From owner-dev-commits-ports-all@freebsd.org Sun Apr 18 16:22:46 2021 Return-Path: Delivered-To: dev-commits-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 98FA35EE2CB; Sun, 18 Apr 2021 16:22:46 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4FNZx23vFWz3pXZ; Sun, 18 Apr 2021 16:22:46 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 783FA6FB9; Sun, 18 Apr 2021 16:22:46 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 13IGMkQ4054318; Sun, 18 Apr 2021 16:22:46 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 13IGMkIW054317; Sun, 18 Apr 2021 16:22:46 GMT (envelope-from git) Date: Sun, 18 Apr 2021 16:22:46 GMT Message-Id: <202104181622.13IGMkIW054317@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: 15458dfbacb8 - main - biology/bbmap: BBMap short read aligner, and other bioinformatic tools MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 15458dfbacb842d71a41dcfdb6be83301ef0b7b6 Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commit messages for all branches of the ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 18 Apr 2021 16:22:46 -0000 The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=15458dfbacb842d71a41dcfdb6be83301ef0b7b6 commit 15458dfbacb842d71a41dcfdb6be83301ef0b7b6 Author: Jason W. Bacon AuthorDate: 2021-04-18 16:21:29 +0000 Commit: Jason W. Bacon 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 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 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