MANIFEST.in
README.md
setup.cfg
setup.py
ARGs_OAP/ARGs_OAP.py
ARGs_OAP/README.md
ARGs_OAP/__init__.py
ARGs_OAP/argoap_pipeline_stageone_version2
ARGs_OAP/argoap_pipeline_stageone_version2.3
ARGs_OAP/argoap_pipeline_stagetwo_version2
ARGs_OAP/index.rst
ARGs_OAP/stage_one.py
ARGs_OAP/stage_two.py
ARGs_OAP.egg-info/PKG-INFO
ARGs_OAP.egg-info/SOURCES.txt
ARGs_OAP.egg-info/dependency_links.txt
ARGs_OAP.egg-info/entry_points.txt
ARGs_OAP.egg-info/top_level.txt
ARGs_OAP/DB/KO30_DIAMOND.dmnd
ARGs_OAP/DB/SARG.2.2.diamondv0.9.24.dmnd
ARGs_OAP/DB/SARG.2.2.fasta
ARGs_OAP/DB/SARG.2.2.fasta.phr
ARGs_OAP/DB/SARG.2.2.fasta.pin
ARGs_OAP/DB/SARG.2.2.fasta.psq
ARGs_OAP/DB/all_KO30_name.list
ARGs_OAP/DB/gg85.fasta
ARGs_OAP/DB/gg85_yinxiaole.fasta.mmi
ARGs_OAP/DB/structure_20181107.LIST
ARGs_OAP/DB/update_45_sarg2.0_16s.table_201704.txt
ARGs_OAP/DB/update_45_sarg2.0_cell.table_201704.txt
ARGs_OAP/bin/Fq2fa.pl
ARGs_OAP/bin/blastx
ARGs_OAP/bin/copy_correction.pl
ARGs_OAP/bin/de-replicate.pl
ARGs_OAP/bin/diamond
ARGs_OAP/bin/diamondv0.9.24
ARGs_OAP/bin/divide_extract.fa_meta_data_online.pl
ARGs_OAP/bin/extract_usearch_reads.pl
ARGs_OAP/bin/fastp
ARGs_OAP/bin/merge_extracted_fa_update_metadate.v2.3.pl
ARGs_OAP/bin/minimap2
ARGs_OAP/bin/obtain_community.pl
ARGs_OAP/bin/samtools
ARGs_OAP/bin/bbmap/README.md
ARGs_OAP/bin/bbmap/a_sample_mt.sh
ARGs_OAP/bin/bbmap/addadapters.sh
ARGs_OAP/bin/bbmap/addssu.sh
ARGs_OAP/bin/bbmap/adjusthomopolymers.sh
ARGs_OAP/bin/bbmap/alltoall.sh
ARGs_OAP/bin/bbmap/analyzeaccession.sh
ARGs_OAP/bin/bbmap/analyzegenes.sh
ARGs_OAP/bin/bbmap/analyzesketchresults.sh
ARGs_OAP/bin/bbmap/applyvariants.sh
ARGs_OAP/bin/bbmap/bbcms.sh
ARGs_OAP/bin/bbmap/bbcountunique.sh
ARGs_OAP/bin/bbmap/bbduk.sh
ARGs_OAP/bin/bbmap/bbest.sh
ARGs_OAP/bin/bbmap/bbfakereads.sh
ARGs_OAP/bin/bbmap/bbmap.sh
ARGs_OAP/bin/bbmap/bbmapskimmer.sh
ARGs_OAP/bin/bbmap/bbmask.sh
ARGs_OAP/bin/bbmap/bbmerge-auto.sh
ARGs_OAP/bin/bbmap/bbmerge.sh
ARGs_OAP/bin/bbmap/bbnorm.sh
ARGs_OAP/bin/bbmap/bbrealign.sh
ARGs_OAP/bin/bbmap/bbrename.sh
ARGs_OAP/bin/bbmap/bbsketch.sh
ARGs_OAP/bin/bbmap/bbsplit.sh
ARGs_OAP/bin/bbmap/bbsplitpairs.sh
ARGs_OAP/bin/bbmap/bbstats.sh
ARGs_OAP/bin/bbmap/bbversion.sh
ARGs_OAP/bin/bbmap/bbwrap.sh
ARGs_OAP/bin/bbmap/bloomfilter.sh
ARGs_OAP/bin/bbmap/calcmem.sh
ARGs_OAP/bin/bbmap/calctruequality.sh
ARGs_OAP/bin/bbmap/callgenes.sh
ARGs_OAP/bin/bbmap/callpeaks.sh
ARGs_OAP/bin/bbmap/callvariants.sh
ARGs_OAP/bin/bbmap/callvariants2.sh
ARGs_OAP/bin/bbmap/clumpify.sh
ARGs_OAP/bin/bbmap/commonkmers.sh
ARGs_OAP/bin/bbmap/comparegff.sh
ARGs_OAP/bin/bbmap/comparesketch.sh
ARGs_OAP/bin/bbmap/comparessu.sh
ARGs_OAP/bin/bbmap/comparevcf.sh
ARGs_OAP/bin/bbmap/consect.sh
ARGs_OAP/bin/bbmap/consensus.sh
ARGs_OAP/bin/bbmap/countbarcodes.sh
ARGs_OAP/bin/bbmap/countgc.sh
ARGs_OAP/bin/bbmap/countsharedlines.sh
ARGs_OAP/bin/bbmap/crossblock.sh
ARGs_OAP/bin/bbmap/crosscontaminate.sh
ARGs_OAP/bin/bbmap/cutgff.sh
ARGs_OAP/bin/bbmap/cutprimers.sh
ARGs_OAP/bin/bbmap/decontaminate.sh
ARGs_OAP/bin/bbmap/dedupe.sh
ARGs_OAP/bin/bbmap/dedupe2.sh
ARGs_OAP/bin/bbmap/dedupebymapping.sh
ARGs_OAP/bin/bbmap/demuxbyname.sh
ARGs_OAP/bin/bbmap/diskbench.sh
ARGs_OAP/bin/bbmap/estherfilter.sh
ARGs_OAP/bin/bbmap/explodetree.sh
ARGs_OAP/bin/bbmap/fetchproks.sh
ARGs_OAP/bin/bbmap/filterassemblysummary.sh
ARGs_OAP/bin/bbmap/filterbarcodes.sh
ARGs_OAP/bin/bbmap/filterbycoverage.sh
ARGs_OAP/bin/bbmap/filterbyname.sh
ARGs_OAP/bin/bbmap/filterbysequence.sh
ARGs_OAP/bin/bbmap/filterbytaxa.sh
ARGs_OAP/bin/bbmap/filterbytile.sh
ARGs_OAP/bin/bbmap/filterlines.sh
ARGs_OAP/bin/bbmap/filterqc.sh
ARGs_OAP/bin/bbmap/filtersam.sh
ARGs_OAP/bin/bbmap/filtersilva.sh
ARGs_OAP/bin/bbmap/filtersubs.sh
ARGs_OAP/bin/bbmap/filtervcf.sh
ARGs_OAP/bin/bbmap/fixgaps.sh
ARGs_OAP/bin/bbmap/fungalrelease.sh
ARGs_OAP/bin/bbmap/fuse.sh
ARGs_OAP/bin/bbmap/gbff2gff.sh
ARGs_OAP/bin/bbmap/getreads.sh
ARGs_OAP/bin/bbmap/gi2ancestors.sh
ARGs_OAP/bin/bbmap/gi2taxid.sh
ARGs_OAP/bin/bbmap/gitable.sh
ARGs_OAP/bin/bbmap/grademerge.sh
ARGs_OAP/bin/bbmap/gradesam.sh
ARGs_OAP/bin/bbmap/icecreamfinder.sh
ARGs_OAP/bin/bbmap/icecreamgrader.sh
ARGs_OAP/bin/bbmap/icecreammaker.sh
ARGs_OAP/bin/bbmap/idmatrix.sh
ARGs_OAP/bin/bbmap/idtree.sh
ARGs_OAP/bin/bbmap/invertkey.sh
ARGs_OAP/bin/bbmap/kapastats.sh
ARGs_OAP/bin/bbmap/kcompress.sh
ARGs_OAP/bin/bbmap/keepbestcopy.sh
ARGs_OAP/bin/bbmap/khist.sh
ARGs_OAP/bin/bbmap/kmercountexact.sh
ARGs_OAP/bin/bbmap/kmercountmulti.sh
ARGs_OAP/bin/bbmap/kmercoverage.sh
ARGs_OAP/bin/bbmap/kmerfilterset.sh
ARGs_OAP/bin/bbmap/kmerlimit.sh
ARGs_OAP/bin/bbmap/kmerlimit2.sh
ARGs_OAP/bin/bbmap/license.txt
ARGs_OAP/bin/bbmap/lilypad.sh
ARGs_OAP/bin/bbmap/loadreads.sh
ARGs_OAP/bin/bbmap/loglog.sh
ARGs_OAP/bin/bbmap/makechimeras.sh
ARGs_OAP/bin/bbmap/makecontaminatedgenomes.sh
ARGs_OAP/bin/bbmap/makepolymers.sh
ARGs_OAP/bin/bbmap/mapPacBio.sh
ARGs_OAP/bin/bbmap/matrixtocolumns.sh
ARGs_OAP/bin/bbmap/mergeOTUs.sh
ARGs_OAP/bin/bbmap/mergebarcodes.sh
ARGs_OAP/bin/bbmap/mergepgm.sh
ARGs_OAP/bin/bbmap/mergeribo.sh
ARGs_OAP/bin/bbmap/mergesam.sh
ARGs_OAP/bin/bbmap/mergesketch.sh
ARGs_OAP/bin/bbmap/mergesorted.sh
ARGs_OAP/bin/bbmap/msa.sh
ARGs_OAP/bin/bbmap/mutate.sh
ARGs_OAP/bin/bbmap/muxbyname.sh
ARGs_OAP/bin/bbmap/partition.sh
ARGs_OAP/bin/bbmap/phylip2fasta.sh
ARGs_OAP/bin/bbmap/pileup.sh
ARGs_OAP/bin/bbmap/plotflowcell.sh
ARGs_OAP/bin/bbmap/plotgc.sh
ARGs_OAP/bin/bbmap/postfilter.sh
ARGs_OAP/bin/bbmap/printtime.sh
ARGs_OAP/bin/bbmap/processfrag.sh
ARGs_OAP/bin/bbmap/processhi-c.sh
ARGs_OAP/bin/bbmap/processspeed.sh
ARGs_OAP/bin/bbmap/randomgenome.sh
ARGs_OAP/bin/bbmap/randomreads.sh
ARGs_OAP/bin/bbmap/readlength.sh
ARGs_OAP/bin/bbmap/readqc.sh
ARGs_OAP/bin/bbmap/reducesilva.sh
ARGs_OAP/bin/bbmap/reformat.sh
ARGs_OAP/bin/bbmap/removebadbarcodes.sh
ARGs_OAP/bin/bbmap/removecatdogmousehuman.sh
ARGs_OAP/bin/bbmap/removehuman.sh
ARGs_OAP/bin/bbmap/removehuman2.sh
ARGs_OAP/bin/bbmap/removemicrobes.sh
ARGs_OAP/bin/bbmap/removesmartbell.sh
ARGs_OAP/bin/bbmap/rename.sh
ARGs_OAP/bin/bbmap/renameimg.sh
ARGs_OAP/bin/bbmap/repair.sh
ARGs_OAP/bin/bbmap/replaceheaders.sh
ARGs_OAP/bin/bbmap/representative.sh
ARGs_OAP/bin/bbmap/rqcfilter.sh
ARGs_OAP/bin/bbmap/rqcfilter2.sh
ARGs_OAP/bin/bbmap/samtoroc.sh
ARGs_OAP/bin/bbmap/seal.sh
ARGs_OAP/bin/bbmap/sendsketch.sh
ARGs_OAP/bin/bbmap/shred.sh
ARGs_OAP/bin/bbmap/shrinkaccession.sh
ARGs_OAP/bin/bbmap/shuffle.sh
ARGs_OAP/bin/bbmap/shuffle2.sh
ARGs_OAP/bin/bbmap/sketch.sh
ARGs_OAP/bin/bbmap/sketchblacklist.sh
ARGs_OAP/bin/bbmap/sketchblacklist2.sh
ARGs_OAP/bin/bbmap/sortbyname.sh
ARGs_OAP/bin/bbmap/splitbytaxa.sh
ARGs_OAP/bin/bbmap/splitnextera.sh
ARGs_OAP/bin/bbmap/splitribo.sh
ARGs_OAP/bin/bbmap/splitsam.sh
ARGs_OAP/bin/bbmap/splitsam4way.sh
ARGs_OAP/bin/bbmap/splitsam6way.sh
ARGs_OAP/bin/bbmap/stats.sh
ARGs_OAP/bin/bbmap/statswrapper.sh
ARGs_OAP/bin/bbmap/streamsam.sh
ARGs_OAP/bin/bbmap/subsketch.sh
ARGs_OAP/bin/bbmap/summarizecontam.sh
ARGs_OAP/bin/bbmap/summarizecoverage.sh
ARGs_OAP/bin/bbmap/summarizecrossblock.sh
ARGs_OAP/bin/bbmap/summarizemerge.sh
ARGs_OAP/bin/bbmap/summarizequast.sh
ARGs_OAP/bin/bbmap/summarizescafstats.sh
ARGs_OAP/bin/bbmap/summarizeseal.sh
ARGs_OAP/bin/bbmap/summarizesketch.sh
ARGs_OAP/bin/bbmap/synthmda.sh
ARGs_OAP/bin/bbmap/tadpipe.sh
ARGs_OAP/bin/bbmap/tadpole.sh
ARGs_OAP/bin/bbmap/tadwrapper.sh
ARGs_OAP/bin/bbmap/taxonomy.sh
ARGs_OAP/bin/bbmap/taxserver.sh
ARGs_OAP/bin/bbmap/taxsize.sh
ARGs_OAP/bin/bbmap/taxtree.sh
ARGs_OAP/bin/bbmap/testfilesystem.sh
ARGs_OAP/bin/bbmap/testformat.sh
ARGs_OAP/bin/bbmap/testformat2.sh
ARGs_OAP/bin/bbmap/tetramerfreq.sh
ARGs_OAP/bin/bbmap/textfile.sh
ARGs_OAP/bin/bbmap/translate6frames.sh
ARGs_OAP/bin/bbmap/unicode2ascii.sh
ARGs_OAP/bin/bbmap/unzip.sh
ARGs_OAP/bin/bbmap/vcf2gff.sh
ARGs_OAP/bin/bbmap/webcheck.sh
ARGs_OAP/bin/bbmap/config/cluster16s.txt
ARGs_OAP/bin/bbmap/config/filter16s.txt
ARGs_OAP/bin/bbmap/config/histograms.txt
ARGs_OAP/bin/bbmap/config/recalibrate.txt
ARGs_OAP/bin/bbmap/config/rnaseq.txt
ARGs_OAP/bin/bbmap/config/trimadapters.txt
ARGs_OAP/bin/bbmap/current/align2/AbstractIndex.class
ARGs_OAP/bin/bbmap/current/align2/AbstractIndex.java
ARGs_OAP/bin/bbmap/current/align2/AbstractMapThread.class
ARGs_OAP/bin/bbmap/current/align2/AbstractMapThread.java
ARGs_OAP/bin/bbmap/current/align2/AbstractMapper.class
ARGs_OAP/bin/bbmap/current/align2/AbstractMapper.java
ARGs_OAP/bin/bbmap/current/align2/BBIndex.class
ARGs_OAP/bin/bbmap/current/align2/BBIndex.java
ARGs_OAP/bin/bbmap/current/align2/BBIndex5.class
ARGs_OAP/bin/bbmap/current/align2/BBIndex5.java
ARGs_OAP/bin/bbmap/current/align2/BBIndexAcc.class
ARGs_OAP/bin/bbmap/current/align2/BBIndexAcc.java
ARGs_OAP/bin/bbmap/current/align2/BBIndexPacBio.class
ARGs_OAP/bin/bbmap/current/align2/BBIndexPacBio.java
ARGs_OAP/bin/bbmap/current/align2/BBIndexPacBioSkimmer.class
ARGs_OAP/bin/bbmap/current/align2/BBIndexPacBioSkimmer.java
ARGs_OAP/bin/bbmap/current/align2/BBMap.class
ARGs_OAP/bin/bbmap/current/align2/BBMap.java
ARGs_OAP/bin/bbmap/current/align2/BBMap5.class
ARGs_OAP/bin/bbmap/current/align2/BBMap5.java
ARGs_OAP/bin/bbmap/current/align2/BBMapAcc.class
ARGs_OAP/bin/bbmap/current/align2/BBMapAcc.java
ARGs_OAP/bin/bbmap/current/align2/BBMapPacBio.class
ARGs_OAP/bin/bbmap/current/align2/BBMapPacBio.java
ARGs_OAP/bin/bbmap/current/align2/BBMapPacBioSkimmer.class
ARGs_OAP/bin/bbmap/current/align2/BBMapPacBioSkimmer.java
ARGs_OAP/bin/bbmap/current/align2/BBMapThread$1.class
ARGs_OAP/bin/bbmap/current/align2/BBMapThread.class
ARGs_OAP/bin/bbmap/current/align2/BBMapThread.java
ARGs_OAP/bin/bbmap/current/align2/BBMapThread5$1.class
ARGs_OAP/bin/bbmap/current/align2/BBMapThread5.class
ARGs_OAP/bin/bbmap/current/align2/BBMapThread5.java
ARGs_OAP/bin/bbmap/current/align2/BBMapThreadAcc$1.class
ARGs_OAP/bin/bbmap/current/align2/BBMapThreadAcc.class
ARGs_OAP/bin/bbmap/current/align2/BBMapThreadAcc.java
ARGs_OAP/bin/bbmap/current/align2/BBMapThreadPacBio$1.class
ARGs_OAP/bin/bbmap/current/align2/BBMapThreadPacBio.class
ARGs_OAP/bin/bbmap/current/align2/BBMapThreadPacBio.java
ARGs_OAP/bin/bbmap/current/align2/BBMapThreadPacBioSkimmer.class
ARGs_OAP/bin/bbmap/current/align2/BBMapThreadPacBioSkimmer.java
ARGs_OAP/bin/bbmap/current/align2/BBSplitter$1.class
ARGs_OAP/bin/bbmap/current/align2/BBSplitter$SetCount.class
ARGs_OAP/bin/bbmap/current/align2/BBSplitter.class
ARGs_OAP/bin/bbmap/current/align2/BBSplitter.java
ARGs_OAP/bin/bbmap/current/align2/BBWrap.class
ARGs_OAP/bin/bbmap/current/align2/BBWrap.java
ARGs_OAP/bin/bbmap/current/align2/BandedAligner.class
ARGs_OAP/bin/bbmap/current/align2/BandedAligner.java
ARGs_OAP/bin/bbmap/current/align2/BandedAlignerConcrete.class
ARGs_OAP/bin/bbmap/current/align2/BandedAlignerConcrete.java
ARGs_OAP/bin/bbmap/current/align2/BandedAlignerJNI.class
ARGs_OAP/bin/bbmap/current/align2/BandedAlignerJNI.java
ARGs_OAP/bin/bbmap/current/align2/Blacklist.class
ARGs_OAP/bin/bbmap/current/align2/Blacklist.java
ARGs_OAP/bin/bbmap/current/align2/Block.class
ARGs_OAP/bin/bbmap/current/align2/Block.java
ARGs_OAP/bin/bbmap/current/align2/ChromLoadThread.class
ARGs_OAP/bin/bbmap/current/align2/ChromLoadThread.java
ARGs_OAP/bin/bbmap/current/align2/CompareSamFiles$1.class
ARGs_OAP/bin/bbmap/current/align2/CompareSamFiles.class
ARGs_OAP/bin/bbmap/current/align2/CompareSamFiles.java
ARGs_OAP/bin/bbmap/current/align2/CompressString.class
ARGs_OAP/bin/bbmap/current/align2/CompressString.java
ARGs_OAP/bin/bbmap/current/align2/GapTools$Range.class
ARGs_OAP/bin/bbmap/current/align2/GapTools.class
ARGs_OAP/bin/bbmap/current/align2/GapTools.java
ARGs_OAP/bin/bbmap/current/align2/GradeSamFile$1.class
ARGs_OAP/bin/bbmap/current/align2/GradeSamFile.class
ARGs_OAP/bin/bbmap/current/align2/GradeSamFile.java
ARGs_OAP/bin/bbmap/current/align2/Index.class
ARGs_OAP/bin/bbmap/current/align2/Index.java
ARGs_OAP/bin/bbmap/current/align2/IndexMaker4$BlockMaker$CountThread.class
ARGs_OAP/bin/bbmap/current/align2/IndexMaker4$BlockMaker.class
ARGs_OAP/bin/bbmap/current/align2/IndexMaker4.class
ARGs_OAP/bin/bbmap/current/align2/IndexMaker4.java
ARGs_OAP/bin/bbmap/current/align2/IndexMaker5$BlockMaker$CountThread.class
ARGs_OAP/bin/bbmap/current/align2/IndexMaker5$BlockMaker.class
ARGs_OAP/bin/bbmap/current/align2/IndexMaker5.class
ARGs_OAP/bin/bbmap/current/align2/IndexMaker5.java
ARGs_OAP/bin/bbmap/current/align2/KeyRing.class
ARGs_OAP/bin/bbmap/current/align2/KeyRing.java
ARGs_OAP/bin/bbmap/current/align2/MSA.class
ARGs_OAP/bin/bbmap/current/align2/MSA.java
ARGs_OAP/bin/bbmap/current/align2/MakeQualityHistogram.class
ARGs_OAP/bin/bbmap/current/align2/MakeQualityHistogram.java
ARGs_OAP/bin/bbmap/current/align2/MakeRocCurve$1.class
ARGs_OAP/bin/bbmap/current/align2/MakeRocCurve.class
ARGs_OAP/bin/bbmap/current/align2/MakeRocCurve.java
ARGs_OAP/bin/bbmap/current/align2/MultiStateAligner10ts.class
ARGs_OAP/bin/bbmap/current/align2/MultiStateAligner10ts.java
ARGs_OAP/bin/bbmap/current/align2/MultiStateAligner11ts.class
ARGs_OAP/bin/bbmap/current/align2/MultiStateAligner11ts.java
ARGs_OAP/bin/bbmap/current/align2/MultiStateAligner11tsJNI.class
ARGs_OAP/bin/bbmap/current/align2/MultiStateAligner11tsJNI.java
ARGs_OAP/bin/bbmap/current/align2/MultiStateAligner9Flat.class
ARGs_OAP/bin/bbmap/current/align2/MultiStateAligner9Flat.java
ARGs_OAP/bin/bbmap/current/align2/MultiStateAligner9PacBio.class
ARGs_OAP/bin/bbmap/current/align2/MultiStateAligner9PacBio.java
ARGs_OAP/bin/bbmap/current/align2/MultiStateAligner9XFlat.class
ARGs_OAP/bin/bbmap/current/align2/MultiStateAligner9XFlat.java
ARGs_OAP/bin/bbmap/current/align2/MultiStateAligner9ts.class
ARGs_OAP/bin/bbmap/current/align2/MultiStateAligner9ts.java
ARGs_OAP/bin/bbmap/current/align2/NeedlemanWunsch.class
ARGs_OAP/bin/bbmap/current/align2/NeedlemanWunsch.java
ARGs_OAP/bin/bbmap/current/align2/PackedHeap.class
ARGs_OAP/bin/bbmap/current/align2/PackedHeap.java
ARGs_OAP/bin/bbmap/current/align2/Pointer.class
ARGs_OAP/bin/bbmap/current/align2/Pointer.java
ARGs_OAP/bin/bbmap/current/align2/PrintTime.class
ARGs_OAP/bin/bbmap/current/align2/PrintTime.java
ARGs_OAP/bin/bbmap/current/align2/Quad.class
ARGs_OAP/bin/bbmap/current/align2/Quad.java
ARGs_OAP/bin/bbmap/current/align2/Quad64.class
ARGs_OAP/bin/bbmap/current/align2/Quad64.java
ARGs_OAP/bin/bbmap/current/align2/Quad64Heap.class
ARGs_OAP/bin/bbmap/current/align2/Quad64Heap.java
ARGs_OAP/bin/bbmap/current/align2/QuadHeap.class
ARGs_OAP/bin/bbmap/current/align2/QuadHeap.java
ARGs_OAP/bin/bbmap/current/align2/QualityTools.class
ARGs_OAP/bin/bbmap/current/align2/QualityTools.java
ARGs_OAP/bin/bbmap/current/align2/RandomReads3$1.class
ARGs_OAP/bin/bbmap/current/align2/RandomReads3.class
ARGs_OAP/bin/bbmap/current/align2/RandomReads3.java
ARGs_OAP/bin/bbmap/current/align2/RefToIndex.class
ARGs_OAP/bin/bbmap/current/align2/RefToIndex.java
ARGs_OAP/bin/bbmap/current/align2/ReformatBatchOutput.class
ARGs_OAP/bin/bbmap/current/align2/ReformatBatchOutput.java
ARGs_OAP/bin/bbmap/current/align2/ReformatBatchOutput2.class
ARGs_OAP/bin/bbmap/current/align2/ReformatBatchOutput2.java
ARGs_OAP/bin/bbmap/current/align2/Solver.class
ARGs_OAP/bin/bbmap/current/align2/Solver.java
ARGs_OAP/bin/bbmap/current/align2/SplitMappedReads.class
ARGs_OAP/bin/bbmap/current/align2/SplitMappedReads.java
ARGs_OAP/bin/bbmap/current/align2/TranslateColorspaceRead.class
ARGs_OAP/bin/bbmap/current/align2/TranslateColorspaceRead.java
ARGs_OAP/bin/bbmap/current/aligner/Aligner.class
ARGs_OAP/bin/bbmap/current/aligner/Aligner.java
ARGs_OAP/bin/bbmap/current/aligner/Alignment.class
ARGs_OAP/bin/bbmap/current/aligner/Alignment.java
ARGs_OAP/bin/bbmap/current/aligner/AlignmentResult.class
ARGs_OAP/bin/bbmap/current/aligner/AlignmentResult.java
ARGs_OAP/bin/bbmap/current/aligner/AllToAll$ProcessThread.class
ARGs_OAP/bin/bbmap/current/aligner/AllToAll.class
ARGs_OAP/bin/bbmap/current/aligner/AllToAll.java
ARGs_OAP/bin/bbmap/current/aligner/FlatAligner.class
ARGs_OAP/bin/bbmap/current/aligner/FlatAligner.java
ARGs_OAP/bin/bbmap/current/aligner/MultiStateAligner9PacBioAdapter.class
ARGs_OAP/bin/bbmap/current/aligner/MultiStateAligner9PacBioAdapter.java
ARGs_OAP/bin/bbmap/current/aligner/MultiStateAligner9PacBioAdapter2.class
ARGs_OAP/bin/bbmap/current/aligner/MultiStateAligner9PacBioAdapter2.java
ARGs_OAP/bin/bbmap/current/aligner/MultiStateAligner9PacBioAdapter3.class
ARGs_OAP/bin/bbmap/current/aligner/MultiStateAligner9PacBioAdapter3.java
ARGs_OAP/bin/bbmap/current/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.class
ARGs_OAP/bin/bbmap/current/aligner/MultiStateAligner9PacBioAdapter_WithBarriers.java
ARGs_OAP/bin/bbmap/current/aligner/SingleStateAlignerFlat.class
ARGs_OAP/bin/bbmap/current/aligner/SingleStateAlignerFlat.java
ARGs_OAP/bin/bbmap/current/aligner/SingleStateAlignerFlat2.class
ARGs_OAP/bin/bbmap/current/aligner/SingleStateAlignerFlat2.java
ARGs_OAP/bin/bbmap/current/aligner/SingleStateAlignerFlat2Amino.class
ARGs_OAP/bin/bbmap/current/aligner/SingleStateAlignerFlat2Amino.java
ARGs_OAP/bin/bbmap/current/aligner/SingleStateAlignerFlat2_1D.class
ARGs_OAP/bin/bbmap/current/aligner/SingleStateAlignerFlat2_1D.java
ARGs_OAP/bin/bbmap/current/aligner/SingleStateAlignerFlat3.class
ARGs_OAP/bin/bbmap/current/aligner/SingleStateAlignerFlat3.java
ARGs_OAP/bin/bbmap/current/aligner/SingleStateAlignerFlatFloat.class
ARGs_OAP/bin/bbmap/current/aligner/SingleStateAlignerFlatFloat.java
ARGs_OAP/bin/bbmap/current/aligner/SingleStateAlignerPacBioAdapter.class
ARGs_OAP/bin/bbmap/current/aligner/SingleStateAlignerPacBioAdapter.java
ARGs_OAP/bin/bbmap/current/assemble/AbstractBuildThread.class
ARGs_OAP/bin/bbmap/current/assemble/AbstractBuildThread.java
ARGs_OAP/bin/bbmap/current/assemble/AbstractExploreThread.class
ARGs_OAP/bin/bbmap/current/assemble/AbstractExploreThread.java
ARGs_OAP/bin/bbmap/current/assemble/AbstractProcessContigThread.class
ARGs_OAP/bin/bbmap/current/assemble/AbstractProcessContigThread.java
ARGs_OAP/bin/bbmap/current/assemble/AbstractRemoveThread$RemoveThread1.class
ARGs_OAP/bin/bbmap/current/assemble/AbstractRemoveThread$RemoveThread2.class
ARGs_OAP/bin/bbmap/current/assemble/AbstractRemoveThread.class
ARGs_OAP/bin/bbmap/current/assemble/AbstractRemoveThread.java
ARGs_OAP/bin/bbmap/current/assemble/AbstractShaveThread.class
ARGs_OAP/bin/bbmap/current/assemble/AbstractShaveThread.java
ARGs_OAP/bin/bbmap/current/assemble/BubblePopper.class
ARGs_OAP/bin/bbmap/current/assemble/BubblePopper.java
ARGs_OAP/bin/bbmap/current/assemble/Contig.class
ARGs_OAP/bin/bbmap/current/assemble/Contig.java
ARGs_OAP/bin/bbmap/current/assemble/Edge.class
ARGs_OAP/bin/bbmap/current/assemble/Edge.java
ARGs_OAP/bin/bbmap/current/assemble/ErrorTracker.class
ARGs_OAP/bin/bbmap/current/assemble/ErrorTracker.java
ARGs_OAP/bin/bbmap/current/assemble/KmerCompressor$BuildThread.class
ARGs_OAP/bin/bbmap/current/assemble/KmerCompressor.class
ARGs_OAP/bin/bbmap/current/assemble/KmerCompressor.java
ARGs_OAP/bin/bbmap/current/assemble/Postfilter.class
ARGs_OAP/bin/bbmap/current/assemble/Postfilter.java
ARGs_OAP/bin/bbmap/current/assemble/Rollback.class
ARGs_OAP/bin/bbmap/current/assemble/Rollback.java
ARGs_OAP/bin/bbmap/current/assemble/ShaveObject.class
ARGs_OAP/bin/bbmap/current/assemble/ShaveObject.java
ARGs_OAP/bin/bbmap/current/assemble/Shaver.class
ARGs_OAP/bin/bbmap/current/assemble/Shaver.java
ARGs_OAP/bin/bbmap/current/assemble/Shaver1$ExploreThread.class
ARGs_OAP/bin/bbmap/current/assemble/Shaver1$ShaveThread.class
ARGs_OAP/bin/bbmap/current/assemble/Shaver1.class
ARGs_OAP/bin/bbmap/current/assemble/Shaver1.java
ARGs_OAP/bin/bbmap/current/assemble/Shaver2$ExploreThread.class
ARGs_OAP/bin/bbmap/current/assemble/Shaver2$ShaveThread.class
ARGs_OAP/bin/bbmap/current/assemble/Shaver2.class
ARGs_OAP/bin/bbmap/current/assemble/Shaver2.java
ARGs_OAP/bin/bbmap/current/assemble/TadPipe.class
ARGs_OAP/bin/bbmap/current/assemble/TadPipe.java
ARGs_OAP/bin/bbmap/current/assemble/Tadpole$DumpKmersThread.class
ARGs_OAP/bin/bbmap/current/assemble/Tadpole$ExtendThread.class
ARGs_OAP/bin/bbmap/current/assemble/Tadpole$MakeKhistThread.class
ARGs_OAP/bin/bbmap/current/assemble/Tadpole.class
ARGs_OAP/bin/bbmap/current/assemble/Tadpole.java
ARGs_OAP/bin/bbmap/current/assemble/Tadpole1$BuildThread.class
ARGs_OAP/bin/bbmap/current/assemble/Tadpole1$ProcessContigThread.class
ARGs_OAP/bin/bbmap/current/assemble/Tadpole1.class
ARGs_OAP/bin/bbmap/current/assemble/Tadpole1.java
ARGs_OAP/bin/bbmap/current/assemble/Tadpole2$BuildThread.class
ARGs_OAP/bin/bbmap/current/assemble/Tadpole2$ProcessContigThread.class
ARGs_OAP/bin/bbmap/current/assemble/Tadpole2.class
ARGs_OAP/bin/bbmap/current/assemble/Tadpole2.java
ARGs_OAP/bin/bbmap/current/assemble/TadpoleWrapper$1.class
ARGs_OAP/bin/bbmap/current/assemble/TadpoleWrapper$Record.class
ARGs_OAP/bin/bbmap/current/assemble/TadpoleWrapper.class
ARGs_OAP/bin/bbmap/current/assemble/TadpoleWrapper.java
ARGs_OAP/bin/bbmap/current/bloom/BloomFilter.class
ARGs_OAP/bin/bbmap/current/bloom/BloomFilter.java
ARGs_OAP/bin/bbmap/current/bloom/BloomFilterCorrector.class
ARGs_OAP/bin/bbmap/current/bloom/BloomFilterCorrector.java
ARGs_OAP/bin/bbmap/current/bloom/BloomFilterCorrectorWrapper$ProcessThread.class
ARGs_OAP/bin/bbmap/current/bloom/BloomFilterCorrectorWrapper.class
ARGs_OAP/bin/bbmap/current/bloom/BloomFilterCorrectorWrapper.java
ARGs_OAP/bin/bbmap/current/bloom/BloomFilterWrapper$ProcessThread.class
ARGs_OAP/bin/bbmap/current/bloom/BloomFilterWrapper.class
ARGs_OAP/bin/bbmap/current/bloom/BloomFilterWrapper.java
ARGs_OAP/bin/bbmap/current/bloom/ErrorCorrect$1.class
ARGs_OAP/bin/bbmap/current/bloom/ErrorCorrect.class
ARGs_OAP/bin/bbmap/current/bloom/ErrorCorrect.java
ARGs_OAP/bin/bbmap/current/bloom/KCountArray$AllocThread.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray.java
ARGs_OAP/bin/bbmap/current/bloom/KCountArray2.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray2.java
ARGs_OAP/bin/bbmap/current/bloom/KCountArray3.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray3.java
ARGs_OAP/bin/bbmap/current/bloom/KCountArray4.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray4.java
ARGs_OAP/bin/bbmap/current/bloom/KCountArray4MT$WriteThread.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray4MT.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray4MT.java
ARGs_OAP/bin/bbmap/current/bloom/KCountArray5MT$WriteThread.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray5MT.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray5MT.java
ARGs_OAP/bin/bbmap/current/bloom/KCountArray6MT$WriteThread.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray6MT.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray6MT.java
ARGs_OAP/bin/bbmap/current/bloom/KCountArray7MT$WriteThread.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray7MT.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray7MT.java
ARGs_OAP/bin/bbmap/current/bloom/KCountArray7MTA$CountUsedThread.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray7MTA.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray7MTA.java
ARGs_OAP/bin/bbmap/current/bloom/KCountArray8MT$WriteThread.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray8MT.class
ARGs_OAP/bin/bbmap/current/bloom/KCountArray8MT.java
ARGs_OAP/bin/bbmap/current/bloom/KmerCount3.class
ARGs_OAP/bin/bbmap/current/bloom/KmerCount3.java
ARGs_OAP/bin/bbmap/current/bloom/KmerCount4.class
ARGs_OAP/bin/bbmap/current/bloom/KmerCount4.java
ARGs_OAP/bin/bbmap/current/bloom/KmerCount5.class
ARGs_OAP/bin/bbmap/current/bloom/KmerCount5.java
ARGs_OAP/bin/bbmap/current/bloom/KmerCount6.class
ARGs_OAP/bin/bbmap/current/bloom/KmerCount6.java
ARGs_OAP/bin/bbmap/current/bloom/KmerCount6MT$CountThread.class
ARGs_OAP/bin/bbmap/current/bloom/KmerCount6MT.class
ARGs_OAP/bin/bbmap/current/bloom/KmerCount6MT.java
ARGs_OAP/bin/bbmap/current/bloom/KmerCount7MT$CountThread.class
ARGs_OAP/bin/bbmap/current/bloom/KmerCount7MT.class
ARGs_OAP/bin/bbmap/current/bloom/KmerCount7MT.java
ARGs_OAP/bin/bbmap/current/bloom/KmerCount7MTA$1.class
ARGs_OAP/bin/bbmap/current/bloom/KmerCount7MTA$CountThread.class
ARGs_OAP/bin/bbmap/current/bloom/KmerCount7MTA$CountThread2.class
ARGs_OAP/bin/bbmap/current/bloom/KmerCount7MTA.class
ARGs_OAP/bin/bbmap/current/bloom/KmerCount7MTA.java
ARGs_OAP/bin/bbmap/current/bloom/KmerCountAbstract.class
ARGs_OAP/bin/bbmap/current/bloom/KmerCountAbstract.java
ARGs_OAP/bin/bbmap/current/bloom/LargeKmerCount.class
ARGs_OAP/bin/bbmap/current/bloom/LargeKmerCount.java
ARGs_OAP/bin/bbmap/current/bloom/LargeKmerCount2.class
ARGs_OAP/bin/bbmap/current/bloom/LargeKmerCount2.java
ARGs_OAP/bin/bbmap/current/bloom/TestLargeKmer.class
ARGs_OAP/bin/bbmap/current/bloom/TestLargeKmer.java
ARGs_OAP/bin/bbmap/current/cardinality/BBLog.class
ARGs_OAP/bin/bbmap/current/cardinality/BBLog.java
ARGs_OAP/bin/bbmap/current/cardinality/BBLog_simple.class
ARGs_OAP/bin/bbmap/current/cardinality/BBLog_simple.java
ARGs_OAP/bin/bbmap/current/cardinality/CardinalityTracker.class
ARGs_OAP/bin/bbmap/current/cardinality/CardinalityTracker.java
ARGs_OAP/bin/bbmap/current/cardinality/LogLog.class
ARGs_OAP/bin/bbmap/current/cardinality/LogLog.java
ARGs_OAP/bin/bbmap/current/cardinality/LogLog16.class
ARGs_OAP/bin/bbmap/current/cardinality/LogLog16.java
ARGs_OAP/bin/bbmap/current/cardinality/LogLog2.class
ARGs_OAP/bin/bbmap/current/cardinality/LogLog2.java
ARGs_OAP/bin/bbmap/current/cardinality/LogLog8.class
ARGs_OAP/bin/bbmap/current/cardinality/LogLog8.java
ARGs_OAP/bin/bbmap/current/cardinality/LogLog8_simple.class
ARGs_OAP/bin/bbmap/current/cardinality/LogLog8_simple.java
ARGs_OAP/bin/bbmap/current/cardinality/LogLogWrapper$LogLogThread.class
ARGs_OAP/bin/bbmap/current/cardinality/LogLogWrapper.class
ARGs_OAP/bin/bbmap/current/cardinality/LogLogWrapper.java
ARGs_OAP/bin/bbmap/current/cardinality/LogLog_old$LogLogWrapper$LogLogThread.class
ARGs_OAP/bin/bbmap/current/cardinality/LogLog_old$LogLogWrapper.class
ARGs_OAP/bin/bbmap/current/cardinality/LogLog_old.class
ARGs_OAP/bin/bbmap/current/cardinality/LogLog_old.java
ARGs_OAP/bin/bbmap/current/cardinality/MultiLogLog.class
ARGs_OAP/bin/bbmap/current/cardinality/MultiLogLog.java
ARGs_OAP/bin/bbmap/current/clump/Clump.class
ARGs_OAP/bin/bbmap/current/clump/Clump.java
ARGs_OAP/bin/bbmap/current/clump/ClumpList$ClumpThread.class
ARGs_OAP/bin/bbmap/current/clump/ClumpList$ProcessThread.class
ARGs_OAP/bin/bbmap/current/clump/ClumpList.class
ARGs_OAP/bin/bbmap/current/clump/ClumpList.java
ARGs_OAP/bin/bbmap/current/clump/ClumpTools.class
ARGs_OAP/bin/bbmap/current/clump/ClumpTools.java
ARGs_OAP/bin/bbmap/current/clump/Clumpify.class
ARGs_OAP/bin/bbmap/current/clump/Clumpify.java
ARGs_OAP/bin/bbmap/current/clump/KmerComparator$HashThread.class
ARGs_OAP/bin/bbmap/current/clump/KmerComparator.class
ARGs_OAP/bin/bbmap/current/clump/KmerComparator.java
ARGs_OAP/bin/bbmap/current/clump/KmerComparator2.class
ARGs_OAP/bin/bbmap/current/clump/KmerComparator2.java
ARGs_OAP/bin/bbmap/current/clump/KmerComparatorX.class
ARGs_OAP/bin/bbmap/current/clump/KmerComparatorX.java
ARGs_OAP/bin/bbmap/current/clump/KmerComparatorY.class
ARGs_OAP/bin/bbmap/current/clump/KmerComparatorY.java
ARGs_OAP/bin/bbmap/current/clump/KmerReduce$HashThread.class
ARGs_OAP/bin/bbmap/current/clump/KmerReduce.class
ARGs_OAP/bin/bbmap/current/clump/KmerReduce.java
ARGs_OAP/bin/bbmap/current/clump/KmerSort$FetchThread1.class
ARGs_OAP/bin/bbmap/current/clump/KmerSort$HashSplitThread.class
ARGs_OAP/bin/bbmap/current/clump/KmerSort.class
ARGs_OAP/bin/bbmap/current/clump/KmerSort.java
ARGs_OAP/bin/bbmap/current/clump/KmerSort1.class
ARGs_OAP/bin/bbmap/current/clump/KmerSort1.java
ARGs_OAP/bin/bbmap/current/clump/KmerSort2.class
ARGs_OAP/bin/bbmap/current/clump/KmerSort2.java
ARGs_OAP/bin/bbmap/current/clump/KmerSort3$FetchThread3$FetchSubThread.class
ARGs_OAP/bin/bbmap/current/clump/KmerSort3$FetchThread3.class
ARGs_OAP/bin/bbmap/current/clump/KmerSort3.class
ARGs_OAP/bin/bbmap/current/clump/KmerSort3.java
ARGs_OAP/bin/bbmap/current/clump/KmerSplit$HashThread.class
ARGs_OAP/bin/bbmap/current/clump/KmerSplit.class
ARGs_OAP/bin/bbmap/current/clump/KmerSplit.java
ARGs_OAP/bin/bbmap/current/clump/PivotSet$HashThread.class
ARGs_OAP/bin/bbmap/current/clump/PivotSet.class
ARGs_OAP/bin/bbmap/current/clump/PivotSet.java
ARGs_OAP/bin/bbmap/current/clump/ReadKey.class
ARGs_OAP/bin/bbmap/current/clump/ReadKey.java
ARGs_OAP/bin/bbmap/current/clump/Splitter.class
ARGs_OAP/bin/bbmap/current/clump/Splitter.java
ARGs_OAP/bin/bbmap/current/clump/StreamToOutput.class
ARGs_OAP/bin/bbmap/current/clump/StreamToOutput.java
ARGs_OAP/bin/bbmap/current/cluster/Cluster.class
ARGs_OAP/bin/bbmap/current/cluster/Cluster.java
ARGs_OAP/bin/bbmap/current/cluster/ClusterTools.class
ARGs_OAP/bin/bbmap/current/cluster/ClusterTools.java
ARGs_OAP/bin/bbmap/current/cluster/MergeReadHeaders.class
ARGs_OAP/bin/bbmap/current/cluster/MergeReadHeaders.java
ARGs_OAP/bin/bbmap/current/cluster/ReadTag.class
ARGs_OAP/bin/bbmap/current/cluster/ReadTag.java
ARGs_OAP/bin/bbmap/current/cluster/ReclusterByKmer$ClusterThread.class
ARGs_OAP/bin/bbmap/current/cluster/ReclusterByKmer.class
ARGs_OAP/bin/bbmap/current/cluster/ReclusterByKmer.java
ARGs_OAP/bin/bbmap/current/consensus/BaseGraph.class
ARGs_OAP/bin/bbmap/current/consensus/BaseGraph.java
ARGs_OAP/bin/bbmap/current/consensus/BaseGraphPart.class
ARGs_OAP/bin/bbmap/current/consensus/BaseGraphPart.java
ARGs_OAP/bin/bbmap/current/consensus/BaseNode.class
ARGs_OAP/bin/bbmap/current/consensus/BaseNode.java
ARGs_OAP/bin/bbmap/current/consensus/ConsensusMaker$ProcessThread.class
ARGs_OAP/bin/bbmap/current/consensus/ConsensusMaker.class
ARGs_OAP/bin/bbmap/current/consensus/ConsensusMaker.java
ARGs_OAP/bin/bbmap/current/consensus/ConsensusObject.class
ARGs_OAP/bin/bbmap/current/consensus/ConsensusObject.java
ARGs_OAP/bin/bbmap/current/consensus/FixScaffoldGaps$ProcessThread.class
ARGs_OAP/bin/bbmap/current/consensus/FixScaffoldGaps$Scaffold.class
ARGs_OAP/bin/bbmap/current/consensus/FixScaffoldGaps.class
ARGs_OAP/bin/bbmap/current/consensus/FixScaffoldGaps.java
ARGs_OAP/bin/bbmap/current/consensus/Lilypad$Contig.class
ARGs_OAP/bin/bbmap/current/consensus/Lilypad$Edge.class
ARGs_OAP/bin/bbmap/current/consensus/Lilypad$ProcessThread.class
ARGs_OAP/bin/bbmap/current/consensus/Lilypad.class
ARGs_OAP/bin/bbmap/current/consensus/Lilypad.java
ARGs_OAP/bin/bbmap/current/covid/SummarizeCoverage.class
ARGs_OAP/bin/bbmap/current/covid/SummarizeCoverage.java
ARGs_OAP/bin/bbmap/current/dna/AminoAcid.class
ARGs_OAP/bin/bbmap/current/dna/AminoAcid.java
ARGs_OAP/bin/bbmap/current/dna/ChromArrayMaker.class
ARGs_OAP/bin/bbmap/current/dna/ChromArrayMaker.java
ARGs_OAP/bin/bbmap/current/dna/ChromToFasta$1.class
ARGs_OAP/bin/bbmap/current/dna/ChromToFasta.class
ARGs_OAP/bin/bbmap/current/dna/ChromToFasta.java
ARGs_OAP/bin/bbmap/current/dna/ChromosomeArray.class
ARGs_OAP/bin/bbmap/current/dna/ChromosomeArray.java
ARGs_OAP/bin/bbmap/current/dna/Data.class
ARGs_OAP/bin/bbmap/current/dna/Data.java
ARGs_OAP/bin/bbmap/current/dna/Exon.class
ARGs_OAP/bin/bbmap/current/dna/Exon.java
ARGs_OAP/bin/bbmap/current/dna/FastaToChromArrays2$1.class
ARGs_OAP/bin/bbmap/current/dna/FastaToChromArrays2.class
ARGs_OAP/bin/bbmap/current/dna/FastaToChromArrays2.java
ARGs_OAP/bin/bbmap/current/dna/Gene.class
ARGs_OAP/bin/bbmap/current/dna/Gene.java
ARGs_OAP/bin/bbmap/current/dna/GeneSet.class
ARGs_OAP/bin/bbmap/current/dna/GeneSet.java
ARGs_OAP/bin/bbmap/current/dna/Matrix.class
ARGs_OAP/bin/bbmap/current/dna/Matrix.java
ARGs_OAP/bin/bbmap/current/dna/Motif.class
ARGs_OAP/bin/bbmap/current/dna/Motif.java
ARGs_OAP/bin/bbmap/current/dna/MotifMulti.class
ARGs_OAP/bin/bbmap/current/dna/MotifMulti.java
ARGs_OAP/bin/bbmap/current/dna/MotifProbsN.class
ARGs_OAP/bin/bbmap/current/dna/MotifProbsN.java
ARGs_OAP/bin/bbmap/current/dna/MotifSimple.class
ARGs_OAP/bin/bbmap/current/dna/MotifSimple.java
ARGs_OAP/bin/bbmap/current/dna/ScafLoc.class
ARGs_OAP/bin/bbmap/current/dna/ScafLoc.java
ARGs_OAP/bin/bbmap/current/dna/Scaffold.class
ARGs_OAP/bin/bbmap/current/dna/Scaffold.java
ARGs_OAP/bin/bbmap/current/driver/BBVersion.class
ARGs_OAP/bin/bbmap/current/driver/BBVersion.java
ARGs_OAP/bin/bbmap/current/driver/ClearRam.class
ARGs_OAP/bin/bbmap/current/driver/ClearRam.java
ARGs_OAP/bin/bbmap/current/driver/CollateSpikeIn.class
ARGs_OAP/bin/bbmap/current/driver/CollateSpikeIn.java
ARGs_OAP/bin/bbmap/current/driver/CompareReferenceGenomes.class
ARGs_OAP/bin/bbmap/current/driver/CompareReferenceGenomes.java
ARGs_OAP/bin/bbmap/current/driver/CompareSequences.class
ARGs_OAP/bin/bbmap/current/driver/CompareSequences.java
ARGs_OAP/bin/bbmap/current/driver/ConcatenateFiles.class
ARGs_OAP/bin/bbmap/current/driver/ConcatenateFiles.java
ARGs_OAP/bin/bbmap/current/driver/ConcatenateTextFiles$1.class
ARGs_OAP/bin/bbmap/current/driver/ConcatenateTextFiles$WriteThread.class
ARGs_OAP/bin/bbmap/current/driver/ConcatenateTextFiles.class
ARGs_OAP/bin/bbmap/current/driver/ConcatenateTextFiles.java
ARGs_OAP/bin/bbmap/current/driver/Concatenator.class
ARGs_OAP/bin/bbmap/current/driver/Concatenator.java
ARGs_OAP/bin/bbmap/current/driver/ConvertSamToAln.class
ARGs_OAP/bin/bbmap/current/driver/ConvertSamToAln.java
ARGs_OAP/bin/bbmap/current/driver/CorrelateIdentity.class
ARGs_OAP/bin/bbmap/current/driver/CorrelateIdentity.java
ARGs_OAP/bin/bbmap/current/driver/CountRNAs.class
ARGs_OAP/bin/bbmap/current/driver/CountRNAs.java
ARGs_OAP/bin/bbmap/current/driver/CountSharedLines.class
ARGs_OAP/bin/bbmap/current/driver/CountSharedLines.java
ARGs_OAP/bin/bbmap/current/driver/EstherFilter.class
ARGs_OAP/bin/bbmap/current/driver/EstherFilter.java
ARGs_OAP/bin/bbmap/current/driver/FilterAssemblySummary.class
ARGs_OAP/bin/bbmap/current/driver/FilterAssemblySummary.java
ARGs_OAP/bin/bbmap/current/driver/FilterLines.class
ARGs_OAP/bin/bbmap/current/driver/FilterLines.java
ARGs_OAP/bin/bbmap/current/driver/FilterReadsByName.class
ARGs_OAP/bin/bbmap/current/driver/FilterReadsByName.java
ARGs_OAP/bin/bbmap/current/driver/FindMotifs.class
ARGs_OAP/bin/bbmap/current/driver/FindMotifs.java
ARGs_OAP/bin/bbmap/current/driver/FixChr.class
ARGs_OAP/bin/bbmap/current/driver/FixChr.java
ARGs_OAP/bin/bbmap/current/driver/FixDumbFile.class
ARGs_OAP/bin/bbmap/current/driver/FixDumbFile.java
ARGs_OAP/bin/bbmap/current/driver/GenerateNoCallsFromCoverage.class
ARGs_OAP/bin/bbmap/current/driver/GenerateNoCallsFromCoverage.java
ARGs_OAP/bin/bbmap/current/driver/GetSequence.class
ARGs_OAP/bin/bbmap/current/driver/GetSequence.java
ARGs_OAP/bin/bbmap/current/driver/GetUniquePrefixes.class
ARGs_OAP/bin/bbmap/current/driver/GetUniquePrefixes.java
ARGs_OAP/bin/bbmap/current/driver/Grep.class
ARGs_OAP/bin/bbmap/current/driver/Grep.java
ARGs_OAP/bin/bbmap/current/driver/Life.class
ARGs_OAP/bin/bbmap/current/driver/Life.java
ARGs_OAP/bin/bbmap/current/driver/LineCount.class
ARGs_OAP/bin/bbmap/current/driver/LineCount.java
ARGs_OAP/bin/bbmap/current/driver/LoadReads.class
ARGs_OAP/bin/bbmap/current/driver/LoadReads.java
ARGs_OAP/bin/bbmap/current/driver/LookAtID.class
ARGs_OAP/bin/bbmap/current/driver/LookAtID.java
ARGs_OAP/bin/bbmap/current/driver/MakeTestScript.class
ARGs_OAP/bin/bbmap/current/driver/MakeTestScript.java
ARGs_OAP/bin/bbmap/current/driver/MakeTestScriptScoreOnly.class
ARGs_OAP/bin/bbmap/current/driver/MakeTestScriptScoreOnly.java
ARGs_OAP/bin/bbmap/current/driver/MeasureGene.class
ARGs_OAP/bin/bbmap/current/driver/MeasureGene.java
ARGs_OAP/bin/bbmap/current/driver/MergeBigelow.class
ARGs_OAP/bin/bbmap/current/driver/MergeBigelow.java
ARGs_OAP/bin/bbmap/current/driver/MergeCoverageOTU.class
ARGs_OAP/bin/bbmap/current/driver/MergeCoverageOTU.java
ARGs_OAP/bin/bbmap/current/driver/MergeTextFiles.class
ARGs_OAP/bin/bbmap/current/driver/MergeTextFiles.java
ARGs_OAP/bin/bbmap/current/driver/MergeTextFiles2.class
ARGs_OAP/bin/bbmap/current/driver/MergeTextFiles2.java
ARGs_OAP/bin/bbmap/current/driver/MoveFiles.class
ARGs_OAP/bin/bbmap/current/driver/MoveFiles.java
ARGs_OAP/bin/bbmap/current/driver/ParseCrossblockResults$ResultsLine.class
ARGs_OAP/bin/bbmap/current/driver/ParseCrossblockResults.class
ARGs_OAP/bin/bbmap/current/driver/ParseCrossblockResults.java
ARGs_OAP/bin/bbmap/current/driver/PlotGC.class
ARGs_OAP/bin/bbmap/current/driver/PlotGC.java
ARGs_OAP/bin/bbmap/current/driver/PrintEnv.class
ARGs_OAP/bin/bbmap/current/driver/PrintEnv.java
ARGs_OAP/bin/bbmap/current/driver/ProcessFragMerging.class
ARGs_OAP/bin/bbmap/current/driver/ProcessFragMerging.java
ARGs_OAP/bin/bbmap/current/driver/ProcessSpeed.class
ARGs_OAP/bin/bbmap/current/driver/ProcessSpeed.java
ARGs_OAP/bin/bbmap/current/driver/ProcessSpeed2.class
ARGs_OAP/bin/bbmap/current/driver/ProcessSpeed2.java
ARGs_OAP/bin/bbmap/current/driver/ProcessWebcheck.class
ARGs_OAP/bin/bbmap/current/driver/ProcessWebcheck.java
ARGs_OAP/bin/bbmap/current/driver/ReduceSilva.class
ARGs_OAP/bin/bbmap/current/driver/ReduceSilva.java
ARGs_OAP/bin/bbmap/current/driver/RenameAndMux$MuxThread.class
ARGs_OAP/bin/bbmap/current/driver/RenameAndMux.class
ARGs_OAP/bin/bbmap/current/driver/RenameAndMux.java
ARGs_OAP/bin/bbmap/current/driver/RenameByHeader.class
ARGs_OAP/bin/bbmap/current/driver/RenameByHeader.java
ARGs_OAP/bin/bbmap/current/driver/RenameNcbiToTid.class
ARGs_OAP/bin/bbmap/current/driver/RenameNcbiToTid.java
ARGs_OAP/bin/bbmap/current/driver/RenameRefseqFiles.class
ARGs_OAP/bin/bbmap/current/driver/RenameRefseqFiles.java
ARGs_OAP/bin/bbmap/current/driver/Sample.class
ARGs_OAP/bin/bbmap/current/driver/Sample.java
ARGs_OAP/bin/bbmap/current/driver/Search.class
ARGs_OAP/bin/bbmap/current/driver/Search.java
ARGs_OAP/bin/bbmap/current/driver/SelectReads.class
ARGs_OAP/bin/bbmap/current/driver/SelectReads.java
ARGs_OAP/bin/bbmap/current/driver/SniffSplices.class
ARGs_OAP/bin/bbmap/current/driver/SniffSplices.java
ARGs_OAP/bin/bbmap/current/driver/SummarizeContamReport$ComparatorA.class
ARGs_OAP/bin/bbmap/current/driver/SummarizeContamReport$ComparatorB.class
ARGs_OAP/bin/bbmap/current/driver/SummarizeContamReport$StringLongLong.class
ARGs_OAP/bin/bbmap/current/driver/SummarizeContamReport.class
ARGs_OAP/bin/bbmap/current/driver/SummarizeContamReport.java
ARGs_OAP/bin/bbmap/current/driver/SummarizeCoverage.class
ARGs_OAP/bin/bbmap/current/driver/SummarizeCoverage.java
ARGs_OAP/bin/bbmap/current/driver/SummarizeCrossblock.class
ARGs_OAP/bin/bbmap/current/driver/SummarizeCrossblock.java
ARGs_OAP/bin/bbmap/current/driver/SummarizeMSDIN.class
ARGs_OAP/bin/bbmap/current/driver/SummarizeMSDIN.java
ARGs_OAP/bin/bbmap/current/driver/SummarizeQuast$Entry.class
ARGs_OAP/bin/bbmap/current/driver/SummarizeQuast$QuastSummary.class
ARGs_OAP/bin/bbmap/current/driver/SummarizeQuast.class
ARGs_OAP/bin/bbmap/current/driver/SummarizeQuast.java
ARGs_OAP/bin/bbmap/current/driver/SummarizeSealStats$SealSummary.class
ARGs_OAP/bin/bbmap/current/driver/SummarizeSealStats.class
ARGs_OAP/bin/bbmap/current/driver/SummarizeSealStats.java
ARGs_OAP/bin/bbmap/current/driver/TestCompressionSpeed.class
ARGs_OAP/bin/bbmap/current/driver/TestCompressionSpeed.java
ARGs_OAP/bin/bbmap/current/driver/TestLockSpeed$1.class
ARGs_OAP/bin/bbmap/current/driver/TestLockSpeed$AtomBox.class
ARGs_OAP/bin/bbmap/current/driver/TestLockSpeed$CountBox.class
ARGs_OAP/bin/bbmap/current/driver/TestLockSpeed$CountThread.class
ARGs_OAP/bin/bbmap/current/driver/TestLockSpeed$LockBox.class
ARGs_OAP/bin/bbmap/current/driver/TestLockSpeed$VolatileBox.class
ARGs_OAP/bin/bbmap/current/driver/TestLockSpeed.class
ARGs_OAP/bin/bbmap/current/driver/TestLockSpeed.java
ARGs_OAP/bin/bbmap/current/driver/Translator.class
ARGs_OAP/bin/bbmap/current/driver/Translator.java
ARGs_OAP/bin/bbmap/current/driver/Translator2.class
ARGs_OAP/bin/bbmap/current/driver/Translator2.java
ARGs_OAP/bin/bbmap/current/driver/TransposeTextFile.class
ARGs_OAP/bin/bbmap/current/driver/TransposeTextFile.java
ARGs_OAP/bin/bbmap/current/driver/TrimSamFile.class
ARGs_OAP/bin/bbmap/current/driver/TrimSamFile.java
ARGs_OAP/bin/bbmap/current/fileIO/ArrayFile.class
ARGs_OAP/bin/bbmap/current/fileIO/ArrayFile.java
ARGs_OAP/bin/bbmap/current/fileIO/ByteFile.class
ARGs_OAP/bin/bbmap/current/fileIO/ByteFile.java
ARGs_OAP/bin/bbmap/current/fileIO/ByteFile1.class
ARGs_OAP/bin/bbmap/current/fileIO/ByteFile1.java
ARGs_OAP/bin/bbmap/current/fileIO/ByteFile2$BF1Thread.class
ARGs_OAP/bin/bbmap/current/fileIO/ByteFile2.class
ARGs_OAP/bin/bbmap/current/fileIO/ByteFile2.java
ARGs_OAP/bin/bbmap/current/fileIO/ByteStreamWriter.class
ARGs_OAP/bin/bbmap/current/fileIO/ByteStreamWriter.java
ARGs_OAP/bin/bbmap/current/fileIO/ChainBlock.class
ARGs_OAP/bin/bbmap/current/fileIO/ChainBlock.java
ARGs_OAP/bin/bbmap/current/fileIO/ChainLine.class
ARGs_OAP/bin/bbmap/current/fileIO/ChainLine.java
ARGs_OAP/bin/bbmap/current/fileIO/CompressFiles.class
ARGs_OAP/bin/bbmap/current/fileIO/CompressFiles.java
ARGs_OAP/bin/bbmap/current/fileIO/CopyFile$1.class
ARGs_OAP/bin/bbmap/current/fileIO/CopyFile.class
ARGs_OAP/bin/bbmap/current/fileIO/CopyFile.java
ARGs_OAP/bin/bbmap/current/fileIO/CopyFiles.class
ARGs_OAP/bin/bbmap/current/fileIO/CopyFiles.java
ARGs_OAP/bin/bbmap/current/fileIO/CopyFiles2.class
ARGs_OAP/bin/bbmap/current/fileIO/CopyFiles2.java
ARGs_OAP/bin/bbmap/current/fileIO/FileFormat.class
ARGs_OAP/bin/bbmap/current/fileIO/FileFormat.java
ARGs_OAP/bin/bbmap/current/fileIO/FindFiles.class
ARGs_OAP/bin/bbmap/current/fileIO/FindFiles.java
ARGs_OAP/bin/bbmap/current/fileIO/GenericTextFile.class
ARGs_OAP/bin/bbmap/current/fileIO/GenericTextFile.java
ARGs_OAP/bin/bbmap/current/fileIO/LoadThread.class
ARGs_OAP/bin/bbmap/current/fileIO/LoadThread.java
ARGs_OAP/bin/bbmap/current/fileIO/MatrixFile.class
ARGs_OAP/bin/bbmap/current/fileIO/MatrixFile.java
ARGs_OAP/bin/bbmap/current/fileIO/OpenFile.class
ARGs_OAP/bin/bbmap/current/fileIO/OpenFile.java
ARGs_OAP/bin/bbmap/current/fileIO/PipeThread.class
ARGs_OAP/bin/bbmap/current/fileIO/PipeThread.java
ARGs_OAP/bin/bbmap/current/fileIO/QuickFile.class
ARGs_OAP/bin/bbmap/current/fileIO/QuickFile.java
ARGs_OAP/bin/bbmap/current/fileIO/ReadWrite$1.class
ARGs_OAP/bin/bbmap/current/fileIO/ReadWrite$WriteObjectThread.class
ARGs_OAP/bin/bbmap/current/fileIO/ReadWrite$WriteStringThread.class
ARGs_OAP/bin/bbmap/current/fileIO/ReadWrite.class
ARGs_OAP/bin/bbmap/current/fileIO/ReadWrite.java
ARGs_OAP/bin/bbmap/current/fileIO/SummaryFile$1.class
ARGs_OAP/bin/bbmap/current/fileIO/SummaryFile.class
ARGs_OAP/bin/bbmap/current/fileIO/SummaryFile.java
ARGs_OAP/bin/bbmap/current/fileIO/TextFile.class
ARGs_OAP/bin/bbmap/current/fileIO/TextFile.java
ARGs_OAP/bin/bbmap/current/fileIO/TextStreamWriter.class
ARGs_OAP/bin/bbmap/current/fileIO/TextStreamWriter.java
ARGs_OAP/bin/bbmap/current/fun/Calc.class
ARGs_OAP/bin/bbmap/current/fun/Calc.java
ARGs_OAP/bin/bbmap/current/fun/Chance.class
ARGs_OAP/bin/bbmap/current/fun/Chance.java
ARGs_OAP/bin/bbmap/current/fun/DiskBench$ReadThread.class
ARGs_OAP/bin/bbmap/current/fun/DiskBench$WriteThread.class
ARGs_OAP/bin/bbmap/current/fun/DiskBench.class
ARGs_OAP/bin/bbmap/current/fun/DiskBench.java
ARGs_OAP/bin/bbmap/current/fun/FindPath$Edge.class
ARGs_OAP/bin/bbmap/current/fun/FindPath$Node.class
ARGs_OAP/bin/bbmap/current/fun/FindPath$Path.class
ARGs_OAP/bin/bbmap/current/fun/FindPath.class
ARGs_OAP/bin/bbmap/current/fun/FindPath.java
ARGs_OAP/bin/bbmap/current/fun/Genetic$Bug.class
ARGs_OAP/bin/bbmap/current/fun/Genetic.class
ARGs_OAP/bin/bbmap/current/fun/Genetic.java
ARGs_OAP/bin/bbmap/current/fun/Life.class
ARGs_OAP/bin/bbmap/current/fun/Life.java
ARGs_OAP/bin/bbmap/current/fun/MakeAdjacencyList$1.class
ARGs_OAP/bin/bbmap/current/fun/MakeAdjacencyList.class
ARGs_OAP/bin/bbmap/current/fun/MakeAdjacencyList.java
ARGs_OAP/bin/bbmap/current/fun/Palindrome.class
ARGs_OAP/bin/bbmap/current/fun/Palindrome.java
ARGs_OAP/bin/bbmap/current/fun/ProbShared.class
ARGs_OAP/bin/bbmap/current/fun/ProbShared.java
ARGs_OAP/bin/bbmap/current/fun/ProbShared2.class
ARGs_OAP/bin/bbmap/current/fun/ProbShared2.java
ARGs_OAP/bin/bbmap/current/fun/ProbShared3.class
ARGs_OAP/bin/bbmap/current/fun/ProbShared3.java
ARGs_OAP/bin/bbmap/current/gff/CompareGff.class
ARGs_OAP/bin/bbmap/current/gff/CompareGff.java
ARGs_OAP/bin/bbmap/current/gff/CompareGff_old.class
ARGs_OAP/bin/bbmap/current/gff/CompareGff_old.java
ARGs_OAP/bin/bbmap/current/gff/CutGff$ProcessThread.class
ARGs_OAP/bin/bbmap/current/gff/CutGff.class
ARGs_OAP/bin/bbmap/current/gff/CutGff.java
ARGs_OAP/bin/bbmap/current/gff/CutGff_ST.class
ARGs_OAP/bin/bbmap/current/gff/CutGff_ST.java
ARGs_OAP/bin/bbmap/current/gff/GbffFeature.class
ARGs_OAP/bin/bbmap/current/gff/GbffFeature.java
ARGs_OAP/bin/bbmap/current/gff/GbffFile.class
ARGs_OAP/bin/bbmap/current/gff/GbffFile.java
ARGs_OAP/bin/bbmap/current/gff/GbffLocus.class
ARGs_OAP/bin/bbmap/current/gff/GbffLocus.java
ARGs_OAP/bin/bbmap/current/gff/GffLine.class
ARGs_OAP/bin/bbmap/current/gff/GffLine.java
ARGs_OAP/bin/bbmap/current/gff/VcfToGff$1.class
ARGs_OAP/bin/bbmap/current/gff/VcfToGff.class
ARGs_OAP/bin/bbmap/current/gff/VcfToGff.java
ARGs_OAP/bin/bbmap/current/hiseq/AnalyzeFlowCell.class
ARGs_OAP/bin/bbmap/current/hiseq/AnalyzeFlowCell.java
ARGs_OAP/bin/bbmap/current/hiseq/CycleTracker.class
ARGs_OAP/bin/bbmap/current/hiseq/CycleTracker.java
ARGs_OAP/bin/bbmap/current/hiseq/FlowCell.class
ARGs_OAP/bin/bbmap/current/hiseq/FlowCell.java
ARGs_OAP/bin/bbmap/current/hiseq/FlowcellCoordinate.class
ARGs_OAP/bin/bbmap/current/hiseq/FlowcellCoordinate.java
ARGs_OAP/bin/bbmap/current/hiseq/IlluminaHeaderParser.class
ARGs_OAP/bin/bbmap/current/hiseq/IlluminaHeaderParser.java
ARGs_OAP/bin/bbmap/current/hiseq/Lane.class
ARGs_OAP/bin/bbmap/current/hiseq/Lane.java
ARGs_OAP/bin/bbmap/current/hiseq/MicroTile.class
ARGs_OAP/bin/bbmap/current/hiseq/MicroTile.java
ARGs_OAP/bin/bbmap/current/hiseq/PlotFlowCell.class
ARGs_OAP/bin/bbmap/current/hiseq/PlotFlowCell.java
ARGs_OAP/bin/bbmap/current/hiseq/Tile.class
ARGs_OAP/bin/bbmap/current/hiseq/Tile.java
ARGs_OAP/bin/bbmap/current/icecream/IceCreamAligner.class
ARGs_OAP/bin/bbmap/current/icecream/IceCreamAligner.java
ARGs_OAP/bin/bbmap/current/icecream/IceCreamAlignerJNI.class
ARGs_OAP/bin/bbmap/current/icecream/IceCreamAlignerJNI.java
ARGs_OAP/bin/bbmap/current/icecream/IceCreamAlignerJava.class
ARGs_OAP/bin/bbmap/current/icecream/IceCreamAlignerJava.java
ARGs_OAP/bin/bbmap/current/icecream/IceCreamFinder$ProcessThread.class
ARGs_OAP/bin/bbmap/current/icecream/IceCreamFinder.class
ARGs_OAP/bin/bbmap/current/icecream/IceCreamFinder.java
ARGs_OAP/bin/bbmap/current/icecream/IceCreamGrader.class
ARGs_OAP/bin/bbmap/current/icecream/IceCreamGrader.java
ARGs_OAP/bin/bbmap/current/icecream/IceCreamMaker$ProcessThread.class
ARGs_OAP/bin/bbmap/current/icecream/IceCreamMaker.class
ARGs_OAP/bin/bbmap/current/icecream/IceCreamMaker.java
ARGs_OAP/bin/bbmap/current/icecream/PolymerTrimmer.class
ARGs_OAP/bin/bbmap/current/icecream/PolymerTrimmer.java
ARGs_OAP/bin/bbmap/current/icecream/ReadBuilder.class
ARGs_OAP/bin/bbmap/current/icecream/ReadBuilder.java
ARGs_OAP/bin/bbmap/current/jgi/AddAdapters.class
ARGs_OAP/bin/bbmap/current/jgi/AddAdapters.java
ARGs_OAP/bin/bbmap/current/jgi/AdjustHomopolymers.class
ARGs_OAP/bin/bbmap/current/jgi/AdjustHomopolymers.java
ARGs_OAP/bin/bbmap/current/jgi/AssemblyStats2$Triple.class
ARGs_OAP/bin/bbmap/current/jgi/AssemblyStats2.class
ARGs_OAP/bin/bbmap/current/jgi/AssemblyStats2.java
ARGs_OAP/bin/bbmap/current/jgi/AssemblyStatsWrapper.class
ARGs_OAP/bin/bbmap/current/jgi/AssemblyStatsWrapper.java
ARGs_OAP/bin/bbmap/current/jgi/BBDuk$LoadThread.class
ARGs_OAP/bin/bbmap/current/jgi/BBDuk$ProcessThread.class
ARGs_OAP/bin/bbmap/current/jgi/BBDuk.class
ARGs_OAP/bin/bbmap/current/jgi/BBDuk.java
ARGs_OAP/bin/bbmap/current/jgi/BBDuk2$LoadThread.class
ARGs_OAP/bin/bbmap/current/jgi/BBDuk2$ProcessThread.class
ARGs_OAP/bin/bbmap/current/jgi/BBDuk2.class
ARGs_OAP/bin/bbmap/current/jgi/BBDuk2.java
ARGs_OAP/bin/bbmap/current/jgi/BBMask$MaskLowEntropyThread.class
ARGs_OAP/bin/bbmap/current/jgi/BBMask$MaskRepeatThread.class
ARGs_OAP/bin/bbmap/current/jgi/BBMask$MaskSamThread.class
ARGs_OAP/bin/bbmap/current/jgi/BBMask.class
ARGs_OAP/bin/bbmap/current/jgi/BBMask.java
ARGs_OAP/bin/bbmap/current/jgi/BBMerge$MateThread.class
ARGs_OAP/bin/bbmap/current/jgi/BBMerge.class
ARGs_OAP/bin/bbmap/current/jgi/BBMerge.java
ARGs_OAP/bin/bbmap/current/jgi/BBMergeOverlapper.class
ARGs_OAP/bin/bbmap/current/jgi/BBMergeOverlapper.java
ARGs_OAP/bin/bbmap/current/jgi/BBQC.class
ARGs_OAP/bin/bbmap/current/jgi/BBQC.java
ARGs_OAP/bin/bbmap/current/jgi/CalcTrueQuality$CountMatrixSet.class
ARGs_OAP/bin/bbmap/current/jgi/CalcTrueQuality$GBMatrixSet.class
ARGs_OAP/bin/bbmap/current/jgi/CalcTrueQuality$Worker.class
ARGs_OAP/bin/bbmap/current/jgi/CalcTrueQuality.class
ARGs_OAP/bin/bbmap/current/jgi/CalcTrueQuality.java
ARGs_OAP/bin/bbmap/current/jgi/CalcUniqueness$Counter.class
ARGs_OAP/bin/bbmap/current/jgi/CalcUniqueness.class
ARGs_OAP/bin/bbmap/current/jgi/CalcUniqueness.java
ARGs_OAP/bin/bbmap/current/jgi/CallPeaks$Peak.class
ARGs_OAP/bin/bbmap/current/jgi/CallPeaks.class
ARGs_OAP/bin/bbmap/current/jgi/CallPeaks.java
ARGs_OAP/bin/bbmap/current/jgi/Consect.class
ARGs_OAP/bin/bbmap/current/jgi/Consect.java
ARGs_OAP/bin/bbmap/current/jgi/CorrelateBarcodes.class
ARGs_OAP/bin/bbmap/current/jgi/CorrelateBarcodes.java
ARGs_OAP/bin/bbmap/current/jgi/CountBarcodes.class
ARGs_OAP/bin/bbmap/current/jgi/CountBarcodes.java
ARGs_OAP/bin/bbmap/current/jgi/CountGC$1.class
ARGs_OAP/bin/bbmap/current/jgi/CountGC.class
ARGs_OAP/bin/bbmap/current/jgi/CountGC.java
ARGs_OAP/bin/bbmap/current/jgi/CountUniqueness.class
ARGs_OAP/bin/bbmap/current/jgi/CountUniqueness.java
ARGs_OAP/bin/bbmap/current/jgi/CovStatsLine.class
ARGs_OAP/bin/bbmap/current/jgi/CovStatsLine.java
ARGs_OAP/bin/bbmap/current/jgi/CoveragePileup.class
ARGs_OAP/bin/bbmap/current/jgi/CoveragePileup.java
ARGs_OAP/bin/bbmap/current/jgi/CrossContaminate$Vessel.class
ARGs_OAP/bin/bbmap/current/jgi/CrossContaminate.class
ARGs_OAP/bin/bbmap/current/jgi/CrossContaminate.java
ARGs_OAP/bin/bbmap/current/jgi/CutPrimers.class
ARGs_OAP/bin/bbmap/current/jgi/CutPrimers.java
ARGs_OAP/bin/bbmap/current/jgi/DecontaminateByNormalization.class
ARGs_OAP/bin/bbmap/current/jgi/DecontaminateByNormalization.java
ARGs_OAP/bin/bbmap/current/jgi/Dedupe$ClusterLengthComparator.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe$ClusterThread.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe$HashThread.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe$MstThread.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe$Overlap.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe$Unit.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe$UnitOffsetComparator.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe.java
ARGs_OAP/bin/bbmap/current/jgi/Dedupe2$ClusterLengthComparator.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe2$ClusterThread.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe2$HashThread.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe2$MstThread.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe2$Overlap.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe2$Unit.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe2$UnitOffsetComparator.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe2.class
ARGs_OAP/bin/bbmap/current/jgi/Dedupe2.java
ARGs_OAP/bin/bbmap/current/jgi/DedupeByMapping$Quad.class
ARGs_OAP/bin/bbmap/current/jgi/DedupeByMapping.class
ARGs_OAP/bin/bbmap/current/jgi/DedupeByMapping.java
ARGs_OAP/bin/bbmap/current/jgi/DedupeProtein$ClusterLengthComparator.class
ARGs_OAP/bin/bbmap/current/jgi/DedupeProtein$ClusterThread.class
ARGs_OAP/bin/bbmap/current/jgi/DedupeProtein$HashThread.class
ARGs_OAP/bin/bbmap/current/jgi/DedupeProtein$MstThread.class
ARGs_OAP/bin/bbmap/current/jgi/DedupeProtein$Overlap.class
ARGs_OAP/bin/bbmap/current/jgi/DedupeProtein$Unit.class
ARGs_OAP/bin/bbmap/current/jgi/DedupeProtein$UnitOffsetComparator.class
ARGs_OAP/bin/bbmap/current/jgi/DedupeProtein.class
ARGs_OAP/bin/bbmap/current/jgi/DedupeProtein.java
ARGs_OAP/bin/bbmap/current/jgi/DemuxByName.class
ARGs_OAP/bin/bbmap/current/jgi/DemuxByName.java
ARGs_OAP/bin/bbmap/current/jgi/DemuxByName2.class
ARGs_OAP/bin/bbmap/current/jgi/DemuxByName2.java
ARGs_OAP/bin/bbmap/current/jgi/Difference.class
ARGs_OAP/bin/bbmap/current/jgi/Difference.java
ARGs_OAP/bin/bbmap/current/jgi/FakeReads.class
ARGs_OAP/bin/bbmap/current/jgi/FakeReads.java
ARGs_OAP/bin/bbmap/current/jgi/FilterByCoverage.class
ARGs_OAP/bin/bbmap/current/jgi/FilterByCoverage.java
ARGs_OAP/bin/bbmap/current/jgi/FilterBySequence$Code.class
ARGs_OAP/bin/bbmap/current/jgi/FilterBySequence$LoadThread.class
ARGs_OAP/bin/bbmap/current/jgi/FilterBySequence$ProcessThread.class
ARGs_OAP/bin/bbmap/current/jgi/FilterBySequence.class
ARGs_OAP/bin/bbmap/current/jgi/FilterBySequence.java
ARGs_OAP/bin/bbmap/current/jgi/FilterReadsWithSubs.class
ARGs_OAP/bin/bbmap/current/jgi/FilterReadsWithSubs.java
ARGs_OAP/bin/bbmap/current/jgi/FindHiCJunctions.class
ARGs_OAP/bin/bbmap/current/jgi/FindHiCJunctions.java
ARGs_OAP/bin/bbmap/current/jgi/FindPrimers$ProcessThread.class
ARGs_OAP/bin/bbmap/current/jgi/FindPrimers.class
ARGs_OAP/bin/bbmap/current/jgi/FindPrimers.java
ARGs_OAP/bin/bbmap/current/jgi/FindPrimers_old.class
ARGs_OAP/bin/bbmap/current/jgi/FindPrimers_old.java
ARGs_OAP/bin/bbmap/current/jgi/FindString.class
ARGs_OAP/bin/bbmap/current/jgi/FindString.java
ARGs_OAP/bin/bbmap/current/jgi/FungalRelease.class
ARGs_OAP/bin/bbmap/current/jgi/FungalRelease.java
ARGs_OAP/bin/bbmap/current/jgi/FuseSequence.class
ARGs_OAP/bin/bbmap/current/jgi/FuseSequence.java
ARGs_OAP/bin/bbmap/current/jgi/GatherKapaStats$KapaEntry.class
ARGs_OAP/bin/bbmap/current/jgi/GatherKapaStats$Plate.class
ARGs_OAP/bin/bbmap/current/jgi/GatherKapaStats$TagData.class
ARGs_OAP/bin/bbmap/current/jgi/GatherKapaStats$Well.class
ARGs_OAP/bin/bbmap/current/jgi/GatherKapaStats.class
ARGs_OAP/bin/bbmap/current/jgi/GatherKapaStats.java
ARGs_OAP/bin/bbmap/current/jgi/GetReads.class
ARGs_OAP/bin/bbmap/current/jgi/GetReads.java
ARGs_OAP/bin/bbmap/current/jgi/GradeMergedReads.class
ARGs_OAP/bin/bbmap/current/jgi/GradeMergedReads.java
ARGs_OAP/bin/bbmap/current/jgi/GreedyBarCodeFinder.class
ARGs_OAP/bin/bbmap/current/jgi/GreedyBarCodeFinder.java
ARGs_OAP/bin/bbmap/current/jgi/IdentityMatrix$ProcessThread.class
ARGs_OAP/bin/bbmap/current/jgi/IdentityMatrix.class
ARGs_OAP/bin/bbmap/current/jgi/IdentityMatrix.java
ARGs_OAP/bin/bbmap/current/jgi/Info.class
ARGs_OAP/bin/bbmap/current/jgi/Info.java
ARGs_OAP/bin/bbmap/current/jgi/KeepBestCopy.class
ARGs_OAP/bin/bbmap/current/jgi/KeepBestCopy.java
ARGs_OAP/bin/bbmap/current/jgi/KmerCountExact$DumpKmersThread.class
ARGs_OAP/bin/bbmap/current/jgi/KmerCountExact$MakeKhistThread.class
ARGs_OAP/bin/bbmap/current/jgi/KmerCountExact.class
ARGs_OAP/bin/bbmap/current/jgi/KmerCountExact.java
ARGs_OAP/bin/bbmap/current/jgi/KmerCountMulti$ProcessThread.class
ARGs_OAP/bin/bbmap/current/jgi/KmerCountMulti.class
ARGs_OAP/bin/bbmap/current/jgi/KmerCountMulti.java
ARGs_OAP/bin/bbmap/current/jgi/KmerCoverage$1.class
ARGs_OAP/bin/bbmap/current/jgi/KmerCoverage$ProcessThread.class
ARGs_OAP/bin/bbmap/current/jgi/KmerCoverage.class
ARGs_OAP/bin/bbmap/current/jgi/KmerCoverage.java
ARGs_OAP/bin/bbmap/current/jgi/KmerFilterSetMaker.class
ARGs_OAP/bin/bbmap/current/jgi/KmerFilterSetMaker.java
ARGs_OAP/bin/bbmap/current/jgi/KmerNormalize$1.class
ARGs_OAP/bin/bbmap/current/jgi/KmerNormalize$ProcessThread.class
ARGs_OAP/bin/bbmap/current/jgi/KmerNormalize.class
ARGs_OAP/bin/bbmap/current/jgi/KmerNormalize.java
ARGs_OAP/bin/bbmap/current/jgi/KmerSample.class
ARGs_OAP/bin/bbmap/current/jgi/KmerSample.java
ARGs_OAP/bin/bbmap/current/jgi/MakeChimeras.class
ARGs_OAP/bin/bbmap/current/jgi/MakeChimeras.java
ARGs_OAP/bin/bbmap/current/jgi/MakeContaminatedGenomes.class
ARGs_OAP/bin/bbmap/current/jgi/MakeContaminatedGenomes.java
ARGs_OAP/bin/bbmap/current/jgi/MakeLengthHistogram$1.class
ARGs_OAP/bin/bbmap/current/jgi/MakeLengthHistogram.class
ARGs_OAP/bin/bbmap/current/jgi/MakeLengthHistogram.java
ARGs_OAP/bin/bbmap/current/jgi/MakePolymers.class
ARGs_OAP/bin/bbmap/current/jgi/MakePolymers.java
ARGs_OAP/bin/bbmap/current/jgi/MergeBarcodes.class
ARGs_OAP/bin/bbmap/current/jgi/MergeBarcodes.java
ARGs_OAP/bin/bbmap/current/jgi/MergeSam.class
ARGs_OAP/bin/bbmap/current/jgi/MergeSam.java
ARGs_OAP/bin/bbmap/current/jgi/MutateGenome$SmallVar.class
ARGs_OAP/bin/bbmap/current/jgi/MutateGenome.class
ARGs_OAP/bin/bbmap/current/jgi/MutateGenome.java
ARGs_OAP/bin/bbmap/current/jgi/MutateGenome2$SmallVar.class
ARGs_OAP/bin/bbmap/current/jgi/MutateGenome2.class
ARGs_OAP/bin/bbmap/current/jgi/MutateGenome2.java
ARGs_OAP/bin/bbmap/current/jgi/Orf.class
ARGs_OAP/bin/bbmap/current/jgi/Orf.java
ARGs_OAP/bin/bbmap/current/jgi/PartitionReads.class
ARGs_OAP/bin/bbmap/current/jgi/PartitionReads.java
ARGs_OAP/bin/bbmap/current/jgi/PhylipToFasta.class
ARGs_OAP/bin/bbmap/current/jgi/PhylipToFasta.java
ARGs_OAP/bin/bbmap/current/jgi/RQCFilter2.class
ARGs_OAP/bin/bbmap/current/jgi/RQCFilter2.java
ARGs_OAP/bin/bbmap/current/jgi/RQCFilterStats.class
ARGs_OAP/bin/bbmap/current/jgi/RQCFilterStats.java
ARGs_OAP/bin/bbmap/current/jgi/RandomGenome.class
ARGs_OAP/bin/bbmap/current/jgi/RandomGenome.java
ARGs_OAP/bin/bbmap/current/jgi/ReadKmerDepthDistribution$1.class
ARGs_OAP/bin/bbmap/current/jgi/ReadKmerDepthDistribution$ProcessThread.class
ARGs_OAP/bin/bbmap/current/jgi/ReadKmerDepthDistribution.class
ARGs_OAP/bin/bbmap/current/jgi/ReadKmerDepthDistribution.java
ARGs_OAP/bin/bbmap/current/jgi/RedirectTest.class
ARGs_OAP/bin/bbmap/current/jgi/RedirectTest.java
ARGs_OAP/bin/bbmap/current/jgi/ReformatReads.class
ARGs_OAP/bin/bbmap/current/jgi/ReformatReads.java
ARGs_OAP/bin/bbmap/current/jgi/RemapQuality.class
ARGs_OAP/bin/bbmap/current/jgi/RemapQuality.java
ARGs_OAP/bin/bbmap/current/jgi/RemoveBadBarcodes.class
ARGs_OAP/bin/bbmap/current/jgi/RemoveBadBarcodes.java
ARGs_OAP/bin/bbmap/current/jgi/RenameReads.class
ARGs_OAP/bin/bbmap/current/jgi/RenameReads.java
ARGs_OAP/bin/bbmap/current/jgi/ReplaceHeaders.class
ARGs_OAP/bin/bbmap/current/jgi/ReplaceHeaders.java
ARGs_OAP/bin/bbmap/current/jgi/RepresentativeSet$Edge.class
ARGs_OAP/bin/bbmap/current/jgi/RepresentativeSet$Node.class
ARGs_OAP/bin/bbmap/current/jgi/RepresentativeSet.class
ARGs_OAP/bin/bbmap/current/jgi/RepresentativeSet.java
ARGs_OAP/bin/bbmap/current/jgi/SamToEst$1.class
ARGs_OAP/bin/bbmap/current/jgi/SamToEst$EST.class
ARGs_OAP/bin/bbmap/current/jgi/SamToEst.class
ARGs_OAP/bin/bbmap/current/jgi/SamToEst.java
ARGs_OAP/bin/bbmap/current/jgi/Seal$LoadThread.class
ARGs_OAP/bin/bbmap/current/jgi/Seal$ProcessThread.class
ARGs_OAP/bin/bbmap/current/jgi/Seal.class
ARGs_OAP/bin/bbmap/current/jgi/Seal.java
ARGs_OAP/bin/bbmap/current/jgi/Shred.class
ARGs_OAP/bin/bbmap/current/jgi/Shred.java
ARGs_OAP/bin/bbmap/current/jgi/SmallKmerFrequency$CountComparator.class
ARGs_OAP/bin/bbmap/current/jgi/SmallKmerFrequency$Kmer.class
ARGs_OAP/bin/bbmap/current/jgi/SmallKmerFrequency$NumComparator.class
ARGs_OAP/bin/bbmap/current/jgi/SmallKmerFrequency.class
ARGs_OAP/bin/bbmap/current/jgi/SmallKmerFrequency.java
ARGs_OAP/bin/bbmap/current/jgi/SplitNexteraLMP.class
ARGs_OAP/bin/bbmap/current/jgi/SplitNexteraLMP.java
ARGs_OAP/bin/bbmap/current/jgi/SplitPairsAndSingles.class
ARGs_OAP/bin/bbmap/current/jgi/SplitPairsAndSingles.java
ARGs_OAP/bin/bbmap/current/jgi/SplitSam4Way.class
ARGs_OAP/bin/bbmap/current/jgi/SplitSam4Way.java
ARGs_OAP/bin/bbmap/current/jgi/SplitSam6Way.class
ARGs_OAP/bin/bbmap/current/jgi/SplitSam6Way.java
ARGs_OAP/bin/bbmap/current/jgi/SplitSamFile.class
ARGs_OAP/bin/bbmap/current/jgi/SplitSamFile.java
ARGs_OAP/bin/bbmap/current/jgi/StringCount.class
ARGs_OAP/bin/bbmap/current/jgi/StringCount.java
ARGs_OAP/bin/bbmap/current/jgi/SynthMDA.class
ARGs_OAP/bin/bbmap/current/jgi/SynthMDA.java
ARGs_OAP/bin/bbmap/current/jgi/TestFilesystem$WriteThread.class
ARGs_OAP/bin/bbmap/current/jgi/TestFilesystem.class
ARGs_OAP/bin/bbmap/current/jgi/TestFilesystem.java
ARGs_OAP/bin/bbmap/current/jgi/TestFormat$Barcode.class
ARGs_OAP/bin/bbmap/current/jgi/TestFormat$TestThread.class
ARGs_OAP/bin/bbmap/current/jgi/TestFormat.class
ARGs_OAP/bin/bbmap/current/jgi/TestFormat.java
ARGs_OAP/bin/bbmap/current/jgi/TetramerFrequencies$Line.class
ARGs_OAP/bin/bbmap/current/jgi/TetramerFrequencies$PrintThread.class
ARGs_OAP/bin/bbmap/current/jgi/TetramerFrequencies.class
ARGs_OAP/bin/bbmap/current/jgi/TetramerFrequencies.java
ARGs_OAP/bin/bbmap/current/jgi/TranslateSixFrames.class
ARGs_OAP/bin/bbmap/current/jgi/TranslateSixFrames.java
ARGs_OAP/bin/bbmap/current/jgi/UnicodeToAscii.class
ARGs_OAP/bin/bbmap/current/jgi/UnicodeToAscii.java
ARGs_OAP/bin/bbmap/current/jgi/Unzip.class
ARGs_OAP/bin/bbmap/current/jgi/Unzip.java
ARGs_OAP/bin/bbmap/current/json/JsonLiteral.class
ARGs_OAP/bin/bbmap/current/json/JsonLiteral.java
ARGs_OAP/bin/bbmap/current/json/JsonObject.class
ARGs_OAP/bin/bbmap/current/json/JsonObject.java
ARGs_OAP/bin/bbmap/current/json/JsonParser.class
ARGs_OAP/bin/bbmap/current/json/JsonParser.java
ARGs_OAP/bin/bbmap/current/kmer/AbstractKmerTable$AllocThread.class
ARGs_OAP/bin/bbmap/current/kmer/AbstractKmerTable.class
ARGs_OAP/bin/bbmap/current/kmer/AbstractKmerTable.java
ARGs_OAP/bin/bbmap/current/kmer/AbstractKmerTableSet.class
ARGs_OAP/bin/bbmap/current/kmer/AbstractKmerTableSet.java
ARGs_OAP/bin/bbmap/current/kmer/AtomicShortArray.class
ARGs_OAP/bin/bbmap/current/kmer/AtomicShortArray.java
ARGs_OAP/bin/bbmap/current/kmer/DumpThread.class
ARGs_OAP/bin/bbmap/current/kmer/DumpThread.java
ARGs_OAP/bin/bbmap/current/kmer/HashArray.class
ARGs_OAP/bin/bbmap/current/kmer/HashArray.java
ARGs_OAP/bin/bbmap/current/kmer/HashArray1D.class
ARGs_OAP/bin/bbmap/current/kmer/HashArray1D.java
ARGs_OAP/bin/bbmap/current/kmer/HashArray2D.class
ARGs_OAP/bin/bbmap/current/kmer/HashArray2D.java
ARGs_OAP/bin/bbmap/current/kmer/HashArrayHybrid.class
ARGs_OAP/bin/bbmap/current/kmer/HashArrayHybrid.java
ARGs_OAP/bin/bbmap/current/kmer/HashArrayHybridFast.class
ARGs_OAP/bin/bbmap/current/kmer/HashArrayHybridFast.java
ARGs_OAP/bin/bbmap/current/kmer/HashBuffer.class
ARGs_OAP/bin/bbmap/current/kmer/HashBuffer.java
ARGs_OAP/bin/bbmap/current/kmer/HashForest.class
ARGs_OAP/bin/bbmap/current/kmer/HashForest.java
ARGs_OAP/bin/bbmap/current/kmer/HistogramMaker$FillThread.class
ARGs_OAP/bin/bbmap/current/kmer/HistogramMaker.class
ARGs_OAP/bin/bbmap/current/kmer/HistogramMaker.java
ARGs_OAP/bin/bbmap/current/kmer/KmerBuffer.class
ARGs_OAP/bin/bbmap/current/kmer/KmerBuffer.java
ARGs_OAP/bin/bbmap/current/kmer/KmerLink.class
ARGs_OAP/bin/bbmap/current/kmer/KmerLink.java
ARGs_OAP/bin/bbmap/current/kmer/KmerNode.class
ARGs_OAP/bin/bbmap/current/kmer/KmerNode.java
ARGs_OAP/bin/bbmap/current/kmer/KmerNode1D.class
ARGs_OAP/bin/bbmap/current/kmer/KmerNode1D.java
ARGs_OAP/bin/bbmap/current/kmer/KmerNode2D.class
ARGs_OAP/bin/bbmap/current/kmer/KmerNode2D.java
ARGs_OAP/bin/bbmap/current/kmer/KmerTable.class
ARGs_OAP/bin/bbmap/current/kmer/KmerTable.java
ARGs_OAP/bin/bbmap/current/kmer/KmerTableSet$LoadThread.class
ARGs_OAP/bin/bbmap/current/kmer/KmerTableSet.class
ARGs_OAP/bin/bbmap/current/kmer/KmerTableSet.java
ARGs_OAP/bin/bbmap/current/kmer/OwnershipThread.class
ARGs_OAP/bin/bbmap/current/kmer/OwnershipThread.java
ARGs_OAP/bin/bbmap/current/kmer/ScheduleMaker.class
ARGs_OAP/bin/bbmap/current/kmer/ScheduleMaker.java
ARGs_OAP/bin/bbmap/current/kmer/TableLoaderLockFree$LoadThread.class
ARGs_OAP/bin/bbmap/current/kmer/TableLoaderLockFree.class
ARGs_OAP/bin/bbmap/current/kmer/TableLoaderLockFree.java
ARGs_OAP/bin/bbmap/current/kmer/TableReader.class
ARGs_OAP/bin/bbmap/current/kmer/TableReader.java
ARGs_OAP/bin/bbmap/current/ml/ProcessBBMergeHeaders$Header.class
ARGs_OAP/bin/bbmap/current/ml/ProcessBBMergeHeaders.class
ARGs_OAP/bin/bbmap/current/ml/ProcessBBMergeHeaders.java
ARGs_OAP/bin/bbmap/current/pacbio/CalcCoverageFromSites$1.class
ARGs_OAP/bin/bbmap/current/pacbio/CalcCoverageFromSites.class
ARGs_OAP/bin/bbmap/current/pacbio/CalcCoverageFromSites.java
ARGs_OAP/bin/bbmap/current/pacbio/GenerateMultiChrom.class
ARGs_OAP/bin/bbmap/current/pacbio/GenerateMultiChrom.java
ARGs_OAP/bin/bbmap/current/pacbio/MakePacBioScript.class
ARGs_OAP/bin/bbmap/current/pacbio/MakePacBioScript.java
ARGs_OAP/bin/bbmap/current/pacbio/MergeFastaContigs$1.class
ARGs_OAP/bin/bbmap/current/pacbio/MergeFastaContigs.class
ARGs_OAP/bin/bbmap/current/pacbio/MergeFastaContigs.java
ARGs_OAP/bin/bbmap/current/pacbio/MergeReadsAndGenome$1.class
ARGs_OAP/bin/bbmap/current/pacbio/MergeReadsAndGenome.class
ARGs_OAP/bin/bbmap/current/pacbio/MergeReadsAndGenome.java
ARGs_OAP/bin/bbmap/current/pacbio/PartitionFastaFile.class
ARGs_OAP/bin/bbmap/current/pacbio/PartitionFastaFile.java
ARGs_OAP/bin/bbmap/current/pacbio/PartitionReads$1.class
ARGs_OAP/bin/bbmap/current/pacbio/PartitionReads.class
ARGs_OAP/bin/bbmap/current/pacbio/PartitionReads.java
ARGs_OAP/bin/bbmap/current/pacbio/ProcessStackedSitesNormalized$1.class
ARGs_OAP/bin/bbmap/current/pacbio/ProcessStackedSitesNormalized$Buffer.class
ARGs_OAP/bin/bbmap/current/pacbio/ProcessStackedSitesNormalized$Ssra.class
ARGs_OAP/bin/bbmap/current/pacbio/ProcessStackedSitesNormalized.class
ARGs_OAP/bin/bbmap/current/pacbio/ProcessStackedSitesNormalized.java
ARGs_OAP/bin/bbmap/current/pacbio/RemoveAdapters2$1.class
ARGs_OAP/bin/bbmap/current/pacbio/RemoveAdapters2$ProcessThread.class
ARGs_OAP/bin/bbmap/current/pacbio/RemoveAdapters2.class
ARGs_OAP/bin/bbmap/current/pacbio/RemoveAdapters2.java
ARGs_OAP/bin/bbmap/current/pacbio/RemoveAdapters3$ProcessThread.class
ARGs_OAP/bin/bbmap/current/pacbio/RemoveAdapters3.class
ARGs_OAP/bin/bbmap/current/pacbio/RemoveAdapters3.java
ARGs_OAP/bin/bbmap/current/pacbio/SiteR.class
ARGs_OAP/bin/bbmap/current/pacbio/SiteR.java
ARGs_OAP/bin/bbmap/current/pacbio/SortSites$1.class
ARGs_OAP/bin/bbmap/current/pacbio/SortSites.class
ARGs_OAP/bin/bbmap/current/pacbio/SortSites.java
ARGs_OAP/bin/bbmap/current/pacbio/SplitOffPerfectContigs$1.class
ARGs_OAP/bin/bbmap/current/pacbio/SplitOffPerfectContigs.class
ARGs_OAP/bin/bbmap/current/pacbio/SplitOffPerfectContigs.java
ARGs_OAP/bin/bbmap/current/pacbio/StackSites$1.class
ARGs_OAP/bin/bbmap/current/pacbio/StackSites$Glob.class
ARGs_OAP/bin/bbmap/current/pacbio/StackSites.class
ARGs_OAP/bin/bbmap/current/pacbio/StackSites.java
ARGs_OAP/bin/bbmap/current/pacbio/StackSites2$1.class
ARGs_OAP/bin/bbmap/current/pacbio/StackSites2$Glob.class
ARGs_OAP/bin/bbmap/current/pacbio/StackSites2.class
ARGs_OAP/bin/bbmap/current/pacbio/StackSites2.java
ARGs_OAP/bin/bbmap/current/prok/AnalyzeGenes$FileThread.class
ARGs_OAP/bin/bbmap/current/prok/AnalyzeGenes.class
ARGs_OAP/bin/bbmap/current/prok/AnalyzeGenes.java
ARGs_OAP/bin/bbmap/current/prok/CallGenes$ProcessThread.class
ARGs_OAP/bin/bbmap/current/prok/CallGenes.class
ARGs_OAP/bin/bbmap/current/prok/CallGenes.java
ARGs_OAP/bin/bbmap/current/prok/Feature$FeatureComparatorScore.class
ARGs_OAP/bin/bbmap/current/prok/Feature.class
ARGs_OAP/bin/bbmap/current/prok/Feature.java
ARGs_OAP/bin/bbmap/current/prok/FetchProks$ProcessThread.class
ARGs_OAP/bin/bbmap/current/prok/FetchProks$Stats.class
ARGs_OAP/bin/bbmap/current/prok/FetchProks.class
ARGs_OAP/bin/bbmap/current/prok/FetchProks.java
ARGs_OAP/bin/bbmap/current/prok/FilterSilva.class
ARGs_OAP/bin/bbmap/current/prok/FilterSilva.java
ARGs_OAP/bin/bbmap/current/prok/FrameStats.class
ARGs_OAP/bin/bbmap/current/prok/FrameStats.java
ARGs_OAP/bin/bbmap/current/prok/GeneCaller.class
ARGs_OAP/bin/bbmap/current/prok/GeneCaller.java
ARGs_OAP/bin/bbmap/current/prok/GeneModel.class
ARGs_OAP/bin/bbmap/current/prok/GeneModel.java
ARGs_OAP/bin/bbmap/current/prok/GeneModelParser.class
ARGs_OAP/bin/bbmap/current/prok/GeneModelParser.java
ARGs_OAP/bin/bbmap/current/prok/MergeRibo$ListComparator.class
ARGs_OAP/bin/bbmap/current/prok/MergeRibo$ProcessThread.class
ARGs_OAP/bin/bbmap/current/prok/MergeRibo$Ribo.class
ARGs_OAP/bin/bbmap/current/prok/MergeRibo.class
ARGs_OAP/bin/bbmap/current/prok/MergeRibo.java
ARGs_OAP/bin/bbmap/current/prok/MergeRibo_Fast$ProcessThread.class
ARGs_OAP/bin/bbmap/current/prok/MergeRibo_Fast$Ribo.class
ARGs_OAP/bin/bbmap/current/prok/MergeRibo_Fast.class
ARGs_OAP/bin/bbmap/current/prok/MergeRibo_Fast.java
ARGs_OAP/bin/bbmap/current/prok/Orf.class
ARGs_OAP/bin/bbmap/current/prok/Orf.java
ARGs_OAP/bin/bbmap/current/prok/PGMTools$1.class
ARGs_OAP/bin/bbmap/current/prok/PGMTools.class
ARGs_OAP/bin/bbmap/current/prok/PGMTools.java
ARGs_OAP/bin/bbmap/current/prok/ProkObject.class
ARGs_OAP/bin/bbmap/current/prok/ProkObject.java
ARGs_OAP/bin/bbmap/current/prok/RiboMaker$ProcessThread.class
ARGs_OAP/bin/bbmap/current/prok/RiboMaker.class
ARGs_OAP/bin/bbmap/current/prok/RiboMaker.java
ARGs_OAP/bin/bbmap/current/prok/ScafData.class
ARGs_OAP/bin/bbmap/current/prok/ScafData.java
ARGs_OAP/bin/bbmap/current/prok/ScoreTracker.class
ARGs_OAP/bin/bbmap/current/prok/ScoreTracker.java
ARGs_OAP/bin/bbmap/current/prok/SplitRibo$ProcessThread.class
ARGs_OAP/bin/bbmap/current/prok/SplitRibo.class
ARGs_OAP/bin/bbmap/current/prok/SplitRibo.java
ARGs_OAP/bin/bbmap/current/prok/StatsContainer.class
ARGs_OAP/bin/bbmap/current/prok/StatsContainer.java
ARGs_OAP/bin/bbmap/current/server/PercentEncoding.class
ARGs_OAP/bin/bbmap/current/server/PercentEncoding.java
ARGs_OAP/bin/bbmap/current/server/ServerTools.class
ARGs_OAP/bin/bbmap/current/server/ServerTools.java
ARGs_OAP/bin/bbmap/current/server/SimpleHttpServer$GetHandler.class
ARGs_OAP/bin/bbmap/current/server/SimpleHttpServer.class
ARGs_OAP/bin/bbmap/current/server/SimpleHttpServer.java
ARGs_OAP/bin/bbmap/current/shared/Colors.class
ARGs_OAP/bin/bbmap/current/shared/Colors.java
ARGs_OAP/bin/bbmap/current/shared/KillSwitch.class
ARGs_OAP/bin/bbmap/current/shared/KillSwitch.java
ARGs_OAP/bin/bbmap/current/shared/MetadataWriter.class
ARGs_OAP/bin/bbmap/current/shared/MetadataWriter.java
ARGs_OAP/bin/bbmap/current/shared/Parser.class
ARGs_OAP/bin/bbmap/current/shared/Parser.java
ARGs_OAP/bin/bbmap/current/shared/PreParser.class
ARGs_OAP/bin/bbmap/current/shared/PreParser.java
ARGs_OAP/bin/bbmap/current/shared/Primes.class
ARGs_OAP/bin/bbmap/current/shared/Primes.java
ARGs_OAP/bin/bbmap/current/shared/ReadStats.class
ARGs_OAP/bin/bbmap/current/shared/ReadStats.java
ARGs_OAP/bin/bbmap/current/shared/Shared.class
ARGs_OAP/bin/bbmap/current/shared/Shared.java
ARGs_OAP/bin/bbmap/current/shared/Timer.class
ARGs_OAP/bin/bbmap/current/shared/Timer.java
ARGs_OAP/bin/bbmap/current/shared/Tools.class
ARGs_OAP/bin/bbmap/current/shared/Tools.java
ARGs_OAP/bin/bbmap/current/shared/TrimRead.class
ARGs_OAP/bin/bbmap/current/shared/TrimRead.java
ARGs_OAP/bin/bbmap/current/sketch/AddSSU$SketchHeader.class
ARGs_OAP/bin/bbmap/current/sketch/AddSSU.class
ARGs_OAP/bin/bbmap/current/sketch/AddSSU.java
ARGs_OAP/bin/bbmap/current/sketch/AlignmentJob.class
ARGs_OAP/bin/bbmap/current/sketch/AlignmentJob.java
ARGs_OAP/bin/bbmap/current/sketch/AlignmentThreadPool$AlignmentThread.class
ARGs_OAP/bin/bbmap/current/sketch/AlignmentThreadPool.class
ARGs_OAP/bin/bbmap/current/sketch/AlignmentThreadPool.java
ARGs_OAP/bin/bbmap/current/sketch/AnalyzeSketchResults$SSUThread.class
ARGs_OAP/bin/bbmap/current/sketch/AnalyzeSketchResults.class
ARGs_OAP/bin/bbmap/current/sketch/AnalyzeSketchResults.java
ARGs_OAP/bin/bbmap/current/sketch/Blacklist.class
ARGs_OAP/bin/bbmap/current/sketch/Blacklist.java
ARGs_OAP/bin/bbmap/current/sketch/BlacklistMaker$ProcessThread.class
ARGs_OAP/bin/bbmap/current/sketch/BlacklistMaker.class
ARGs_OAP/bin/bbmap/current/sketch/BlacklistMaker.java
ARGs_OAP/bin/bbmap/current/sketch/BlacklistMaker2$KeyPair.class
ARGs_OAP/bin/bbmap/current/sketch/BlacklistMaker2$ProcessThread.class
ARGs_OAP/bin/bbmap/current/sketch/BlacklistMaker2.class
ARGs_OAP/bin/bbmap/current/sketch/BlacklistMaker2.java
ARGs_OAP/bin/bbmap/current/sketch/CompareBuffer.class
ARGs_OAP/bin/bbmap/current/sketch/CompareBuffer.java
ARGs_OAP/bin/bbmap/current/sketch/CompareSSU$ProcessThread.class
ARGs_OAP/bin/bbmap/current/sketch/CompareSSU.class
ARGs_OAP/bin/bbmap/current/sketch/CompareSSU.java
ARGs_OAP/bin/bbmap/current/sketch/CompareSketch$CompareThread.class
ARGs_OAP/bin/bbmap/current/sketch/CompareSketch.class
ARGs_OAP/bin/bbmap/current/sketch/CompareSketch.java
ARGs_OAP/bin/bbmap/current/sketch/Comparison$Depth2Comparator.class
ARGs_OAP/bin/bbmap/current/sketch/Comparison$DepthComparator.class
ARGs_OAP/bin/bbmap/current/sketch/Comparison$HitsComparator.class
ARGs_OAP/bin/bbmap/current/sketch/Comparison$KIDComparator.class
ARGs_OAP/bin/bbmap/current/sketch/Comparison$SSUComparator.class
ARGs_OAP/bin/bbmap/current/sketch/Comparison$ScoreComparator.class
ARGs_OAP/bin/bbmap/current/sketch/Comparison$VolumeComparator.class
ARGs_OAP/bin/bbmap/current/sketch/Comparison$WKIDComparator.class
ARGs_OAP/bin/bbmap/current/sketch/Comparison.class
ARGs_OAP/bin/bbmap/current/sketch/Comparison.java
ARGs_OAP/bin/bbmap/current/sketch/DisplayParams.class
ARGs_OAP/bin/bbmap/current/sketch/DisplayParams.java
ARGs_OAP/bin/bbmap/current/sketch/GlocalAligner.class
ARGs_OAP/bin/bbmap/current/sketch/GlocalAligner.java
ARGs_OAP/bin/bbmap/current/sketch/InvertKey.class
ARGs_OAP/bin/bbmap/current/sketch/InvertKey.java
ARGs_OAP/bin/bbmap/current/sketch/KmerLimit$ProcessThread.class
ARGs_OAP/bin/bbmap/current/sketch/KmerLimit.class
ARGs_OAP/bin/bbmap/current/sketch/KmerLimit.java
ARGs_OAP/bin/bbmap/current/sketch/KmerLimit2$ProcessThread.class
ARGs_OAP/bin/bbmap/current/sketch/KmerLimit2.class
ARGs_OAP/bin/bbmap/current/sketch/KmerLimit2.java
ARGs_OAP/bin/bbmap/current/sketch/MergeSketch.class
ARGs_OAP/bin/bbmap/current/sketch/MergeSketch.java
ARGs_OAP/bin/bbmap/current/sketch/Record.class
ARGs_OAP/bin/bbmap/current/sketch/Record.java
ARGs_OAP/bin/bbmap/current/sketch/RecordSet.class
ARGs_OAP/bin/bbmap/current/sketch/RecordSet.java
ARGs_OAP/bin/bbmap/current/sketch/ResultLineParser.class
ARGs_OAP/bin/bbmap/current/sketch/ResultLineParser.java
ARGs_OAP/bin/bbmap/current/sketch/SSUMap.class
ARGs_OAP/bin/bbmap/current/sketch/SSUMap.java
ARGs_OAP/bin/bbmap/current/sketch/SendSketch.class
ARGs_OAP/bin/bbmap/current/sketch/SendSketch.java
ARGs_OAP/bin/bbmap/current/sketch/Sketch.class
ARGs_OAP/bin/bbmap/current/sketch/Sketch.java
ARGs_OAP/bin/bbmap/current/sketch/SketchHeap.class
ARGs_OAP/bin/bbmap/current/sketch/SketchHeap.java
ARGs_OAP/bin/bbmap/current/sketch/SketchIdComparator.class
ARGs_OAP/bin/bbmap/current/sketch/SketchIdComparator.java
ARGs_OAP/bin/bbmap/current/sketch/SketchIndex$IndexThread.class
ARGs_OAP/bin/bbmap/current/sketch/SketchIndex.class
ARGs_OAP/bin/bbmap/current/sketch/SketchIndex.java
ARGs_OAP/bin/bbmap/current/sketch/SketchMaker$ProcessThread.class
ARGs_OAP/bin/bbmap/current/sketch/SketchMaker$WriteThread.class
ARGs_OAP/bin/bbmap/current/sketch/SketchMaker.class
ARGs_OAP/bin/bbmap/current/sketch/SketchMaker.java
ARGs_OAP/bin/bbmap/current/sketch/SketchMakerMini.class
ARGs_OAP/bin/bbmap/current/sketch/SketchMakerMini.java
ARGs_OAP/bin/bbmap/current/sketch/SketchObject.class
ARGs_OAP/bin/bbmap/current/sketch/SketchObject.java
ARGs_OAP/bin/bbmap/current/sketch/SketchResults.class
ARGs_OAP/bin/bbmap/current/sketch/SketchResults.java
ARGs_OAP/bin/bbmap/current/sketch/SketchSearcher$CompareThread.class
ARGs_OAP/bin/bbmap/current/sketch/SketchSearcher.class
ARGs_OAP/bin/bbmap/current/sketch/SketchSearcher.java
ARGs_OAP/bin/bbmap/current/sketch/SketchTool$LoadThread.class
ARGs_OAP/bin/bbmap/current/sketch/SketchTool$LoadThread2.class
ARGs_OAP/bin/bbmap/current/sketch/SketchTool$SketchThread.class
ARGs_OAP/bin/bbmap/current/sketch/SketchTool.class
ARGs_OAP/bin/bbmap/current/sketch/SketchTool.java
ARGs_OAP/bin/bbmap/current/sketch/SubSketch.class
ARGs_OAP/bin/bbmap/current/sketch/SubSketch.java
ARGs_OAP/bin/bbmap/current/sketch/SummarizeSketchStats$SketchResultsLine.class
ARGs_OAP/bin/bbmap/current/sketch/SummarizeSketchStats$SketchResultsSummary.class
ARGs_OAP/bin/bbmap/current/sketch/SummarizeSketchStats.class
ARGs_OAP/bin/bbmap/current/sketch/SummarizeSketchStats.java
ARGs_OAP/bin/bbmap/current/sketch/Whitelist.class
ARGs_OAP/bin/bbmap/current/sketch/Whitelist.java
ARGs_OAP/bin/bbmap/current/sort/ContigLengthComparator.class
ARGs_OAP/bin/bbmap/current/sort/ContigLengthComparator.java
ARGs_OAP/bin/bbmap/current/sort/MergeSorted.class
ARGs_OAP/bin/bbmap/current/sort/MergeSorted.java
ARGs_OAP/bin/bbmap/current/sort/ReadComparator.class
ARGs_OAP/bin/bbmap/current/sort/ReadComparator.java
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorFlowcell.class
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorFlowcell.java
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorID.class
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorID.java
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorList.class
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorList.java
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorMapping.class
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorMapping.java
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorName.class
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorName.java
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorPosition.class
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorPosition.java
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorRandom.class
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorRandom.java
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorTaxa.class
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorTaxa.java
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorTopological.class
ARGs_OAP/bin/bbmap/current/sort/ReadComparatorTopological.java
ARGs_OAP/bin/bbmap/current/sort/ReadErrorComparator.class
ARGs_OAP/bin/bbmap/current/sort/ReadErrorComparator.java
ARGs_OAP/bin/bbmap/current/sort/ReadLengthComparator.class
ARGs_OAP/bin/bbmap/current/sort/ReadLengthComparator.java
ARGs_OAP/bin/bbmap/current/sort/ReadQualityComparator.class
ARGs_OAP/bin/bbmap/current/sort/ReadQualityComparator.java
ARGs_OAP/bin/bbmap/current/sort/Shuffle$ShuffleThread.class
ARGs_OAP/bin/bbmap/current/sort/Shuffle.class
ARGs_OAP/bin/bbmap/current/sort/Shuffle.java
ARGs_OAP/bin/bbmap/current/sort/Shuffle2$WriteThread.class
ARGs_OAP/bin/bbmap/current/sort/Shuffle2.class
ARGs_OAP/bin/bbmap/current/sort/Shuffle2.java
ARGs_OAP/bin/bbmap/current/sort/SortByName$WriteThread.class
ARGs_OAP/bin/bbmap/current/sort/SortByName.class
ARGs_OAP/bin/bbmap/current/sort/SortByName.java
ARGs_OAP/bin/bbmap/current/sort/SortReadsByID$1.class
ARGs_OAP/bin/bbmap/current/sort/SortReadsByID$Block.class
ARGs_OAP/bin/bbmap/current/sort/SortReadsByID.class
ARGs_OAP/bin/bbmap/current/sort/SortReadsByID.java
ARGs_OAP/bin/bbmap/current/stream/ArrayListSet$Pack.class
ARGs_OAP/bin/bbmap/current/stream/ArrayListSet.class
ARGs_OAP/bin/bbmap/current/stream/ArrayListSet.java
ARGs_OAP/bin/bbmap/current/stream/BufferedMultiCros.class
ARGs_OAP/bin/bbmap/current/stream/BufferedMultiCros.java
ARGs_OAP/bin/bbmap/current/stream/ConcurrentCollectionReadInputStream.class
ARGs_OAP/bin/bbmap/current/stream/ConcurrentCollectionReadInputStream.java
ARGs_OAP/bin/bbmap/current/stream/ConcurrentDepot.class
ARGs_OAP/bin/bbmap/current/stream/ConcurrentDepot.java
ARGs_OAP/bin/bbmap/current/stream/ConcurrentGenericReadInputStream$1.class
ARGs_OAP/bin/bbmap/current/stream/ConcurrentGenericReadInputStream$ReadThread.class
ARGs_OAP/bin/bbmap/current/stream/ConcurrentGenericReadInputStream.class
ARGs_OAP/bin/bbmap/current/stream/ConcurrentGenericReadInputStream.java
ARGs_OAP/bin/bbmap/current/stream/ConcurrentGenericReadOutputStream.class
ARGs_OAP/bin/bbmap/current/stream/ConcurrentGenericReadOutputStream.java
ARGs_OAP/bin/bbmap/current/stream/ConcurrentLegacyReadInputStream.class
ARGs_OAP/bin/bbmap/current/stream/ConcurrentLegacyReadInputStream.java
ARGs_OAP/bin/bbmap/current/stream/ConcurrentReadInputStream.class
ARGs_OAP/bin/bbmap/current/stream/ConcurrentReadInputStream.java
ARGs_OAP/bin/bbmap/current/stream/ConcurrentReadInputStreamD.class
ARGs_OAP/bin/bbmap/current/stream/ConcurrentReadInputStreamD.java
ARGs_OAP/bin/bbmap/current/stream/ConcurrentReadListDepot.class
ARGs_OAP/bin/bbmap/current/stream/ConcurrentReadListDepot.java
ARGs_OAP/bin/bbmap/current/stream/ConcurrentReadOutputStream.class
ARGs_OAP/bin/bbmap/current/stream/ConcurrentReadOutputStream.java
ARGs_OAP/bin/bbmap/current/stream/ConcurrentReadOutputStreamD$ListenThread.class
ARGs_OAP/bin/bbmap/current/stream/ConcurrentReadOutputStreamD.class
ARGs_OAP/bin/bbmap/current/stream/ConcurrentReadOutputStreamD.java
ARGs_OAP/bin/bbmap/current/stream/ConcurrentReadStreamInterface.class
ARGs_OAP/bin/bbmap/current/stream/ConcurrentReadStreamInterface.java
ARGs_OAP/bin/bbmap/current/stream/CrisContainer.class
ARGs_OAP/bin/bbmap/current/stream/CrisContainer.java
ARGs_OAP/bin/bbmap/current/stream/CrisWrapper.class
ARGs_OAP/bin/bbmap/current/stream/CrisWrapper.java
ARGs_OAP/bin/bbmap/current/stream/DualCris.class
ARGs_OAP/bin/bbmap/current/stream/DualCris.java
ARGs_OAP/bin/bbmap/current/stream/EmblReadInputStream.class
ARGs_OAP/bin/bbmap/current/stream/EmblReadInputStream.java
ARGs_OAP/bin/bbmap/current/stream/FASTQ.class
ARGs_OAP/bin/bbmap/current/stream/FASTQ.java
ARGs_OAP/bin/bbmap/current/stream/FastaQualReadInputStream.class
ARGs_OAP/bin/bbmap/current/stream/FastaQualReadInputStream.java
ARGs_OAP/bin/bbmap/current/stream/FastaReadInputStream.class
ARGs_OAP/bin/bbmap/current/stream/FastaReadInputStream.java
ARGs_OAP/bin/bbmap/current/stream/FastaShredInputStream.class
ARGs_OAP/bin/bbmap/current/stream/FastaShredInputStream.java
ARGs_OAP/bin/bbmap/current/stream/FastqReadInputStream.class
ARGs_OAP/bin/bbmap/current/stream/FastqReadInputStream.java
ARGs_OAP/bin/bbmap/current/stream/GbkReadInputStream.class
ARGs_OAP/bin/bbmap/current/stream/GbkReadInputStream.java
ARGs_OAP/bin/bbmap/current/stream/Header.class
ARGs_OAP/bin/bbmap/current/stream/Header.java
ARGs_OAP/bin/bbmap/current/stream/HeaderInputStream.class
ARGs_OAP/bin/bbmap/current/stream/HeaderInputStream.java
ARGs_OAP/bin/bbmap/current/stream/MDWalker.class
ARGs_OAP/bin/bbmap/current/stream/MDWalker.java
ARGs_OAP/bin/bbmap/current/stream/MultiCros.class
ARGs_OAP/bin/bbmap/current/stream/MultiCros.java
ARGs_OAP/bin/bbmap/current/stream/MultiCros2$Buffer.class
ARGs_OAP/bin/bbmap/current/stream/MultiCros2.class
ARGs_OAP/bin/bbmap/current/stream/MultiCros2.java
ARGs_OAP/bin/bbmap/current/stream/MultiCros3$Buffer.class
ARGs_OAP/bin/bbmap/current/stream/MultiCros3.class
ARGs_OAP/bin/bbmap/current/stream/MultiCros3.java
ARGs_OAP/bin/bbmap/current/stream/NullOutputStream.class
ARGs_OAP/bin/bbmap/current/stream/NullOutputStream.java
ARGs_OAP/bin/bbmap/current/stream/OnelineReadInputStream.class
ARGs_OAP/bin/bbmap/current/stream/OnelineReadInputStream.java
ARGs_OAP/bin/bbmap/current/stream/RTextInputStream.class
ARGs_OAP/bin/bbmap/current/stream/RTextInputStream.java
ARGs_OAP/bin/bbmap/current/stream/RandomReadInputStream3.class
ARGs_OAP/bin/bbmap/current/stream/RandomReadInputStream3.java
ARGs_OAP/bin/bbmap/current/stream/Read.class
ARGs_OAP/bin/bbmap/current/stream/Read.java
ARGs_OAP/bin/bbmap/current/stream/ReadInputStream.class
ARGs_OAP/bin/bbmap/current/stream/ReadInputStream.java
ARGs_OAP/bin/bbmap/current/stream/ReadStreamByteWriter.class
ARGs_OAP/bin/bbmap/current/stream/ReadStreamByteWriter.java
ARGs_OAP/bin/bbmap/current/stream/ReadStreamWriter$Job.class
ARGs_OAP/bin/bbmap/current/stream/ReadStreamWriter.class
ARGs_OAP/bin/bbmap/current/stream/ReadStreamWriter.java
ARGs_OAP/bin/bbmap/current/stream/SamHeader.class
ARGs_OAP/bin/bbmap/current/stream/SamHeader.java
ARGs_OAP/bin/bbmap/current/stream/SamLine.class
ARGs_OAP/bin/bbmap/current/stream/SamLine.java
ARGs_OAP/bin/bbmap/current/stream/SamLineStreamer$ProcessThread.class
ARGs_OAP/bin/bbmap/current/stream/SamLineStreamer.class
ARGs_OAP/bin/bbmap/current/stream/SamLineStreamer.java
ARGs_OAP/bin/bbmap/current/stream/SamReadInputStream.class
ARGs_OAP/bin/bbmap/current/stream/SamReadInputStream.java
ARGs_OAP/bin/bbmap/current/stream/SamReadStreamer$ProcessThread.class
ARGs_OAP/bin/bbmap/current/stream/SamReadStreamer.class
ARGs_OAP/bin/bbmap/current/stream/SamReadStreamer.java
ARGs_OAP/bin/bbmap/current/stream/SamStreamer.class
ARGs_OAP/bin/bbmap/current/stream/SamStreamer.java
ARGs_OAP/bin/bbmap/current/stream/SamStreamerMF.class
ARGs_OAP/bin/bbmap/current/stream/SamStreamerMF.java
ARGs_OAP/bin/bbmap/current/stream/SamStreamerWrapper.class
ARGs_OAP/bin/bbmap/current/stream/SamStreamerWrapper.java
ARGs_OAP/bin/bbmap/current/stream/ScaffoldCoordinates.class
ARGs_OAP/bin/bbmap/current/stream/ScaffoldCoordinates.java
ARGs_OAP/bin/bbmap/current/stream/ScarfReadInputStream.class
ARGs_OAP/bin/bbmap/current/stream/ScarfReadInputStream.java
ARGs_OAP/bin/bbmap/current/stream/SequentialReadInputStream.class
ARGs_OAP/bin/bbmap/current/stream/SequentialReadInputStream.java
ARGs_OAP/bin/bbmap/current/stream/SiteScore$PositionComparator.class
ARGs_OAP/bin/bbmap/current/stream/SiteScore.class
ARGs_OAP/bin/bbmap/current/stream/SiteScore.java
ARGs_OAP/bin/bbmap/current/stream/SiteScoreR$IDComparator.class
ARGs_OAP/bin/bbmap/current/stream/SiteScoreR$NormalizedComparator.class
ARGs_OAP/bin/bbmap/current/stream/SiteScoreR$PositionComparator.class
ARGs_OAP/bin/bbmap/current/stream/SiteScoreR.class
ARGs_OAP/bin/bbmap/current/stream/SiteScoreR.java
ARGs_OAP/bin/bbmap/current/structures/AbstractBitSet.class
ARGs_OAP/bin/bbmap/current/structures/AbstractBitSet.java
ARGs_OAP/bin/bbmap/current/structures/AbstractIntHashMap.class
ARGs_OAP/bin/bbmap/current/structures/AbstractIntHashMap.java
ARGs_OAP/bin/bbmap/current/structures/AtomicBitSet.class
ARGs_OAP/bin/bbmap/current/structures/AtomicBitSet.java
ARGs_OAP/bin/bbmap/current/structures/ByteBuilder.class
ARGs_OAP/bin/bbmap/current/structures/ByteBuilder.java
ARGs_OAP/bin/bbmap/current/structures/CoverageArray.class
ARGs_OAP/bin/bbmap/current/structures/CoverageArray.java
ARGs_OAP/bin/bbmap/current/structures/CoverageArray2.class
ARGs_OAP/bin/bbmap/current/structures/CoverageArray2.java
ARGs_OAP/bin/bbmap/current/structures/CoverageArray3.class
ARGs_OAP/bin/bbmap/current/structures/CoverageArray3.java
ARGs_OAP/bin/bbmap/current/structures/CoverageArray3A.class
ARGs_OAP/bin/bbmap/current/structures/CoverageArray3A.java
ARGs_OAP/bin/bbmap/current/structures/DoubleList.class
ARGs_OAP/bin/bbmap/current/structures/DoubleList.java
ARGs_OAP/bin/bbmap/current/structures/EntropyTracker.class
ARGs_OAP/bin/bbmap/current/structures/EntropyTracker.java
ARGs_OAP/bin/bbmap/current/structures/FloatList.class
ARGs_OAP/bin/bbmap/current/structures/FloatList.java
ARGs_OAP/bin/bbmap/current/structures/Heap.class
ARGs_OAP/bin/bbmap/current/structures/Heap.java
ARGs_OAP/bin/bbmap/current/structures/IntHashMap.class
ARGs_OAP/bin/bbmap/current/structures/IntHashMap.java
ARGs_OAP/bin/bbmap/current/structures/IntHashMapBinary.class
ARGs_OAP/bin/bbmap/current/structures/IntHashMapBinary.java
ARGs_OAP/bin/bbmap/current/structures/IntHashSet.class
ARGs_OAP/bin/bbmap/current/structures/IntHashSet.java
ARGs_OAP/bin/bbmap/current/structures/IntHashSetList.class
ARGs_OAP/bin/bbmap/current/structures/IntHashSetList.java
ARGs_OAP/bin/bbmap/current/structures/IntList.class
ARGs_OAP/bin/bbmap/current/structures/IntList.java
ARGs_OAP/bin/bbmap/current/structures/IntList2.class
ARGs_OAP/bin/bbmap/current/structures/IntList2.java
ARGs_OAP/bin/bbmap/current/structures/IntList3.class
ARGs_OAP/bin/bbmap/current/structures/IntList3.java
ARGs_OAP/bin/bbmap/current/structures/IntListCompressor.class
ARGs_OAP/bin/bbmap/current/structures/IntListCompressor.java
ARGs_OAP/bin/bbmap/current/structures/IntLongHashMap.class
ARGs_OAP/bin/bbmap/current/structures/IntLongHashMap.java
ARGs_OAP/bin/bbmap/current/structures/IntMap.class
ARGs_OAP/bin/bbmap/current/structures/IntMap.java
ARGs_OAP/bin/bbmap/current/structures/ListNum.class
ARGs_OAP/bin/bbmap/current/structures/ListNum.java
ARGs_OAP/bin/bbmap/current/structures/LongHashMap.class
ARGs_OAP/bin/bbmap/current/structures/LongHashMap.java
ARGs_OAP/bin/bbmap/current/structures/LongHashSet.class
ARGs_OAP/bin/bbmap/current/structures/LongHashSet.java
ARGs_OAP/bin/bbmap/current/structures/LongHeap.class
ARGs_OAP/bin/bbmap/current/structures/LongHeap.java
ARGs_OAP/bin/bbmap/current/structures/LongHeapMap.class
ARGs_OAP/bin/bbmap/current/structures/LongHeapMap.java
ARGs_OAP/bin/bbmap/current/structures/LongHeapSet.class
ARGs_OAP/bin/bbmap/current/structures/LongHeapSet.java
ARGs_OAP/bin/bbmap/current/structures/LongHeapSetInterface.class
ARGs_OAP/bin/bbmap/current/structures/LongHeapSetInterface.java
ARGs_OAP/bin/bbmap/current/structures/LongList.class
ARGs_OAP/bin/bbmap/current/structures/LongList.java
ARGs_OAP/bin/bbmap/current/structures/LongLongHashMap.class
ARGs_OAP/bin/bbmap/current/structures/LongLongHashMap.java
ARGs_OAP/bin/bbmap/current/structures/LongM.class
ARGs_OAP/bin/bbmap/current/structures/LongM.java
ARGs_OAP/bin/bbmap/current/structures/LongPair.class
ARGs_OAP/bin/bbmap/current/structures/LongPair.java
ARGs_OAP/bin/bbmap/current/structures/MultiBitSet.class
ARGs_OAP/bin/bbmap/current/structures/MultiBitSet.java
ARGs_OAP/bin/bbmap/current/structures/PolymerTracker.class
ARGs_OAP/bin/bbmap/current/structures/PolymerTracker.java
ARGs_OAP/bin/bbmap/current/structures/Quantizer.class
ARGs_OAP/bin/bbmap/current/structures/Quantizer.java
ARGs_OAP/bin/bbmap/current/structures/Range.class
ARGs_OAP/bin/bbmap/current/structures/Range.java
ARGs_OAP/bin/bbmap/current/structures/RawBitSet.class
ARGs_OAP/bin/bbmap/current/structures/RawBitSet.java
ARGs_OAP/bin/bbmap/current/structures/StringNum.class
ARGs_OAP/bin/bbmap/current/structures/StringNum.java
ARGs_OAP/bin/bbmap/current/structures/StringPair.class
ARGs_OAP/bin/bbmap/current/structures/StringPair.java
ARGs_OAP/bin/bbmap/current/structures/SuperLongList.class
ARGs_OAP/bin/bbmap/current/structures/SuperLongList.java
ARGs_OAP/bin/bbmap/current/tax/AccessionToTaxid$HashThread.class
ARGs_OAP/bin/bbmap/current/tax/AccessionToTaxid.class
ARGs_OAP/bin/bbmap/current/tax/AccessionToTaxid.java
ARGs_OAP/bin/bbmap/current/tax/AccessionToTaxid_old$HashThread.class
ARGs_OAP/bin/bbmap/current/tax/AccessionToTaxid_old.class
ARGs_OAP/bin/bbmap/current/tax/AccessionToTaxid_old.java
ARGs_OAP/bin/bbmap/current/tax/AnalyzeAccession$ProcessThread.class
ARGs_OAP/bin/bbmap/current/tax/AnalyzeAccession.class
ARGs_OAP/bin/bbmap/current/tax/AnalyzeAccession.java
ARGs_OAP/bin/bbmap/current/tax/AnalyzeAccession_ST.class
ARGs_OAP/bin/bbmap/current/tax/AnalyzeAccession_ST.java
ARGs_OAP/bin/bbmap/current/tax/ExplodeTree.class
ARGs_OAP/bin/bbmap/current/tax/ExplodeTree.java
ARGs_OAP/bin/bbmap/current/tax/FilterByTaxa.class
ARGs_OAP/bin/bbmap/current/tax/FilterByTaxa.java
ARGs_OAP/bin/bbmap/current/tax/FindAncestor.class
ARGs_OAP/bin/bbmap/current/tax/FindAncestor.java
ARGs_OAP/bin/bbmap/current/tax/GiToTaxid.class
ARGs_OAP/bin/bbmap/current/tax/GiToTaxid.java
ARGs_OAP/bin/bbmap/current/tax/IDNode.class
ARGs_OAP/bin/bbmap/current/tax/IDNode.java
ARGs_OAP/bin/bbmap/current/tax/IDTree.class
ARGs_OAP/bin/bbmap/current/tax/IDTree.java
ARGs_OAP/bin/bbmap/current/tax/ImgRecord.class
ARGs_OAP/bin/bbmap/current/tax/ImgRecord.java
ARGs_OAP/bin/bbmap/current/tax/ImgRecord2.class
ARGs_OAP/bin/bbmap/current/tax/ImgRecord2.java
ARGs_OAP/bin/bbmap/current/tax/PrintTaxonomy.class
ARGs_OAP/bin/bbmap/current/tax/PrintTaxonomy.java
ARGs_OAP/bin/bbmap/current/tax/Query.class
ARGs_OAP/bin/bbmap/current/tax/Query.java
ARGs_OAP/bin/bbmap/current/tax/RenameGiToTaxid.class
ARGs_OAP/bin/bbmap/current/tax/RenameGiToTaxid.java
ARGs_OAP/bin/bbmap/current/tax/RenameIMG.class
ARGs_OAP/bin/bbmap/current/tax/RenameIMG.java
ARGs_OAP/bin/bbmap/current/tax/ShrinkAccession.class
ARGs_OAP/bin/bbmap/current/tax/ShrinkAccession.java
ARGs_OAP/bin/bbmap/current/tax/SplitByTaxa.class
ARGs_OAP/bin/bbmap/current/tax/SplitByTaxa.java
ARGs_OAP/bin/bbmap/current/tax/TaxApp$1.class
ARGs_OAP/bin/bbmap/current/tax/TaxApp.class
ARGs_OAP/bin/bbmap/current/tax/TaxApp.java
ARGs_OAP/bin/bbmap/current/tax/TaxClient.class
ARGs_OAP/bin/bbmap/current/tax/TaxClient.java
ARGs_OAP/bin/bbmap/current/tax/TaxFilter$1.class
ARGs_OAP/bin/bbmap/current/tax/TaxFilter.class
ARGs_OAP/bin/bbmap/current/tax/TaxFilter.java
ARGs_OAP/bin/bbmap/current/tax/TaxNode$CountComparator.class
ARGs_OAP/bin/bbmap/current/tax/TaxNode.class
ARGs_OAP/bin/bbmap/current/tax/TaxNode.java
ARGs_OAP/bin/bbmap/current/tax/TaxServer$CompareThread.class
ARGs_OAP/bin/bbmap/current/tax/TaxServer$HelpHandler.class
ARGs_OAP/bin/bbmap/current/tax/TaxServer$IconHandler.class
ARGs_OAP/bin/bbmap/current/tax/TaxServer$KillHandler.class
ARGs_OAP/bin/bbmap/current/tax/TaxServer$SketchHandler$SketchInstance.class
ARGs_OAP/bin/bbmap/current/tax/TaxServer$SketchHandler.class
ARGs_OAP/bin/bbmap/current/tax/TaxServer$StatsHandler.class
ARGs_OAP/bin/bbmap/current/tax/TaxServer$TaxHandler.class
ARGs_OAP/bin/bbmap/current/tax/TaxServer.class
ARGs_OAP/bin/bbmap/current/tax/TaxServer.java
ARGs_OAP/bin/bbmap/current/tax/TaxSize.class
ARGs_OAP/bin/bbmap/current/tax/TaxSize.java
ARGs_OAP/bin/bbmap/current/tax/TaxTree.class
ARGs_OAP/bin/bbmap/current/tax/TaxTree.java
ARGs_OAP/bin/bbmap/current/template/A_Sample.class
ARGs_OAP/bin/bbmap/current/template/A_Sample.java
ARGs_OAP/bin/bbmap/current/template/A_Sample2.class
ARGs_OAP/bin/bbmap/current/template/A_Sample2.java
ARGs_OAP/bin/bbmap/current/template/A_SampleBasic.class
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ARGs_OAP/bin/bbmap/current/template/A_SampleBasic2.class
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ARGs_OAP/bin/bbmap/current/template/A_SampleByteFile.class
ARGs_OAP/bin/bbmap/current/template/A_SampleByteFile.java
ARGs_OAP/bin/bbmap/current/template/A_SampleD.class
ARGs_OAP/bin/bbmap/current/template/A_SampleD.java
ARGs_OAP/bin/bbmap/current/template/A_SampleMT$ProcessThread.class
ARGs_OAP/bin/bbmap/current/template/A_SampleMT.class
ARGs_OAP/bin/bbmap/current/template/A_SampleMT.java
ARGs_OAP/bin/bbmap/current/template/A_SampleSamStreamer$ProcessThread.class
ARGs_OAP/bin/bbmap/current/template/A_SampleSamStreamer.class
ARGs_OAP/bin/bbmap/current/template/A_SampleSamStreamer.java
ARGs_OAP/bin/bbmap/current/template/A_Sample_Generator$ProcessThread.class
ARGs_OAP/bin/bbmap/current/template/A_Sample_Generator.class
ARGs_OAP/bin/bbmap/current/template/A_Sample_Generator.java
ARGs_OAP/bin/bbmap/current/template/A_Sample_Unpaired.class
ARGs_OAP/bin/bbmap/current/template/A_Sample_Unpaired.java
ARGs_OAP/bin/bbmap/current/template/Accumulator.class
ARGs_OAP/bin/bbmap/current/template/Accumulator.java
ARGs_OAP/bin/bbmap/current/template/BBTool_ST.class
ARGs_OAP/bin/bbmap/current/template/BBTool_ST.java
ARGs_OAP/bin/bbmap/current/template/DoWorker.class
ARGs_OAP/bin/bbmap/current/template/DoWorker.java
ARGs_OAP/bin/bbmap/current/template/ThreadPoolJob.class
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ARGs_OAP/bin/bbmap/current/template/ThreadWaiter.class
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ARGs_OAP/bin/bbmap/current/ukmer/AbstractKmerTableU.java
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ARGs_OAP/bin/bbmap/current/ukmer/DumpThreadU.java
ARGs_OAP/bin/bbmap/current/ukmer/HashArrayU.class
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ARGs_OAP/bin/bbmap/current/ukmer/Kmer.class
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ARGs_OAP/bin/bbmap/current/var2/VarMap.java
ARGs_OAP/bin/bbmap/current/var2/VcfLoader$ProcessThread.class
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ARGs_OAP/bin/bbmap/current/var2/VcfLoader.java
ARGs_OAP/bin/bbmap/current/var2/VcfWriter$ProcessThread.class
ARGs_OAP/bin/bbmap/current/var2/VcfWriter.class
ARGs_OAP/bin/bbmap/current/var2/VcfWriter.java
ARGs_OAP/bin/bbmap/docs/Legal.txt
ARGs_OAP/bin/bbmap/docs/Legal_Illumina.txt
ARGs_OAP/bin/bbmap/docs/RestartingServers.txt
ARGs_OAP/bin/bbmap/docs/TableOfContents.txt
ARGs_OAP/bin/bbmap/docs/ToolDescriptions.txt
ARGs_OAP/bin/bbmap/docs/UsageGuide.txt
ARGs_OAP/bin/bbmap/docs/changelog.txt
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ARGs_OAP/bin/bbmap/docs/readme_config.txt
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ARGs_OAP/bin/bbmap/docs/guides/BBDukGuide.txt
ARGs_OAP/bin/bbmap/docs/guides/BBMapGuide.txt
ARGs_OAP/bin/bbmap/docs/guides/BBMap_old_readme.txt
ARGs_OAP/bin/bbmap/docs/guides/BBMaskGuide.txt
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ARGs_OAP/bin/bbmap/docs/guides/StatsGuide.txt
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ARGs_OAP/bin/bbmap/jni/BBMergeOverlapper.o
ARGs_OAP/bin/bbmap/jni/BandedAlignerJNI.c
ARGs_OAP/bin/bbmap/jni/BandedAlignerJNI.o
ARGs_OAP/bin/bbmap/jni/CMakeLists.txt
ARGs_OAP/bin/bbmap/jni/IceCreamAlignerJNI.c
ARGs_OAP/bin/bbmap/jni/IceCreamAlignerJNI.o
ARGs_OAP/bin/bbmap/jni/MultiStateAligner11tsJNI.c
ARGs_OAP/bin/bbmap/jni/MultiStateAligner11tsJNI.o
ARGs_OAP/bin/bbmap/jni/README.txt
ARGs_OAP/bin/bbmap/jni/align2_BandedAlignerJNI.h
ARGs_OAP/bin/bbmap/jni/align2_MultiStateAligner11tsJNI.h
ARGs_OAP/bin/bbmap/jni/icecream_IceCreamAlignerJNI.h
ARGs_OAP/bin/bbmap/jni/jgi_BBMergeOverlapper.h
ARGs_OAP/bin/bbmap/jni/libbbtoolsjni.dylib
ARGs_OAP/bin/bbmap/jni/libbbtoolsjni.so
ARGs_OAP/bin/bbmap/jni/makefile.linux
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ARGs_OAP/bin/bbmap/jni/run.sh
ARGs_OAP/bin/bbmap/pipelines/assembleMito_Illumina.sh
ARGs_OAP/bin/bbmap/pipelines/assembleMito_PacBio.sh
ARGs_OAP/bin/bbmap/pipelines/assemblyPipeline.sh
ARGs_OAP/bin/bbmap/pipelines/callInsertions.sh
ARGs_OAP/bin/bbmap/pipelines/cutRna.sh
ARGs_OAP/bin/bbmap/pipelines/makeRiboKmers.sh
ARGs_OAP/bin/bbmap/pipelines/processIMG.sh
ARGs_OAP/bin/bbmap/pipelines/testPlatformQuality.sh
ARGs_OAP/bin/bbmap/pipelines/testsketch.sh
ARGs_OAP/bin/bbmap/pipelines/variantPipeline.sh
ARGs_OAP/bin/bbmap/pipelines/covid/makeSummary.sh
ARGs_OAP/bin/bbmap/pipelines/covid/processCorona.sh
ARGs_OAP/bin/bbmap/pipelines/covid/processCoronaWrapper.sh
ARGs_OAP/bin/bbmap/pipelines/covid/readme.txt
ARGs_OAP/bin/bbmap/pipelines/covid/recal.sh
ARGs_OAP/bin/bbmap/pipelines/fetch/fetchMito.sh
ARGs_OAP/bin/bbmap/pipelines/fetch/fetchNt.sh
ARGs_OAP/bin/bbmap/pipelines/fetch/fetchNtOuter.sh
ARGs_OAP/bin/bbmap/pipelines/fetch/fetchPlasmid.sh
ARGs_OAP/bin/bbmap/pipelines/fetch/fetchPlastid.sh
ARGs_OAP/bin/bbmap/pipelines/fetch/fetchProkByGenus.sh
ARGs_OAP/bin/bbmap/pipelines/fetch/fetchRefSeq.sh
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ARGs_OAP/bin/bbmap/pipelines/fetch/fetchSilva.sh
ARGs_OAP/bin/bbmap/pipelines/fetch/fetchTaxonomy.sh
ARGs_OAP/bin/bbmap/pipelines/fetch/runRefSeqProtein.sh
ARGs_OAP/bin/bbmap/pipelines/fetch/sketchRefSeq.sh
ARGs_OAP/bin/bbmap/pipelines/server/startNtServerVM.sh
ARGs_OAP/bin/bbmap/pipelines/server/startProteinServerVM.sh
ARGs_OAP/bin/bbmap/pipelines/server/startRefseqServerVM.sh
ARGs_OAP/bin/bbmap/pipelines/server/startSilvaServerVM.sh
ARGs_OAP/bin/bbmap/pipelines/server/startTaxServerVM.sh
ARGs_OAP/bin/bbmap/pipelines/silva/fetchSilva.sh
ARGs_OAP/bin/bbmap/pipelines/silva/make15mers.sh
ARGs_OAP/bin/bbmap/pipelines/silva/makeCoveringSetLsu.sh
ARGs_OAP/bin/bbmap/pipelines/silva/makeCoveringSetSsu.sh
ARGs_OAP/bin/bbmap/pipelines/silva/makeRep.sh
ARGs_OAP/bin/bbmap/pytools/.gitignore
ARGs_OAP/bin/bbmap/pytools/ReadMe
ARGs_OAP/bin/bbmap/pytools/filter.py
ARGs_OAP/bin/bbmap/pytools/readqc.py
ARGs_OAP/bin/bbmap/pytools/css/report.css
ARGs_OAP/bin/bbmap/pytools/filter_desc/3primerna.txt
ARGs_OAP/bin/bbmap/pytools/filter_desc/bisulphite.txt
ARGs_OAP/bin/bbmap/pytools/filter_desc/cell-enrichment.txt
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ARGs_OAP/bin/bbmap/pytools/filter_param/cell-enrichment.config
ARGs_OAP/bin/bbmap/pytools/filter_param/chip-seq.config
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ARGs_OAP/bin/bbmap/pytools/lib/rqc_utility.py
ARGs_OAP/bin/bbmap/pytools/template/filter_body_template.html
ARGs_OAP/bin/bbmap/pytools/template/readqc_artifacts.html
ARGs_OAP/bin/bbmap/pytools/template/readqc_body_template.html
ARGs_OAP/bin/bbmap/pytools/template/template.html
ARGs_OAP/bin/bbmap/pytools/tools/patterN_fastq.pl
ARGs_OAP/bin/bbmap/resources/16S_15mers.fa
ARGs_OAP/bin/bbmap/resources/16S_consensus_sequence.fa
ARGs_OAP/bin/bbmap/resources/18S_15mers.fa
ARGs_OAP/bin/bbmap/resources/18S_consensus_sequence.fa
ARGs_OAP/bin/bbmap/resources/23S_15mers.fa
ARGs_OAP/bin/bbmap/resources/23S_consensus_sequence.fa
ARGs_OAP/bin/bbmap/resources/5S_10mers.fa
ARGs_OAP/bin/bbmap/resources/5S_11mers.fa
ARGs_OAP/bin/bbmap/resources/5S_12mers.fa
ARGs_OAP/bin/bbmap/resources/5S_15mers.fa
ARGs_OAP/bin/bbmap/resources/5S_9mers.fa
ARGs_OAP/bin/bbmap/resources/5S_consensus_sequence.fa
ARGs_OAP/bin/bbmap/resources/Covid19_ref.fa
ARGs_OAP/bin/bbmap/resources/ITS_animal_consensus_sequence.fq
ARGs_OAP/bin/bbmap/resources/ITS_consensus_sequence.fq
ARGs_OAP/bin/bbmap/resources/ITS_fungi_consensus_sequence.fq
ARGs_OAP/bin/bbmap/resources/ITS_nonfungi_consensus_sequence.fq
ARGs_OAP/bin/bbmap/resources/ITS_other_consensus_sequence.fq
ARGs_OAP/bin/bbmap/resources/ITS_plant_consensus_sequence.fq
ARGs_OAP/bin/bbmap/resources/ITS_universal_consensus_sequence.fq
ARGs_OAP/bin/bbmap/resources/adapters.fa
ARGs_OAP/bin/bbmap/resources/adapters_no_transposase.fa.gz
ARGs_OAP/bin/bbmap/resources/blacklist_nt_merged.sketch
ARGs_OAP/bin/bbmap/resources/blacklist_prokprot_merged.sketch
ARGs_OAP/bin/bbmap/resources/blacklist_refseq_merged.sketch
ARGs_OAP/bin/bbmap/resources/blacklist_silva_merged.sketch
ARGs_OAP/bin/bbmap/resources/contents.txt
ARGs_OAP/bin/bbmap/resources/crelox.fa.gz
ARGs_OAP/bin/bbmap/resources/favicon.ico
ARGs_OAP/bin/bbmap/resources/kapatags.L40.fa
ARGs_OAP/bin/bbmap/resources/lambda.fa.gz
ARGs_OAP/bin/bbmap/resources/lfpe.linker.fa.gz
ARGs_OAP/bin/bbmap/resources/lsu_15mers.fa
ARGs_OAP/bin/bbmap/resources/m16S_consensus_sequence.fa
ARGs_OAP/bin/bbmap/resources/m18S_consensus_sequence.fa
ARGs_OAP/bin/bbmap/resources/model.pgm
ARGs_OAP/bin/bbmap/resources/mtst.fa
ARGs_OAP/bin/bbmap/resources/nextera.fa.gz
ARGs_OAP/bin/bbmap/resources/nextera_LMP_adapter.fa.gz
ARGs_OAP/bin/bbmap/resources/nextera_LMP_linker.fa.gz
ARGs_OAP/bin/bbmap/resources/p16S_consensus_sequence.fa
ARGs_OAP/bin/bbmap/resources/pJET1.2.fa
ARGs_OAP/bin/bbmap/resources/phix174_ill.ref.fa.gz
ARGs_OAP/bin/bbmap/resources/phix_adapters.fa.gz
ARGs_OAP/bin/bbmap/resources/polyA.fa.gz
ARGs_OAP/bin/bbmap/resources/primes.txt.gz
ARGs_OAP/bin/bbmap/resources/remote_files.txt
ARGs_OAP/bin/bbmap/resources/remote_files_old.txt
ARGs_OAP/bin/bbmap/resources/sample1.fq.gz
ARGs_OAP/bin/bbmap/resources/sample2.fq.gz
ARGs_OAP/bin/bbmap/resources/sequencing_artifacts.fa.gz
ARGs_OAP/bin/bbmap/resources/short.fa
ARGs_OAP/bin/bbmap/resources/ssu_15mers.fa
ARGs_OAP/bin/bbmap/resources/tRNA_10mers.fa
ARGs_OAP/bin/bbmap/resources/tRNA_11mers.fa
ARGs_OAP/bin/bbmap/resources/tRNA_15mers.fa
ARGs_OAP/bin/bbmap/resources/tRNA_16mers.fa
ARGs_OAP/bin/bbmap/resources/tRNA_consensus_sequence.fa
ARGs_OAP/bin/bbmap/resources/tax_server.html
ARGs_OAP/bin/bbmap/resources/truseq.fa.gz
ARGs_OAP/bin/bbmap/resources/truseq_rna.fa.gz