVAJARDIR%%/bbmap/jgi/MakeContaminatedGenomes.java +%%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram$1.class +%%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.class +%%JAVAJARDIR%%/bbmap/jgi/MakeLengthHistogram.java +%%JAVAJARDIR%%/bbmap/jgi/MakePolymers.class +%%JAVAJARDIR%%/bbmap/jgi/MakePolymers.java +%%JAVAJARDIR%%/bbmap/jgi/MergeBarcodes.class +%%JAVAJARDIR%%/bbmap/jgi/MergeBarcodes.java +%%JAVAJARDIR%%/bbmap/jgi/MergeSam.class +%%JAVAJARDIR%%/bbmap/jgi/MergeSam.java +%%JAVAJARDIR%%/bbmap/jgi/MutateGenome$SmallVar.class +%%JAVAJARDIR%%/bbmap/jgi/MutateGenome.class +%%JAVAJARDIR%%/bbmap/jgi/MutateGenome.java +%%JAVAJARDIR%%/bbmap/jgi/MutateGenome2$SmallVar.class +%%JAVAJARDIR%%/bbmap/jgi/MutateGenome2.class +%%JAVAJARDIR%%/bbmap/jgi/MutateGenome2.java +%%JAVAJARDIR%%/bbmap/jgi/Orf.class +%%JAVAJARDIR%%/bbmap/jgi/Orf.java +%%JAVAJARDIR%%/bbmap/jgi/PartitionReads.class +%%JAVAJARDIR%%/bbmap/jgi/PartitionReads.java +%%JAVAJARDIR%%/bbmap/jgi/PhylipToFasta.class +%%JAVAJARDIR%%/bbmap/jgi/PhylipToFasta.java +%%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.class +%%JAVAJARDIR%%/bbmap/jgi/RQCFilter2.java +%%JAVAJARDIR%%/bbmap/jgi/RQCFilterStats.class +%%JAVAJARDIR%%/bbmap/jgi/RQCFilterStats.java +%%JAVAJARDIR%%/bbmap/jgi/RandomGenome.class +%%JAVAJARDIR%%/bbmap/jgi/RandomGenome.java +%%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution$1.class +%%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution$ProcessThread.class +%%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution.class +%%JAVAJARDIR%%/bbmap/jgi/ReadKmerDepthDistribution.java +%%JAVAJARDIR%%/bbmap/jgi/RedirectTest.class +%%JAVAJARDIR%%/bbmap/jgi/RedirectTest.java +%%JAVAJARDIR%%/bbmap/jgi/ReformatReads.class +%%JAVAJARDIR%%/bbmap/jgi/ReformatReads.java +%%JAVAJARDIR%%/bbmap/jgi/RemapQuality.class +%%JAVAJARDIR%%/bbmap/jgi/RemapQuality.java +%%JAVAJARDIR%%/bbmap/jgi/RemoveBadBarcodes.class +%%JAVAJARDIR%%/bbmap/jgi/RemoveBadBarcodes.java +%%JAVAJARDIR%%/bbmap/jgi/RenameReads.class +%%JAVAJARDIR%%/bbmap/jgi/RenameReads.java +%%JAVAJARDIR%%/bbmap/jgi/ReplaceHeaders.class +%%JAVAJARDIR%%/bbmap/jgi/ReplaceHeaders.java +%%JAVAJARDIR%%/bbmap/jgi/RepresentativeSet$Edge.class +%%JAVAJARDIR%%/bbmap/jgi/RepresentativeSet$Node.class +%%JAVAJARDIR%%/bbmap/jgi/RepresentativeSet.class +%%JAVAJARDIR%%/bbmap/jgi/RepresentativeSet.java +%%JAVAJARDIR%%/bbmap/jgi/SamToEst$1.class +%%JAVAJARDIR%%/bbmap/jgi/SamToEst$EST.class +%%JAVAJARDIR%%/bbmap/jgi/SamToEst.class +%%JAVAJARDIR%%/bbmap/jgi/SamToEst.java +%%JAVAJARDIR%%/bbmap/jgi/Seal$LoadThread.class +%%JAVAJARDIR%%/bbmap/jgi/Seal$ProcessThread.class +%%JAVAJARDIR%%/bbmap/jgi/Seal.class +%%JAVAJARDIR%%/bbmap/jgi/Seal.java +%%JAVAJARDIR%%/bbmap/jgi/Shred.class +%%JAVAJARDIR%%/bbmap/jgi/Shred.java +%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$CountComparator.class +%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$Kmer.class +%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency$NumComparator.class +%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency.class +%%JAVAJARDIR%%/bbmap/jgi/SmallKmerFrequency.java +%%JAVAJARDIR%%/bbmap/jgi/SplitNexteraLMP.class +%%JAVAJARDIR%%/bbmap/jgi/SplitNexteraLMP.java +%%JAVAJARDIR%%/bbmap/jgi/SplitPairsAndSingles.class +%%JAVAJARDIR%%/bbmap/jgi/SplitPairsAndSingles.java +%%JAVAJARDIR%%/bbmap/jgi/SplitSam4Way.class +%%JAVAJARDIR%%/bbmap/jgi/SplitSam4Way.java +%%JAVAJARDIR%%/bbmap/jgi/SplitSam6Way.class +%%JAVAJARDIR%%/bbmap/jgi/SplitSam6Way.java +%%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.class +%%JAVAJARDIR%%/bbmap/jgi/SplitSamFile.java +%%JAVAJARDIR%%/bbmap/jgi/StringCount.class +%%JAVAJARDIR%%/bbmap/jgi/StringCount.java +%%JAVAJARDIR%%/bbmap/jgi/SynthMDA.class +%%JAVAJARDIR%%/bbmap/jgi/SynthMDA.java +%%JAVAJARDIR%%/bbmap/jgi/TestFilesystem$WriteThread.class +%%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.class +%%JAVAJARDIR%%/bbmap/jgi/TestFilesystem.java +%%JAVAJARDIR%%/bbmap/jgi/TestFormat$Barcode.class +%%JAVAJARDIR%%/bbmap/jgi/TestFormat$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/TranslateSixFrames.class +%%JAVAJARDIR%%/bbmap/jgi/TranslateSixFrames.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/kmer/AbstractKmerTable$AllocThread.class +%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.class +%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTable.java +%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.class +%%JAVAJARDIR%%/bbmap/kmer/AbstractKmerTableSet.java +%%JAVAJARDIR%%/bbmap/kmer/AtomicShortArray.class +%%JAVAJARDIR%%/bbmap/kmer/AtomicShortArray.java +%%JAVAJARDIR%%/bbmap/kmer/DumpThread.class +%%JAVAJARDIR%%/bbmap/kmer/DumpThread.java +%%JAVAJARDIR%%/bbmap/kmer/HashArray.class +%%JAVAJARDIR%%/bbmap/kmer/HashArray.java +%%JAVAJARDIR%%/bbmap/kmer/HashArray1D$Walker1D.class +%%JAVAJARDIR%%/bbmap/kmer/HashArray1D.class +%%JAVAJARDIR%%/bbmap/kmer/HashArray1D.java +%%JAVAJARDIR%%/bbmap/kmer/HashArray2D.class +%%JAVAJARDIR%%/bbmap/kmer/HashArray2D.java +%%JAVAJARDIR%%/bbmap/kmer/HashArrayHybrid.class +%%JAVAJARDIR%%/bbmap/kmer/HashArrayHybrid.java +%%JAVAJARDIR%%/bbmap/kmer/HashArrayHybridFast.class +%%JAVAJARDIR%%/bbmap/kmer/HashArrayHybridFast.java +%%JAVAJARDIR%%/bbmap/kmer/HashBuffer.class +%%JAVAJARDIR%%/bbmap/kmer/HashBuffer.java +%%JAVAJARDIR%%/bbmap/kmer/HashForest.class +%%JAVAJARDIR%%/bbmap/kmer/HashForest.java +%%JAVAJARDIR%%/bbmap/kmer/HistogramMaker$FillThread.class +%%JAVAJARDIR%%/bbmap/kmer/HistogramMaker.class +%%JAVAJARDIR%%/bbmap/kmer/HistogramMaker.java +%%JAVAJARDIR%%/bbmap/kmer/KmerBuffer.class +%%JAVAJARDIR%%/bbmap/kmer/KmerBuffer.java +%%JAVAJARDIR%%/bbmap/kmer/KmerLink.class +%%JAVAJARDIR%%/bbmap/kmer/KmerLink.java +%%JAVAJARDIR%%/bbmap/kmer/KmerNode.class +%%JAVAJARDIR%%/bbmap/kmer/KmerNode.java +%%JAVAJARDIR%%/bbmap/kmer/KmerNode1D.class +%%JAVAJARDIR%%/bbmap/kmer/KmerNode1D.java +%%JAVAJARDIR%%/bbmap/kmer/KmerNode2D.class +%%JAVAJARDIR%%/bbmap/kmer/KmerNode2D.java +%%JAVAJARDIR%%/bbmap/kmer/KmerTable.class +%%JAVAJARDIR%%/bbmap/kmer/KmerTable.java +%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet$LoadThread.class +%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet$WalkerKST.class +%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet.class +%%JAVAJARDIR%%/bbmap/kmer/KmerTableSet.java +%%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.class +%%JAVAJARDIR%%/bbmap/kmer/OwnershipThread.java +%%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.class +%%JAVAJARDIR%%/bbmap/kmer/ScheduleMaker.java +%%JAVAJARDIR%%/bbmap/kmer/TableLoaderLockFree$LoadThread.class +%%JAVAJARDIR%%/bbmap/kmer/TableLoaderLockFree.class +%%JAVAJARDIR%%/bbmap/kmer/TableLoaderLockFree.java +%%JAVAJARDIR%%/bbmap/kmer/TableReader.class +%%JAVAJARDIR%%/bbmap/kmer/TableReader.java +%%JAVAJARDIR%%/bbmap/kmer/Walker.class +%%JAVAJARDIR%%/bbmap/kmer/Walker.java +%%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders$Header.class +%%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders.class +%%JAVAJARDIR%%/bbmap/ml/ProcessBBMergeHeaders.java +%%JAVAJARDIR%%/bbmap/pacbio/CalcCoverageFromSites$1.class +%%JAVAJARDIR%%/bbmap/pacbio/CalcCoverageFromSites.class +%%JAVAJARDIR%%/bbmap/pacbio/CalcCoverageFromSites.java +%%JAVAJARDIR%%/bbmap/pacbio/GenerateMultiChrom.class +%%JAVAJARDIR%%/bbmap/pacbio/GenerateMultiChrom.java +%%JAVAJARDIR%%/bbmap/pacbio/MakePacBioScript.class +%%JAVAJARDIR%%/bbmap/pacbio/MakePacBioScript.java +%%JAVAJARDIR%%/bbmap/pacbio/MergeFastaContigs$1.class +%%JAVAJARDIR%%/bbmap/pacbio/MergeFastaContigs.class +%%JAVAJARDIR%%/bbmap/pacbio/MergeFastaContigs.java +%%JAVAJARDIR%%/bbmap/pacbio/MergeReadsAndGenome$1.class +%%JAVAJARDIR%%/bbmap/pacbio/MergeReadsAndGenome.class +%%JAVAJARDIR%%/bbmap/pacbio/MergeReadsAndGenome.java +%%JAVAJARDIR%%/bbmap/pacbio/PartitionFastaFile.class +%%JAVAJARDIR%%/bbmap/pacbio/PartitionFastaFile.java +%%JAVAJARDIR%%/bbmap/pacbio/PartitionReads$1.class +%%JAVAJARDIR%%/bbmap/pacbio/PartitionReads.class +%%JAVAJARDIR%%/bbmap/pacbio/PartitionReads.java +%%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized$1.class +%%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized$Buffer.class +%%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized$Ssra.class +%%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized.class +%%JAVAJARDIR%%/bbmap/pacbio/ProcessStackedSitesNormalized.java +%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2$1.class +%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2$ProcessThread.class +%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2.class +%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters2.java +%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters3$ProcessThread.class +%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters3.class +%%JAVAJARDIR%%/bbmap/pacbio/RemoveAdapters3.java +%%JAVAJARDIR%%/bbmap/pacbio/SiteR.class +%%JAVAJARDIR%%/bbmap/pacbio/SiteR.java +%%JAVAJARDIR%%/bbmap/pacbio/SortSites$1.class +%%JAVAJARDIR%%/bbmap/pacbio/SortSites.class +%%JAVAJARDIR%%/bbmap/pacbio/SortSites.java +%%JAVAJARDIR%%/bbmap/pacbio/SplitOffPerfectContigs$1.class +%%JAVAJARDIR%%/bbmap/pacbio/SplitOffPerfectContigs.class +%%JAVAJARDIR%%/bbmap/pacbio/SplitOffPerfectContigs.java +%%JAVAJARDIR%%/bbmap/pacbio/StackSites$1.class +%%JAVAJARDIR%%/bbmap/pacbio/StackSites$Glob.class +%%JAVAJARDIR%%/bbmap/pacbio/StackSites.class +%%JAVAJARDIR%%/bbmap/pacbio/StackSites.java +%%JAVAJARDIR%%/bbmap/pacbio/StackSites2$1.class +%%JAVAJARDIR%%/bbmap/pacbio/StackSites2$Glob.class +%%JAVAJARDIR%%/bbmap/pacbio/StackSites2.class +%%JAVAJARDIR%%/bbmap/pacbio/StackSites2.java +%%JAVAJARDIR%%/bbmap/prok/AnalyzeGenes$FileThread.class +%%JAVAJARDIR%%/bbmap/prok/AnalyzeGenes.class +%%JAVAJARDIR%%/bbmap/prok/AnalyzeGenes.java +%%JAVAJARDIR%%/bbmap/prok/CallGenes$ProcessThread.class +%%JAVAJARDIR%%/bbmap/prok/CallGenes.class +%%JAVAJARDIR%%/bbmap/prok/CallGenes.java +%%JAVAJARDIR%%/bbmap/prok/Feature$FeatureComparatorScore.class +%%JAVAJARDIR%%/bbmap/prok/Feature.class +%%JAVAJARDIR%%/bbmap/prok/Feature.java +%%JAVAJARDIR%%/bbmap/prok/FetchProks$ProcessThread.class +%%JAVAJARDIR%%/bbmap/prok/FetchProks$Stats.class +%%JAVAJARDIR%%/bbmap/prok/FetchProks.class +%%JAVAJARDIR%%/bbmap/prok/FetchProks.java +%%JAVAJARDIR%%/bbmap/prok/FilterSilva.class +%%JAVAJARDIR%%/bbmap/prok/FilterSilva.java +%%JAVAJARDIR%%/bbmap/prok/FrameStats.class +%%JAVAJARDIR%%/bbmap/prok/FrameStats.java +%%JAVAJARDIR%%/bbmap/prok/GeneCaller.class +%%JAVAJARDIR%%/bbmap/prok/GeneCaller.java +%%JAVAJARDIR%%/bbmap/prok/GeneModel.class +%%JAVAJARDIR%%/bbmap/prok/GeneModel.java +%%JAVAJARDIR%%/bbmap/prok/GeneModelParser.class +%%JAVAJARDIR%%/bbmap/prok/GeneModelParser.java +%%JAVAJARDIR%%/bbmap/prok/MergeRibo$ListComparator.class +%%JAVAJARDIR%%/bbmap/prok/MergeRibo$ProcessThread.class +%%JAVAJARDIR%%/bbmap/prok/MergeRibo$Ribo.class +%%JAVAJARDIR%%/bbmap/prok/MergeRibo.class +%%JAVAJARDIR%%/bbmap/prok/MergeRibo.java +%%JAVAJARDIR%%/bbmap/prok/MergeRibo_Fast$ProcessThread.class +%%JAVAJARDIR%%/bbmap/prok/MergeRibo_Fast$Ribo.class +%%JAVAJARDIR%%/bbmap/prok/MergeRibo_Fast.class +%%JAVAJARDIR%%/bbmap/prok/MergeRibo_Fast.java +%%JAVAJARDIR%%/bbmap/prok/Orf.class +%%JAVAJARDIR%%/bbmap/prok/Orf.java +%%JAVAJARDIR%%/bbmap/prok/PGMTools$1.class +%%JAVAJARDIR%%/bbmap/prok/PGMTools.class +%%JAVAJARDIR%%/bbmap/prok/PGMTools.java +%%JAVAJARDIR%%/bbmap/prok/ProkObject.class +%%JAVAJARDIR%%/bbmap/prok/ProkObject.java +%%JAVAJARDIR%%/bbmap/prok/RiboMaker$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$ProcessThread.class +%%JAVAJARDIR%%/bbmap/prok/SplitRibo.class +%%JAVAJARDIR%%/bbmap/prok/SplitRibo.java +%%JAVAJARDIR%%/bbmap/prok/StatsContainer.class +%%JAVAJARDIR%%/bbmap/prok/StatsContainer.java +%%JAVAJARDIR%%/bbmap/server/PercentEncoding.class +%%JAVAJARDIR%%/bbmap/server/PercentEncoding.java +%%JAVAJARDIR%%/bbmap/server/ServerTools.class +%%JAVAJARDIR%%/bbmap/server/ServerTools.java +%%JAVAJARDIR%%/bbmap/server/SimpleHttpServer$GetHandler.class +%%JAVAJARDIR%%/bbmap/server/SimpleHttpServer.class +%%JAVAJARDIR%%/bbmap/server/SimpleHttpServer.java +%%JAVAJARDIR%%/bbmap/shared/Colors.class +%%JAVAJARDIR%%/bbmap/shared/Colors.java +%%JAVAJARDIR%%/bbmap/shared/KillSwitch.class +%%JAVAJARDIR%%/bbmap/shared/KillSwitch.java +%%JAVAJARDIR%%/bbmap/shared/MetadataWriter.class +%%JAVAJARDIR%%/bbmap/shared/MetadataWriter.java +%%JAVAJARDIR%%/bbmap/shared/Parse.class +%%JAVAJARDIR%%/bbmap/shared/Parse.java +%%JAVAJARDIR%%/bbmap/shared/Parser.class +%%JAVAJARDIR%%/bbmap/shared/Parser.java +%%JAVAJARDIR%%/bbmap/shared/PreParser.class +%%JAVAJARDIR%%/bbmap/shared/PreParser.java +%%JAVAJARDIR%%/bbmap/shared/Primes.class +%%JAVAJARDIR%%/bbmap/shared/Primes.java +%%JAVAJARDIR%%/bbmap/shared/ReadStats.class +%%JAVAJARDIR%%/bbmap/shared/ReadStats.java +%%JAVAJARDIR%%/bbmap/shared/Shared.class +%%JAVAJARDIR%%/bbmap/shared/Shared.java +%%JAVAJARDIR%%/bbmap/shared/Timer.class +%%JAVAJARDIR%%/bbmap/shared/Timer.java +%%JAVAJARDIR%%/bbmap/shared/Tools.class +%%JAVAJARDIR%%/bbmap/shared/Tools.java +%%JAVAJARDIR%%/bbmap/shared/TrimRead.class +%%JAVAJARDIR%%/bbmap/shared/TrimRead.java +%%JAVAJARDIR%%/bbmap/sketch/AddSSU$SketchHeader.class +%%JAVAJARDIR%%/bbmap/sketch/AddSSU.class +%%JAVAJARDIR%%/bbmap/sketch/AddSSU.java +%%JAVAJARDIR%%/bbmap/sketch/AlignmentJob.class +%%JAVAJARDIR%%/bbmap/sketch/AlignmentJob.java +%%JAVAJARDIR%%/bbmap/sketch/AlignmentThreadPool$AlignmentThread.class +%%JAVAJARDIR%%/bbmap/sketch/AlignmentThreadPool.class +%%JAVAJARDIR%%/bbmap/sketch/AlignmentThreadPool.java +%%JAVAJARDIR%%/bbmap/sketch/AnalyzeSketchResults$SSUThread.class +%%JAVAJARDIR%%/bbmap/sketch/AnalyzeSketchResults.class +%%JAVAJARDIR%%/bbmap/sketch/AnalyzeSketchResults.java +%%JAVAJARDIR%%/bbmap/sketch/Blacklist.class +%%JAVAJARDIR%%/bbmap/sketch/Blacklist.java +%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker$ProcessThread.class +%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker.class +%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker.java +%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker2$KeyPair.class +%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker2$ProcessThread.class +%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker2.class +%%JAVAJARDIR%%/bbmap/sketch/BlacklistMaker2.java +%%JAVAJARDIR%%/bbmap/sketch/CompareBuffer.class +%%JAVAJARDIR%%/bbmap/sketch/CompareBuffer.java +%%JAVAJARDIR%%/bbmap/sketch/CompareSSU$ProcessThread.class +%%JAVAJARDIR%%/bbmap/sketch/CompareSSU.class +%%JAVAJARDIR%%/bbmap/sketch/CompareSSU.java +%%JAVAJARDIR%%/bbmap/sketch/CompareSketch$CompareThread.class +%%JAVAJARDIR%%/bbmap/sketch/CompareSketch.class +%%JAVAJARDIR%%/bbmap/sketch/CompareSketch.java +%%JAVAJARDIR%%/bbmap/sketch/Comparison$Depth2Comparator.class +%%JAVAJARDIR%%/bbmap/sketch/Comparison$DepthComparator.class +%%JAVAJARDIR%%/bbmap/sketch/Comparison$HitsComparator.class +%%JAVAJARDIR%%/bbmap/sketch/Comparison$KIDComparator.class +%%JAVAJARDIR%%/bbmap/sketch/Comparison$SSUComparator.class +%%JAVAJARDIR%%/bbmap/sketch/Comparison$ScoreComparator.class +%%JAVAJARDIR%%/bbmap/sketch/Comparison$VolumeComparator.class +%%JAVAJARDIR%%/bbmap/sketch/Comparison$WKIDComparator.class +%%JAVAJARDIR%%/bbmap/sketch/Comparison.class +%%JAVAJARDIR%%/bbmap/sketch/Comparison.java +%%JAVAJARDIR%%/bbmap/sketch/DisplayParams.class +%%JAVAJARDIR%%/bbmap/sketch/DisplayParams.java +%%JAVAJARDIR%%/bbmap/sketch/GlocalAligner.class +%%JAVAJARDIR%%/bbmap/sketch/GlocalAligner.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/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$SketchResultsSummary.class +%%JAVAJARDIR%%/bbmap/sketch/SummarizeSketchStats.class +%%JAVAJARDIR%%/bbmap/sketch/SummarizeSketchStats.java +%%JAVAJARDIR%%/bbmap/sketch/Whitelist.class +%%JAVAJARDIR%%/bbmap/sketch/Whitelist.java +%%JAVAJARDIR%%/bbmap/sort/ContigLengthComparator.class +%%JAVAJARDIR%%/bbmap/sort/ContigLengthComparator.java +%%JAVAJARDIR%%/bbmap/sort/MergeSorted.class +%%JAVAJARDIR%%/bbmap/sort/MergeSorted.java +%%JAVAJARDIR%%/bbmap/sort/ReadComparator.class +%%JAVAJARDIR%%/bbmap/sort/ReadComparator.java +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorFlowcell.class +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorFlowcell.java +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorID.class +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorID.java +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorList.class +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorList.java +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorMapping.class +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorMapping.java +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorName.class +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorName.java +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorPosition.class +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorPosition.java +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorRandom.class +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorRandom.java +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTaxa.class +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTaxa.java +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological.class +%%JAVAJARDIR%%/bbmap/sort/ReadComparatorTopological.java +%%JAVAJARDIR%%/bbmap/sort/ReadErrorComparator.class +%%JAVAJARDIR%%/bbmap/sort/ReadErrorComparator.java +%%JAVAJARDIR%%/bbmap/sort/ReadLengthComparator.class +%%JAVAJARDIR%%/bbmap/sort/ReadLengthComparator.java +%%JAVAJARDIR%%/bbmap/sort/ReadQualityComparator.class +%%JAVAJARDIR%%/bbmap/sort/ReadQualityComparator.java +%%JAVAJARDIR%%/bbmap/sort/Shuffle$ShuffleThread.class +%%JAVAJARDIR%%/bbmap/sort/Shuffle.class +%%JAVAJARDIR%%/bbmap/sort/Shuffle.java +%%JAVAJARDIR%%/bbmap/sort/Shuffle2$WriteThread.class +%%JAVAJARDIR%%/bbmap/sort/Shuffle2.class +%%JAVAJARDIR%%/bbmap/sort/Shuffle2.java +%%JAVAJARDIR%%/bbmap/sort/SortByName$WriteThread.class +%%JAVAJARDIR%%/bbmap/sort/SortByName.class +%%JAVAJARDIR%%/bbmap/sort/SortByName.java +%%JAVAJARDIR%%/bbmap/sort/SortReadsByID$1.class +%%JAVAJARDIR%%/bbmap/sort/SortReadsByID$Block.class +%%JAVAJARDIR%%/bbmap/sort/SortReadsByID.class +%%JAVAJARDIR%%/bbmap/sort/SortReadsByID.java +%%JAVAJARDIR%%/bbmap/stream/ArrayListSet$Pack.class +%%JAVAJARDIR%%/bbmap/stream/ArrayListSet.class +%%JAVAJARDIR%%/bbmap/stream/ArrayListSet.java +%%JAVAJARDIR%%/bbmap/stream/BufferedMultiCros.class +%%JAVAJARDIR%%/bbmap/stream/BufferedMultiCros.java +%%JAVAJARDIR%%/bbmap/stream/ConcurrentCollectionReadInputStream.class +%%JAVAJARDIR%%/bbmap/stream/ConcurrentCollectionReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/ConcurrentDepot.class +%%JAVAJARDIR%%/bbmap/stream/ConcurrentDepot.java +%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadInputStream$1.class +%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadInputStream$ReadThread.class +%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadInputStream.class +%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadOutputStream.class +%%JAVAJARDIR%%/bbmap/stream/ConcurrentGenericReadOutputStream.java +%%JAVAJARDIR%%/bbmap/stream/ConcurrentLegacyReadInputStream.class +%%JAVAJARDIR%%/bbmap/stream/ConcurrentLegacyReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadInputStream.class +%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadInputStreamD.class +%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadInputStreamD.java +%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadListDepot.class +%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadListDepot.java +%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStream.class +%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStream.java +%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStreamD$ListenThread.class +%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStreamD.class +%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadOutputStreamD.java +%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadStreamInterface.class +%%JAVAJARDIR%%/bbmap/stream/ConcurrentReadStreamInterface.java +%%JAVAJARDIR%%/bbmap/stream/CrisContainer.class +%%JAVAJARDIR%%/bbmap/stream/CrisContainer.java +%%JAVAJARDIR%%/bbmap/stream/CrisWrapper.class +%%JAVAJARDIR%%/bbmap/stream/CrisWrapper.java +%%JAVAJARDIR%%/bbmap/stream/DualCris.class +%%JAVAJARDIR%%/bbmap/stream/DualCris.java +%%JAVAJARDIR%%/bbmap/stream/EmblReadInputStream.class +%%JAVAJARDIR%%/bbmap/stream/EmblReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/FASTQ.class +%%JAVAJARDIR%%/bbmap/stream/FASTQ.java +%%JAVAJARDIR%%/bbmap/stream/FastaQualReadInputStream.class +%%JAVAJARDIR%%/bbmap/stream/FastaQualReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/FastaReadInputStream.class +%%JAVAJARDIR%%/bbmap/stream/FastaReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/FastaShredInputStream.class +%%JAVAJARDIR%%/bbmap/stream/FastaShredInputStream.java +%%JAVAJARDIR%%/bbmap/stream/FastqReadInputStream.class +%%JAVAJARDIR%%/bbmap/stream/FastqReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/GbkReadInputStream.class +%%JAVAJARDIR%%/bbmap/stream/GbkReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/Header.class +%%JAVAJARDIR%%/bbmap/stream/Header.java +%%JAVAJARDIR%%/bbmap/stream/HeaderInputStream.class +%%JAVAJARDIR%%/bbmap/stream/HeaderInputStream.java +%%JAVAJARDIR%%/bbmap/stream/MDWalker.class +%%JAVAJARDIR%%/bbmap/stream/MDWalker.java +%%JAVAJARDIR%%/bbmap/stream/MultiCros.class +%%JAVAJARDIR%%/bbmap/stream/MultiCros.java +%%JAVAJARDIR%%/bbmap/stream/MultiCros2$Buffer.class +%%JAVAJARDIR%%/bbmap/stream/MultiCros2.class +%%JAVAJARDIR%%/bbmap/stream/MultiCros2.java +%%JAVAJARDIR%%/bbmap/stream/MultiCros3$Buffer.class +%%JAVAJARDIR%%/bbmap/stream/MultiCros3.class +%%JAVAJARDIR%%/bbmap/stream/MultiCros3.java +%%JAVAJARDIR%%/bbmap/stream/NullOutputStream.class +%%JAVAJARDIR%%/bbmap/stream/NullOutputStream.java +%%JAVAJARDIR%%/bbmap/stream/OnelineReadInputStream.class +%%JAVAJARDIR%%/bbmap/stream/OnelineReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/RTextInputStream.class +%%JAVAJARDIR%%/bbmap/stream/RTextInputStream.java +%%JAVAJARDIR%%/bbmap/stream/RandomReadInputStream3.class +%%JAVAJARDIR%%/bbmap/stream/RandomReadInputStream3.java +%%JAVAJARDIR%%/bbmap/stream/Read.class +%%JAVAJARDIR%%/bbmap/stream/Read.java +%%JAVAJARDIR%%/bbmap/stream/ReadInputStream.class +%%JAVAJARDIR%%/bbmap/stream/ReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/ReadStreamByteWriter.class +%%JAVAJARDIR%%/bbmap/stream/ReadStreamByteWriter.java +%%JAVAJARDIR%%/bbmap/stream/ReadStreamWriter$Job.class +%%JAVAJARDIR%%/bbmap/stream/ReadStreamWriter.class +%%JAVAJARDIR%%/bbmap/stream/ReadStreamWriter.java +%%JAVAJARDIR%%/bbmap/stream/SamHeader.class +%%JAVAJARDIR%%/bbmap/stream/SamHeader.java +%%JAVAJARDIR%%/bbmap/stream/SamLine.class +%%JAVAJARDIR%%/bbmap/stream/SamLine.java +%%JAVAJARDIR%%/bbmap/stream/SamLineStreamer$ProcessThread.class +%%JAVAJARDIR%%/bbmap/stream/SamLineStreamer.class +%%JAVAJARDIR%%/bbmap/stream/SamLineStreamer.java +%%JAVAJARDIR%%/bbmap/stream/SamReadInputStream.class +%%JAVAJARDIR%%/bbmap/stream/SamReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/SamReadStreamer$ProcessThread.class +%%JAVAJARDIR%%/bbmap/stream/SamReadStreamer.class +%%JAVAJARDIR%%/bbmap/stream/SamReadStreamer.java +%%JAVAJARDIR%%/bbmap/stream/SamStreamer.class +%%JAVAJARDIR%%/bbmap/stream/SamStreamer.java +%%JAVAJARDIR%%/bbmap/stream/SamStreamerMF.class +%%JAVAJARDIR%%/bbmap/stream/SamStreamerMF.java +%%JAVAJARDIR%%/bbmap/stream/SamStreamerWrapper.class +%%JAVAJARDIR%%/bbmap/stream/SamStreamerWrapper.java +%%JAVAJARDIR%%/bbmap/stream/ScaffoldCoordinates.class +%%JAVAJARDIR%%/bbmap/stream/ScaffoldCoordinates.java +%%JAVAJARDIR%%/bbmap/stream/ScarfReadInputStream.class +%%JAVAJARDIR%%/bbmap/stream/ScarfReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/SequentialReadInputStream.class +%%JAVAJARDIR%%/bbmap/stream/SequentialReadInputStream.java +%%JAVAJARDIR%%/bbmap/stream/SiteScore$PositionComparator.class +%%JAVAJARDIR%%/bbmap/stream/SiteScore.class +%%JAVAJARDIR%%/bbmap/stream/SiteScore.java +%%JAVAJARDIR%%/bbmap/stream/SiteScoreR$IDComparator.class +%%JAVAJARDIR%%/bbmap/stream/SiteScoreR$NormalizedComparator.class +%%JAVAJARDIR%%/bbmap/stream/SiteScoreR$PositionComparator.class +%%JAVAJARDIR%%/bbmap/stream/SiteScoreR.class +%%JAVAJARDIR%%/bbmap/stream/SiteScoreR.java +%%JAVAJARDIR%%/bbmap/structures/AbstractBitSet.class +%%JAVAJARDIR%%/bbmap/structures/AbstractBitSet.java +%%JAVAJARDIR%%/bbmap/structures/AbstractIntHashMap.class +%%JAVAJARDIR%%/bbmap/structures/AbstractIntHashMap.java +%%JAVAJARDIR%%/bbmap/structures/AtomicBitSet.class +%%JAVAJARDIR%%/bbmap/structures/AtomicBitSet.java +%%JAVAJARDIR%%/bbmap/structures/ByteBuilder.class +%%JAVAJARDIR%%/bbmap/structures/ByteBuilder.java +%%JAVAJARDIR%%/bbmap/structures/CoverageArray.class +%%JAVAJARDIR%%/bbmap/structures/CoverageArray.java +%%JAVAJARDIR%%/bbmap/structures/CoverageArray2.class +%%JAVAJARDIR%%/bbmap/structures/CoverageArray2.java +%%JAVAJARDIR%%/bbmap/structures/CoverageArray3.class +%%JAVAJARDIR%%/bbmap/structures/CoverageArray3.java +%%JAVAJARDIR%%/bbmap/structures/CoverageArray3A.class +%%JAVAJARDIR%%/bbmap/structures/CoverageArray3A.java +%%JAVAJARDIR%%/bbmap/structures/DoubleList.class +%%JAVAJARDIR%%/bbmap/structures/DoubleList.java +%%JAVAJARDIR%%/bbmap/structures/EntropyTracker.class +%%JAVAJARDIR%%/bbmap/structures/EntropyTracker.java +%%JAVAJARDIR%%/bbmap/structures/FloatList.class +%%JAVAJARDIR%%/bbmap/structures/FloatList.java +%%JAVAJARDIR%%/bbmap/structures/Heap.class +%%JAVAJARDIR%%/bbmap/structures/Heap.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/IntLongHashMap.class +%%JAVAJARDIR%%/bbmap/structures/IntLongHashMap.java +%%JAVAJARDIR%%/bbmap/structures/IntMap.class +%%JAVAJARDIR%%/bbmap/structures/IntMap.java +%%JAVAJARDIR%%/bbmap/structures/ListNum.class +%%JAVAJARDIR%%/bbmap/structures/ListNum.java +%%JAVAJARDIR%%/bbmap/structures/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/LongListSet$LongListSetIterator.class +%%JAVAJARDIR%%/bbmap/structures/LongListSet.class +%%JAVAJARDIR%%/bbmap/structures/LongListSet.java +%%JAVAJARDIR%%/bbmap/structures/LongLongHashMap.class +%%JAVAJARDIR%%/bbmap/structures/LongLongHashMap.java +%%JAVAJARDIR%%/bbmap/structures/LongM.class +%%JAVAJARDIR%%/bbmap/structures/LongM.java +%%JAVAJARDIR%%/bbmap/structures/LongPair.class +%%JAVAJARDIR%%/bbmap/structures/LongPair.java +%%JAVAJARDIR%%/bbmap/structures/MultiBitSet.class +%%JAVAJARDIR%%/bbmap/structures/MultiBitSet.java +%%JAVAJARDIR%%/bbmap/structures/PolymerTracker.class +%%JAVAJARDIR%%/bbmap/structures/PolymerTracker.java +%%JAVAJARDIR%%/bbmap/structures/Quantizer.class +%%JAVAJARDIR%%/bbmap/structures/Quantizer.java +%%JAVAJARDIR%%/bbmap/structures/Range.class +%%JAVAJARDIR%%/bbmap/structures/Range.java +%%JAVAJARDIR%%/bbmap/structures/RawBitSet.class +%%JAVAJARDIR%%/bbmap/structures/RawBitSet.java +%%JAVAJARDIR%%/bbmap/structures/StringNum.class +%%JAVAJARDIR%%/bbmap/structures/StringNum.java +%%JAVAJARDIR%%/bbmap/structures/StringPair.class +%%JAVAJARDIR%%/bbmap/structures/StringPair.java +%%JAVAJARDIR%%/bbmap/structures/SuperLongList.class +%%JAVAJARDIR%%/bbmap/structures/SuperLongList.java +%%JAVAJARDIR%%/bbmap/tax/AccessionToTaxid$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/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/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/PrintTaxonomy.class +%%JAVAJARDIR%%/bbmap/tax/PrintTaxonomy.java +%%JAVAJARDIR%%/bbmap/tax/Query.class +%%JAVAJARDIR%%/bbmap/tax/Query.java +%%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$TaxHandler.class +%%JAVAJARDIR%%/bbmap/tax/TaxServer.class +%%JAVAJARDIR%%/bbmap/tax/TaxServer.java +%%JAVAJARDIR%%/bbmap/tax/TaxSize.class +%%JAVAJARDIR%%/bbmap/tax/TaxSize.java +%%JAVAJARDIR%%/bbmap/tax/TaxTree.class +%%JAVAJARDIR%%/bbmap/tax/TaxTree.java +%%JAVAJARDIR%%/bbmap/template/A_Sample.class +%%JAVAJARDIR%%/bbmap/template/A_Sample.java +%%JAVAJARDIR%%/bbmap/template/A_Sample2.class +%%JAVAJARDIR%%/bbmap/template/A_Sample2.java +%%JAVAJARDIR%%/bbmap/template/A_SampleBasic.class +%%JAVAJARDIR%%/bbmap/template/A_SampleBasic.java +%%JAVAJARDIR%%/bbmap/template/A_SampleBasic2.class +%%JAVAJARDIR%%/bbmap/template/A_SampleBasic2.java +%%JAVAJARDIR%%/bbmap/template/A_SampleByteFile.class +%%JAVAJARDIR%%/bbmap/template/A_SampleByteFile.java +%%JAVAJARDIR%%/bbmap/template/A_SampleD.class +%%JAVAJARDIR%%/bbmap/template/A_SampleD.java +%%JAVAJARDIR%%/bbmap/template/A_SampleMT$ProcessThread.class +%%JAVAJARDIR%%/bbmap/template/A_SampleMT.class +%%JAVAJARDIR%%/bbmap/template/A_SampleMT.java +%%JAVAJARDIR%%/bbmap/template/A_SampleSamStreamer$ProcessThread.class +%%JAVAJARDIR%%/bbmap/template/A_SampleSamStreamer.class +%%JAVAJARDIR%%/bbmap/template/A_SampleSamStreamer.java +%%JAVAJARDIR%%/bbmap/template/A_SampleSummary.class +%%JAVAJARDIR%%/bbmap/template/A_SampleSummary.java +%%JAVAJARDIR%%/bbmap/template/A_Sample_Generator$ProcessThread.class +%%JAVAJARDIR%%/bbmap/template/A_Sample_Generator.class +%%JAVAJARDIR%%/bbmap/template/A_Sample_Generator.java +%%JAVAJARDIR%%/bbmap/template/A_Sample_Unpaired.class +%%JAVAJARDIR%%/bbmap/template/A_Sample_Unpaired.java +%%JAVAJARDIR%%/bbmap/template/Accumulator.class +%%JAVAJARDIR%%/bbmap/template/Accumulator.java +%%JAVAJARDIR%%/bbmap/template/BBTool_ST.class +%%JAVAJARDIR%%/bbmap/template/BBTool_ST.java +%%JAVAJARDIR%%/bbmap/template/DoWorker.class +%%JAVAJARDIR%%/bbmap/template/DoWorker.java +%%JAVAJARDIR%%/bbmap/template/ThreadPoolJob.class +%%JAVAJARDIR%%/bbmap/template/ThreadPoolJob.java +%%JAVAJARDIR%%/bbmap/template/ThreadWaiter.class +%%JAVAJARDIR%%/bbmap/template/ThreadWaiter.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/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/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/ApplyVariants.class +%%JAVAJARDIR%%/bbmap/var2/ApplyVariants.java +%%JAVAJARDIR%%/bbmap/var2/CallVariants$ProcessThread.class +%%JAVAJARDIR%%/bbmap/var2/CallVariants.class +%%JAVAJARDIR%%/bbmap/var2/CallVariants.java +%%JAVAJARDIR%%/bbmap/var2/CallVariants2$Sample$ProcessThread.class +%%JAVAJARDIR%%/bbmap/var2/CallVariants2$Sample.class +%%JAVAJARDIR%%/bbmap/var2/CallVariants2.class +%%JAVAJARDIR%%/bbmap/var2/CallVariants2.java +%%JAVAJARDIR%%/bbmap/var2/CompareVCF.class +%%JAVAJARDIR%%/bbmap/var2/CompareVCF.java +%%JAVAJARDIR%%/bbmap/var2/FilterSam$ProcessThread.class +%%JAVAJARDIR%%/bbmap/var2/FilterSam.class +%%JAVAJARDIR%%/bbmap/var2/FilterSam.java +%%JAVAJARDIR%%/bbmap/var2/FilterVCF$ProcessThread.class +%%JAVAJARDIR%%/bbmap/var2/FilterVCF.class +%%JAVAJARDIR%%/bbmap/var2/FilterVCF.java +%%JAVAJARDIR%%/bbmap/var2/MergeSamples$MergeThread.class +%%JAVAJARDIR%%/bbmap/var2/MergeSamples.class +%%JAVAJARDIR%%/bbmap/var2/MergeSamples.java +%%JAVAJARDIR%%/bbmap/var2/Realign$ProcessThread.class +%%JAVAJARDIR%%/bbmap/var2/Realign.class +%%JAVAJARDIR%%/bbmap/var2/Realign.java +%%JAVAJARDIR%%/bbmap/var2/Realigner.class +%%JAVAJARDIR%%/bbmap/var2/Realigner.java +%%JAVAJARDIR%%/bbmap/var2/SamFilter.class +%%JAVAJARDIR%%/bbmap/var2/SamFilter.java +%%JAVAJARDIR%%/bbmap/var2/ScafMap.class +%%JAVAJARDIR%%/bbmap/var2/ScafMap.java +%%JAVAJARDIR%%/bbmap/var2/Scaffold.class +%%JAVAJARDIR%%/bbmap/var2/Scaffold.java +%%JAVAJARDIR%%/bbmap/var2/SoftClipper.class +%%JAVAJARDIR%%/bbmap/var2/SoftClipper.java +%%JAVAJARDIR%%/bbmap/var2/VCFFile$1.class +%%JAVAJARDIR%%/bbmap/var2/VCFFile.class +%%JAVAJARDIR%%/bbmap/var2/VCFFile.java +%%JAVAJARDIR%%/bbmap/var2/VCFLine.class +%%JAVAJARDIR%%/bbmap/var2/VCFLine.java +%%JAVAJARDIR%%/bbmap/var2/Var.class +%%JAVAJARDIR%%/bbmap/var2/Var.java +%%JAVAJARDIR%%/bbmap/var2/VarFilter.class +%%JAVAJARDIR%%/bbmap/var2/VarFilter.java +%%JAVAJARDIR%%/bbmap/var2/VarKey.class +%%JAVAJARDIR%%/bbmap/var2/VarKey.java +%%JAVAJARDIR%%/bbmap/var2/VarMap$ProcessThread.class +%%JAVAJARDIR%%/bbmap/var2/VarMap$VarMapIterator.class +%%JAVAJARDIR%%/bbmap/var2/VarMap.class +%%JAVAJARDIR%%/bbmap/var2/VarMap.java +%%JAVAJARDIR%%/bbmap/var2/VcfLoader$ProcessThread.class +%%JAVAJARDIR%%/bbmap/var2/VcfLoader.class +%%JAVAJARDIR%%/bbmap/var2/VcfLoader.java +%%JAVAJARDIR%%/bbmap/var2/VcfWriter$ProcessThread.class +%%JAVAJARDIR%%/bbmap/var2/VcfWriter.class +%%JAVAJARDIR%%/bbmap/var2/VcfWriter.java |