Date: Sun, 18 Apr 2021 16:22:46 GMT From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 15458dfbacb8 - main - biology/bbmap: BBMap short read aligner, and other bioinformatic tools Message-ID: <202104181622.13IGMkIW054317@gitrepo.freebsd.org>
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The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=15458dfbacb842d71a41dcfdb6be83301ef0b7b6 commit 15458dfbacb842d71a41dcfdb6be83301ef0b7b6 Author: Jason W. Bacon <jwb@FreeBSD.org> AuthorDate: 2021-04-18 16:21:29 +0000 Commit: Jason W. Bacon <jwb@FreeBSD.org> CommitDate: 2021-04-18 16:21:29 +0000 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. --- biology/Makefile | 1 + biology/bbmap/Makefile | 45 + biology/bbmap/distinfo | 3 + biology/bbmap/files/patch-calcmem.sh | 33 + biology/bbmap/pkg-descr | 6 + biology/bbmap/pkg-plist | 1976 ++++++++++++++++++++++++++++++++++ 6 files changed, 2064 insertions(+) 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 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+%%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 *** 1143 LINES SKIPPED ***
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