CHANGES.txt
Dockerfile
LICENSE.txt
MANIFEST.in
README.md
VERSION.txt
icarus.py
install.sh
install_full.sh
manual.html
metaquast.py
quast-lg.py
quast.py
setup.py
quast.egg-info/PKG-INFO
quast.egg-info/SOURCES.txt
quast.egg-info/dependency_links.txt
quast.egg-info/not-zip-safe
quast.egg-info/top_level.txt
quast_libs/N50.py
quast_libs/__init__.py
quast_libs/aligned_stats.py
quast_libs/basic_stats.py
quast_libs/circos.py
quast_libs/contigs_analyzer.py
quast_libs/create_meta_summary.py
quast_libs/fastaparser.py
quast_libs/genemark.py
quast_libs/genes_parser.py
quast_libs/genome_analyzer.py
quast_libs/glimmer.py
quast_libs/icarus.py
quast_libs/icarus_builder.py
quast_libs/icarus_parser.py
quast_libs/icarus_utils.py
quast_libs/log.py
quast_libs/metautils.py
quast_libs/optimal_assembly.py
quast_libs/options_parser.py
quast_libs/plotter.py
quast_libs/plotter_data.py
quast_libs/qconfig.py
quast_libs/qutils.py
quast_libs/reads_analyzer.py
quast_libs/reporting.py
quast_libs/run_barrnap.py
quast_libs/run_busco.py
quast_libs/search_references_meta.py
quast_libs/unique_kmers.py
quast_libs/version.py
quast_libs/barrnap/LICENSE
quast_libs/barrnap/LICENSE.Rfam
quast_libs/barrnap/LICENSE.SILVA
quast_libs/barrnap/Makefile
quast_libs/barrnap/README.md
quast_libs/barrnap/bin/barrnap
quast_libs/barrnap/binaries/darwin/nhmmer
quast_libs/barrnap/binaries/linux/nhmmer
quast_libs/barrnap/build/12S.mito.aln
quast_libs/barrnap/build/16S.mito.aln
quast_libs/barrnap/build/build_HMMs.sh
quast_libs/barrnap/build/fix-SILVA.pl
quast_libs/barrnap/db/arc.hmm
quast_libs/barrnap/db/bac.hmm
quast_libs/barrnap/db/euk.hmm
quast_libs/barrnap/db/mito.hmm
quast_libs/bedtools/.gitignore
quast_libs/bedtools/.travis.yml
quast_libs/bedtools/LICENSE
quast_libs/bedtools/Makefile
quast_libs/bedtools/README.md
quast_libs/bedtools/RELEASE_HISTORY
quast_libs/bedtools/make.err
quast_libs/bedtools/make.log
quast_libs/bedtools/bin/annotateBed
quast_libs/bedtools/bin/bamToBed
quast_libs/bedtools/bin/bamToFastq
quast_libs/bedtools/bin/bed12ToBed6
quast_libs/bedtools/bin/bedToBam
quast_libs/bedtools/bin/bedToIgv
quast_libs/bedtools/bin/bedpeToBam
quast_libs/bedtools/bin/bedtools
quast_libs/bedtools/bin/closestBed
quast_libs/bedtools/bin/clusterBed
quast_libs/bedtools/bin/complementBed
quast_libs/bedtools/bin/coverageBed
quast_libs/bedtools/bin/expandCols
quast_libs/bedtools/bin/fastaFromBed
quast_libs/bedtools/bin/flankBed
quast_libs/bedtools/bin/genomeCoverageBed
quast_libs/bedtools/bin/getOverlap
quast_libs/bedtools/bin/groupBy
quast_libs/bedtools/bin/intersectBed
quast_libs/bedtools/bin/linksBed
quast_libs/bedtools/bin/mapBed
quast_libs/bedtools/bin/maskFastaFromBed
quast_libs/bedtools/bin/mergeBed
quast_libs/bedtools/bin/multiBamCov
quast_libs/bedtools/bin/multiIntersectBed
quast_libs/bedtools/bin/nucBed
quast_libs/bedtools/bin/pairToBed
quast_libs/bedtools/bin/pairToPair
quast_libs/bedtools/bin/randomBed
quast_libs/bedtools/bin/shiftBed
quast_libs/bedtools/bin/shuffleBed
quast_libs/bedtools/bin/slopBed
quast_libs/bedtools/bin/sortBed
quast_libs/bedtools/bin/subtractBed
quast_libs/bedtools/bin/tagBam
quast_libs/bedtools/bin/unionBedGraphs
quast_libs/bedtools/bin/windowBed
quast_libs/bedtools/bin/windowMaker
quast_libs/bedtools/obj/BamAncillary.h
quast_libs/bedtools/obj/BamAncillary.o
quast_libs/bedtools/obj/BamFileReader.o
quast_libs/bedtools/obj/BamRecord.o
quast_libs/bedtools/obj/Bed12Interval.o
quast_libs/bedtools/obj/Bed3Interval.o
quast_libs/bedtools/obj/Bed4Interval.o
quast_libs/bedtools/obj/Bed5Interval.o
quast_libs/bedtools/obj/Bed6Interval.o
quast_libs/bedtools/obj/BedGraphInterval.o
quast_libs/bedtools/obj/BedPlusInterval.o
quast_libs/bedtools/obj/BedtoolsDriver.o
quast_libs/bedtools/obj/BinTree.o
quast_libs/bedtools/obj/BlockMgr.o
quast_libs/bedtools/obj/BlockedIntervals.o
quast_libs/bedtools/obj/BufferedStreamMgr.o
quast_libs/bedtools/obj/CloseSweep.o
quast_libs/bedtools/obj/CommonHelp.o
quast_libs/bedtools/obj/CompressionTools.o
quast_libs/bedtools/obj/ContextBase.o
quast_libs/bedtools/obj/ContextClosest.o
quast_libs/bedtools/obj/ContextComplement.o
quast_libs/bedtools/obj/ContextCoverage.o
quast_libs/bedtools/obj/ContextFisher.o
quast_libs/bedtools/obj/ContextGroupBy.o
quast_libs/bedtools/obj/ContextIntersect.o
quast_libs/bedtools/obj/ContextJaccard.o
quast_libs/bedtools/obj/ContextMap.o
quast_libs/bedtools/obj/ContextMerge.o
quast_libs/bedtools/obj/ContextSample.o
quast_libs/bedtools/obj/ContextSpacing.o
quast_libs/bedtools/obj/ContextSubtract.o
quast_libs/bedtools/obj/EmptyRecord.o
quast_libs/bedtools/obj/Fasta.o
quast_libs/bedtools/obj/FileReader.o
quast_libs/bedtools/obj/FileRecordMergeMgr.o
quast_libs/bedtools/obj/FileRecordMgr.o
quast_libs/bedtools/obj/FileRecordTypeChecker.o
quast_libs/bedtools/obj/GenomeFile.o
quast_libs/bedtools/obj/GffPlusRecord.o
quast_libs/bedtools/obj/GffRecord.o
quast_libs/bedtools/obj/InputStreamMgr.o
quast_libs/bedtools/obj/KeyListOps.o
quast_libs/bedtools/obj/KeyListOpsMethods.o
quast_libs/bedtools/obj/NewChromsweep.o
quast_libs/bedtools/obj/NewGenomeFile.o
quast_libs/bedtools/obj/NoPosPlusRecord.o
quast_libs/bedtools/obj/ParseTools.o
quast_libs/bedtools/obj/PlusFields.o
quast_libs/bedtools/obj/PushBackStreamBuf.o
quast_libs/bedtools/obj/Record.o
quast_libs/bedtools/obj/RecordKeyList.o
quast_libs/bedtools/obj/RecordKeyVector.o
quast_libs/bedtools/obj/RecordList.o
quast_libs/bedtools/obj/RecordMgr.o
quast_libs/bedtools/obj/RecordOutputMgr.o
quast_libs/bedtools/obj/RegressTest.o
quast_libs/bedtools/obj/SingleLineDelimTextFileReader.o
quast_libs/bedtools/obj/StrandQueue.o
quast_libs/bedtools/obj/Tokenizer.o
quast_libs/bedtools/obj/ToolBase.o
quast_libs/bedtools/obj/VcfRecord.o
quast_libs/bedtools/obj/VectorOps.o
quast_libs/bedtools/obj/annotateBed.o
quast_libs/bedtools/obj/annotateMain.o
quast_libs/bedtools/obj/bamToBed.o
quast_libs/bedtools/obj/bamToFastq.o
quast_libs/bedtools/obj/bamToFastqMain.o
quast_libs/bedtools/obj/bed12ToBed6.o
quast_libs/bedtools/obj/bedFile.o
quast_libs/bedtools/obj/bedFilePE.o
quast_libs/bedtools/obj/bedGraphFile.o
quast_libs/bedtools/obj/bedToBam.o
quast_libs/bedtools/obj/bedToIgv.o
quast_libs/bedtools/obj/bedpeToBam.o
quast_libs/bedtools/obj/bedtools.o
quast_libs/bedtools/obj/chromsweep.o
quast_libs/bedtools/obj/closestFile.o
quast_libs/bedtools/obj/closestHelp.o
quast_libs/bedtools/obj/clusterBed.o
quast_libs/bedtools/obj/clusterMain.o
quast_libs/bedtools/obj/complementFile.o
quast_libs/bedtools/obj/complementHelp.o
quast_libs/bedtools/obj/coverageFile.o
quast_libs/bedtools/obj/coverageHelp.o
quast_libs/bedtools/obj/expand.o
quast_libs/bedtools/obj/fastaFromBed.o
quast_libs/bedtools/obj/fastaFromBedMain.o
quast_libs/bedtools/obj/fileType.o
quast_libs/bedtools/obj/fisher.o
quast_libs/bedtools/obj/fisherHelp.o
quast_libs/bedtools/obj/flankBed.o
quast_libs/bedtools/obj/flankBedMain.o
quast_libs/bedtools/obj/genomeCoverageBed.o
quast_libs/bedtools/obj/genomeCoverageMain.o
quast_libs/bedtools/obj/getOverlap.o
quast_libs/bedtools/obj/groupBy.o
quast_libs/bedtools/obj/groupByHelp.o
quast_libs/bedtools/obj/gzstream.o
quast_libs/bedtools/obj/intersectFile.o
quast_libs/bedtools/obj/intersectHelp.o
quast_libs/bedtools/obj/jaccard.o
quast_libs/bedtools/obj/jaccardHelp.o
quast_libs/bedtools/obj/kfunc.o
quast_libs/bedtools/obj/linksBed.o
quast_libs/bedtools/obj/linksMain.o
quast_libs/bedtools/obj/mapFile.o
quast_libs/bedtools/obj/mapHelp.o
quast_libs/bedtools/obj/maskFastaFromBed.o
quast_libs/bedtools/obj/maskFastaFromBedMain.o
quast_libs/bedtools/obj/mergeFile.o
quast_libs/bedtools/obj/mergeHelp.o
quast_libs/bedtools/obj/multiBamCov.o
quast_libs/bedtools/obj/multiBamCovMain.o
quast_libs/bedtools/obj/multiIntersectBed.o
quast_libs/bedtools/obj/multiIntersectBedMain.o
quast_libs/bedtools/obj/nucBed.o
quast_libs/bedtools/obj/nucBedMain.o
quast_libs/bedtools/obj/pairToBed.o
quast_libs/bedtools/obj/pairToBedMain.o
quast_libs/bedtools/obj/pairToPair.o
quast_libs/bedtools/obj/pairToPairMain.o
quast_libs/bedtools/obj/randomBed.o
quast_libs/bedtools/obj/randomBedMain.o
quast_libs/bedtools/obj/regressTestMain.o
quast_libs/bedtools/obj/reldist.o
quast_libs/bedtools/obj/reldistMain.o
quast_libs/bedtools/obj/sampleFile.o
quast_libs/bedtools/obj/sampleHelp.o
quast_libs/bedtools/obj/sequenceUtils.o
quast_libs/bedtools/obj/shiftBed.o
quast_libs/bedtools/obj/shiftBedMain.o
quast_libs/bedtools/obj/shuffleBed.o
quast_libs/bedtools/obj/shuffleBedMain.o
quast_libs/bedtools/obj/slopBed.o
quast_libs/bedtools/obj/slopBedMain.o
quast_libs/bedtools/obj/sortBed.o
quast_libs/bedtools/obj/sortMain.o
quast_libs/bedtools/obj/spacingFile.o
quast_libs/bedtools/obj/spacingHelp.o
quast_libs/bedtools/obj/split.o
quast_libs/bedtools/obj/splitBed.o
quast_libs/bedtools/obj/splitBedMain.o
quast_libs/bedtools/obj/subtractFile.o
quast_libs/bedtools/obj/subtractHelp.o
quast_libs/bedtools/obj/tabFile.o
quast_libs/bedtools/obj/tagBam.o
quast_libs/bedtools/obj/tagBamMain.o
quast_libs/bedtools/obj/unionBedGraphs.o
quast_libs/bedtools/obj/unionBedGraphsMain.o
quast_libs/bedtools/obj/version.o
quast_libs/bedtools/obj/windowBed.o
quast_libs/bedtools/obj/windowMain.o
quast_libs/bedtools/obj/windowMaker.o
quast_libs/bedtools/obj/windowMakerMain.o
quast_libs/bedtools/scripts/makeBashScripts.py
quast_libs/bedtools/scripts/vcfsort.sh
quast_libs/bedtools/src/bedtools.cpp
quast_libs/bedtools/src/annotateBed/Makefile
quast_libs/bedtools/src/annotateBed/annotateBed.cpp
quast_libs/bedtools/src/annotateBed/annotateBed.h
quast_libs/bedtools/src/annotateBed/annotateMain.cpp
quast_libs/bedtools/src/bamToBed/Makefile
quast_libs/bedtools/src/bamToBed/bamToBed.cpp
quast_libs/bedtools/src/bamToFastq/Makefile
quast_libs/bedtools/src/bamToFastq/bamToFastq.cpp
quast_libs/bedtools/src/bamToFastq/bamToFastq.h
quast_libs/bedtools/src/bamToFastq/bamToFastqMain.cpp
quast_libs/bedtools/src/bed12ToBed6/Makefile
quast_libs/bedtools/src/bed12ToBed6/bed12ToBed6.cpp
quast_libs/bedtools/src/bedToBam/Makefile
quast_libs/bedtools/src/bedToBam/bedToBam.cpp
quast_libs/bedtools/src/bedToIgv/Makefile
quast_libs/bedtools/src/bedToIgv/bedToIgv.cpp
quast_libs/bedtools/src/bedpeToBam/Makefile
quast_libs/bedtools/src/bedpeToBam/bedpeToBam.cpp
quast_libs/bedtools/src/bedpeToBam/notes.txt
quast_libs/bedtools/src/closestFile/Makefile
quast_libs/bedtools/src/closestFile/closestFile.cpp
quast_libs/bedtools/src/closestFile/closestFile.h
quast_libs/bedtools/src/closestFile/closestHelp.cpp
quast_libs/bedtools/src/clusterBed/Makefile
quast_libs/bedtools/src/clusterBed/clusterBed.cpp
quast_libs/bedtools/src/clusterBed/clusterBed.h
quast_libs/bedtools/src/clusterBed/clusterMain.cpp
quast_libs/bedtools/src/complementFile/Makefile
quast_libs/bedtools/src/complementFile/complementFile.cpp
quast_libs/bedtools/src/complementFile/complementFile.h
quast_libs/bedtools/src/complementFile/complementHelp.cpp
quast_libs/bedtools/src/coverageFile/Makefile
quast_libs/bedtools/src/coverageFile/coverageFile.cpp
quast_libs/bedtools/src/coverageFile/coverageFile.h
quast_libs/bedtools/src/coverageFile/coverageHelp.cpp
quast_libs/bedtools/src/expand/Makefile
quast_libs/bedtools/src/expand/expand.cpp
quast_libs/bedtools/src/fastaFromBed/Makefile
quast_libs/bedtools/src/fastaFromBed/fastaFromBed.cpp
quast_libs/bedtools/src/fastaFromBed/fastaFromBed.h
quast_libs/bedtools/src/fastaFromBed/fastaFromBedMain.cpp
quast_libs/bedtools/src/fisher/Makefile
quast_libs/bedtools/src/fisher/fisher.cpp
quast_libs/bedtools/src/fisher/fisher.h
quast_libs/bedtools/src/fisher/fisherHelp.cpp
quast_libs/bedtools/src/fisher/kfunc.cpp
quast_libs/bedtools/src/fisher/kfunc.h
quast_libs/bedtools/src/flankBed/Makefile
quast_libs/bedtools/src/flankBed/flankBed.cpp
quast_libs/bedtools/src/flankBed/flankBed.h
quast_libs/bedtools/src/flankBed/flankBedMain.cpp
quast_libs/bedtools/src/genomeCoverageBed/Makefile
quast_libs/bedtools/src/genomeCoverageBed/genomeCoverageBed.cpp
quast_libs/bedtools/src/genomeCoverageBed/genomeCoverageBed.h
quast_libs/bedtools/src/genomeCoverageBed/genomeCoverageMain.cpp
quast_libs/bedtools/src/getOverlap/Makefile
quast_libs/bedtools/src/getOverlap/getOverlap.cpp
quast_libs/bedtools/src/groupBy/Makefile
quast_libs/bedtools/src/groupBy/groupBy.cpp
quast_libs/bedtools/src/groupBy/groupBy.h
quast_libs/bedtools/src/groupBy/groupByHelp.cpp
quast_libs/bedtools/src/intersectFile/Makefile
quast_libs/bedtools/src/intersectFile/intersectFile.cpp
quast_libs/bedtools/src/intersectFile/intersectFile.h
quast_libs/bedtools/src/intersectFile/intersectHelp.cpp
quast_libs/bedtools/src/jaccard/Makefile
quast_libs/bedtools/src/jaccard/jaccard.cpp
quast_libs/bedtools/src/jaccard/jaccard.h
quast_libs/bedtools/src/jaccard/jaccardHelp.cpp
quast_libs/bedtools/src/linksBed/Makefile
quast_libs/bedtools/src/linksBed/linksBed.cpp
quast_libs/bedtools/src/linksBed/linksBed.h
quast_libs/bedtools/src/linksBed/linksMain.cpp
quast_libs/bedtools/src/mapFile/Makefile
quast_libs/bedtools/src/mapFile/mapFile.cpp
quast_libs/bedtools/src/mapFile/mapFile.h
quast_libs/bedtools/src/mapFile/mapHelp.cpp
quast_libs/bedtools/src/maskFastaFromBed/Makefile
quast_libs/bedtools/src/maskFastaFromBed/maskFastaFromBed.cpp
quast_libs/bedtools/src/maskFastaFromBed/maskFastaFromBed.h
quast_libs/bedtools/src/maskFastaFromBed/maskFastaFromBedMain.cpp
quast_libs/bedtools/src/mergeFile/Makefile
quast_libs/bedtools/src/mergeFile/mergeFile.cpp
quast_libs/bedtools/src/mergeFile/mergeFile.h
quast_libs/bedtools/src/mergeFile/mergeHelp.cpp
quast_libs/bedtools/src/multiBamCov/Makefile
quast_libs/bedtools/src/multiBamCov/multiBamCov.cpp
quast_libs/bedtools/src/multiBamCov/multiBamCov.h
quast_libs/bedtools/src/multiBamCov/multiBamCovMain.cpp
quast_libs/bedtools/src/multiIntersectBed/Makefile
quast_libs/bedtools/src/multiIntersectBed/multiIntersectBed.cpp
quast_libs/bedtools/src/multiIntersectBed/multiIntersectBed.h
quast_libs/bedtools/src/multiIntersectBed/multiIntersectBedMain.cpp
quast_libs/bedtools/src/nekSandbox1/FormatGuess.h
quast_libs/bedtools/src/nekSandbox1/Makefile
quast_libs/bedtools/src/nekSandbox1/nekSandboxMain.cpp
quast_libs/bedtools/src/nucBed/LargeFileSupport.h
quast_libs/bedtools/src/nucBed/Makefile
quast_libs/bedtools/src/nucBed/nucBed.cpp
quast_libs/bedtools/src/nucBed/nucBed.h
quast_libs/bedtools/src/nucBed/nucBedMain.cpp
quast_libs/bedtools/src/pairToBed/Makefile
quast_libs/bedtools/src/pairToBed/pairToBed.cpp
quast_libs/bedtools/src/pairToBed/pairToBed.h
quast_libs/bedtools/src/pairToBed/pairToBedMain.cpp
quast_libs/bedtools/src/pairToPair/Makefile
quast_libs/bedtools/src/pairToPair/pairToPair.cpp
quast_libs/bedtools/src/pairToPair/pairToPair.h
quast_libs/bedtools/src/pairToPair/pairToPairMain.cpp
quast_libs/bedtools/src/randomBed/Makefile
quast_libs/bedtools/src/randomBed/randomBed.cpp
quast_libs/bedtools/src/randomBed/randomBed.h
quast_libs/bedtools/src/randomBed/randomBedMain.cpp
quast_libs/bedtools/src/regressTest/Makefile
quast_libs/bedtools/src/regressTest/RegressTest.cpp
quast_libs/bedtools/src/regressTest/RegressTest.h
quast_libs/bedtools/src/regressTest/regressTestMain.cpp
quast_libs/bedtools/src/reldist/Makefile
quast_libs/bedtools/src/reldist/reldist.cpp
quast_libs/bedtools/src/reldist/reldist.h
quast_libs/bedtools/src/reldist/reldistMain.cpp
quast_libs/bedtools/src/sampleFile/Makefile
quast_libs/bedtools/src/sampleFile/sampleFile.cpp
quast_libs/bedtools/src/sampleFile/sampleFile.h
quast_libs/bedtools/src/sampleFile/sampleHelp.cpp
quast_libs/bedtools/src/shiftBed/Makefile
quast_libs/bedtools/src/shiftBed/shiftBed.cpp
quast_libs/bedtools/src/shiftBed/shiftBed.h
quast_libs/bedtools/src/shiftBed/shiftBedMain.cpp
quast_libs/bedtools/src/shuffleBed/Makefile
quast_libs/bedtools/src/shuffleBed/shuffleBed.cpp
quast_libs/bedtools/src/shuffleBed/shuffleBed.h
quast_libs/bedtools/src/shuffleBed/shuffleBedMain.cpp
quast_libs/bedtools/src/slopBed/Makefile
quast_libs/bedtools/src/slopBed/slopBed.cpp
quast_libs/bedtools/src/slopBed/slopBed.h
quast_libs/bedtools/src/slopBed/slopBedMain.cpp
quast_libs/bedtools/src/sortBed/Makefile
quast_libs/bedtools/src/sortBed/sortBed.cpp
quast_libs/bedtools/src/sortBed/sortBed.h
quast_libs/bedtools/src/sortBed/sortMain.cpp
quast_libs/bedtools/src/spacingFile/Makefile
quast_libs/bedtools/src/spacingFile/spacingFile.cpp
quast_libs/bedtools/src/spacingFile/spacingFile.h
quast_libs/bedtools/src/spacingFile/spacingHelp.cpp
quast_libs/bedtools/src/split/Makefile
quast_libs/bedtools/src/split/splitBed.cpp
quast_libs/bedtools/src/split/splitBed.h
quast_libs/bedtools/src/split/splitBedMain.cpp
quast_libs/bedtools/src/subtractFile/Makefile
quast_libs/bedtools/src/subtractFile/subtractFile.cpp
quast_libs/bedtools/src/subtractFile/subtractFile.h
quast_libs/bedtools/src/subtractFile/subtractHelp.cpp
quast_libs/bedtools/src/tagBam/Makefile
quast_libs/bedtools/src/tagBam/tagBam.cpp
quast_libs/bedtools/src/tagBam/tagBam.h
quast_libs/bedtools/src/tagBam/tagBamMain.cpp
quast_libs/bedtools/src/unionBedGraphs/Makefile
quast_libs/bedtools/src/unionBedGraphs/unionBedGraphs.cpp
quast_libs/bedtools/src/unionBedGraphs/unionBedGraphs.h
quast_libs/bedtools/src/unionBedGraphs/unionBedGraphsMain.cpp
quast_libs/bedtools/src/utils/BamTools/.gitignore
quast_libs/bedtools/src/utils/BamTools/LICENSE
quast_libs/bedtools/src/utils/BamTools/Makefile
quast_libs/bedtools/src/utils/BamTools-Ancillary/BamAncillary.cpp
quast_libs/bedtools/src/utils/BamTools-Ancillary/BamAncillary.h
quast_libs/bedtools/src/utils/BamTools-Ancillary/Makefile
quast_libs/bedtools/src/utils/BamTools/include/api/BamAlgorithms.h
quast_libs/bedtools/src/utils/BamTools/include/api/BamAlignment.h
quast_libs/bedtools/src/utils/BamTools/include/api/BamAux.h
quast_libs/bedtools/src/utils/BamTools/include/api/BamConstants.h
quast_libs/bedtools/src/utils/BamTools/include/api/BamIndex.h
quast_libs/bedtools/src/utils/BamTools/include/api/BamMultiReader.h
quast_libs/bedtools/src/utils/BamTools/include/api/BamReader.h
quast_libs/bedtools/src/utils/BamTools/include/api/BamWriter.h
quast_libs/bedtools/src/utils/BamTools/include/api/IBamIODevice.h
quast_libs/bedtools/src/utils/BamTools/include/api/SamConstants.h
quast_libs/bedtools/src/utils/BamTools/include/api/SamHeader.h
quast_libs/bedtools/src/utils/BamTools/include/api/SamProgram.h
quast_libs/bedtools/src/utils/BamTools/include/api/SamProgramChain.h
quast_libs/bedtools/src/utils/BamTools/include/api/SamReadGroup.h
quast_libs/bedtools/src/utils/BamTools/include/api/SamReadGroupDictionary.h
quast_libs/bedtools/src/utils/BamTools/include/api/SamSequence.h
quast_libs/bedtools/src/utils/BamTools/include/api/SamSequenceDictionary.h
quast_libs/bedtools/src/utils/BamTools/include/api/api_global.h
quast_libs/bedtools/src/utils/BamTools/include/shared/bamtools_global.h
quast_libs/bedtools/src/utils/BamTools/lib/libbamtools.a
quast_libs/bedtools/src/utils/BamTools/src/api/BamAlgorithms.h
quast_libs/bedtools/src/utils/BamTools/src/api/BamAlignment.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/BamAlignment.h
quast_libs/bedtools/src/utils/BamTools/src/api/BamAlignment.o
quast_libs/bedtools/src/utils/BamTools/src/api/BamAux.h
quast_libs/bedtools/src/utils/BamTools/src/api/BamConstants.h
quast_libs/bedtools/src/utils/BamTools/src/api/BamIndex.h
quast_libs/bedtools/src/utils/BamTools/src/api/BamMultiReader.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/BamMultiReader.h
quast_libs/bedtools/src/utils/BamTools/src/api/BamMultiReader.o
quast_libs/bedtools/src/utils/BamTools/src/api/BamReader.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/BamReader.h
quast_libs/bedtools/src/utils/BamTools/src/api/BamReader.o
quast_libs/bedtools/src/utils/BamTools/src/api/BamWriter.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/BamWriter.h
quast_libs/bedtools/src/utils/BamTools/src/api/BamWriter.o
quast_libs/bedtools/src/utils/BamTools/src/api/IBamIODevice.h
quast_libs/bedtools/src/utils/BamTools/src/api/SamConstants.h
quast_libs/bedtools/src/utils/BamTools/src/api/SamHeader.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/SamHeader.h
quast_libs/bedtools/src/utils/BamTools/src/api/SamHeader.o
quast_libs/bedtools/src/utils/BamTools/src/api/SamProgram.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/SamProgram.h
quast_libs/bedtools/src/utils/BamTools/src/api/SamProgram.o
quast_libs/bedtools/src/utils/BamTools/src/api/SamProgramChain.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/SamProgramChain.h
quast_libs/bedtools/src/utils/BamTools/src/api/SamProgramChain.o
quast_libs/bedtools/src/utils/BamTools/src/api/SamReadGroup.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/SamReadGroup.h
quast_libs/bedtools/src/utils/BamTools/src/api/SamReadGroup.o
quast_libs/bedtools/src/utils/BamTools/src/api/SamReadGroupDictionary.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/SamReadGroupDictionary.h
quast_libs/bedtools/src/utils/BamTools/src/api/SamReadGroupDictionary.o
quast_libs/bedtools/src/utils/BamTools/src/api/SamSequence.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/SamSequence.h
quast_libs/bedtools/src/utils/BamTools/src/api/SamSequence.o
quast_libs/bedtools/src/utils/BamTools/src/api/SamSequenceDictionary.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/SamSequenceDictionary.h
quast_libs/bedtools/src/utils/BamTools/src/api/SamSequenceDictionary.o
quast_libs/bedtools/src/utils/BamTools/src/api/api_global.h
quast_libs/bedtools/src/utils/BamTools/src/api/algorithms/Sort.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamHeader_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamHeader_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamHeader_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamMultiMerger_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamMultiReader_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamMultiReader_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamMultiReader_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamRandomAccessController_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamRandomAccessController_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamRandomAccessController_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamReader_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamReader_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamReader_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamWriter_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamWriter_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/bam/BamWriter_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/index/BamIndexFactory_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/index/BamIndexFactory_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/index/BamIndexFactory_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/index/BamStandardIndex_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/index/BamStandardIndex_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/index/BamStandardIndex_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/index/BamToolsIndex_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/index/BamToolsIndex_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/index/BamToolsIndex_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BamDeviceFactory_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BamFile_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BamFile_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BamFile_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BamFtp_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BamFtp_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BamFtp_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BamHttp_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BamHttp_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BamHttp_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BamPipe_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BamPipe_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BamPipe_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BgzfStream_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BgzfStream_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/BgzfStream_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/ByteArray_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/ByteArray_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/ByteArray_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/HostAddress_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/HostAddress_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/HostAddress_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/HostInfo_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/HostInfo_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/HostInfo_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/HttpHeader_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/HttpHeader_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/HttpHeader_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/ILocalIODevice_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/ILocalIODevice_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/ILocalIODevice_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/NetUnix_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/NetWin_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/RollingBuffer_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/RollingBuffer_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/RollingBuffer_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/StdStreamDevice_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/TcpSocketEngine_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/TcpSocketEngine_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/TcpSocketEngine_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/TcpSocketEngine_unix_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/TcpSocketEngine_unix_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/TcpSocketEngine_win_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/TcpSocket_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/TcpSocket_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/io/TcpSocket_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/sam/SamFormatParser_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/sam/SamFormatParser_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/sam/SamFormatParser_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/sam/SamFormatPrinter_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/sam/SamFormatPrinter_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/sam/SamFormatPrinter_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/sam/SamHeaderValidator_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/sam/SamHeaderValidator_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/sam/SamHeaderValidator_p.o
quast_libs/bedtools/src/utils/BamTools/src/api/internal/sam/SamHeaderVersion_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/utils/BamException_p.cpp
quast_libs/bedtools/src/utils/BamTools/src/api/internal/utils/BamException_p.h
quast_libs/bedtools/src/utils/BamTools/src/api/internal/utils/BamException_p.o
quast_libs/bedtools/src/utils/BamTools/src/shared/bamtools_global.h
quast_libs/bedtools/src/utils/BinTree/BinTree.cpp
quast_libs/bedtools/src/utils/BinTree/BinTree.h
quast_libs/bedtools/src/utils/BinTree/Makefile
quast_libs/bedtools/src/utils/BlockedIntervals/BlockedIntervals.cpp
quast_libs/bedtools/src/utils/BlockedIntervals/BlockedIntervals.h
quast_libs/bedtools/src/utils/BlockedIntervals/Makefile
quast_libs/bedtools/src/utils/Contexts/ContextBase.cpp
quast_libs/bedtools/src/utils/Contexts/ContextBase.h
quast_libs/bedtools/src/utils/Contexts/ContextClosest.cpp
quast_libs/bedtools/src/utils/Contexts/ContextClosest.h
quast_libs/bedtools/src/utils/Contexts/ContextComplement.cpp
quast_libs/bedtools/src/utils/Contexts/ContextComplement.h
quast_libs/bedtools/src/utils/Contexts/ContextCoverage.cpp
quast_libs/bedtools/src/utils/Contexts/ContextCoverage.h
quast_libs/bedtools/src/utils/Contexts/ContextFisher.cpp
quast_libs/bedtools/src/utils/Contexts/ContextFisher.h
quast_libs/bedtools/src/utils/Contexts/ContextGroupBy.cpp
quast_libs/bedtools/src/utils/Contexts/ContextGroupBy.h
quast_libs/bedtools/src/utils/Contexts/ContextIntersect.cpp
quast_libs/bedtools/src/utils/Contexts/ContextIntersect.h
quast_libs/bedtools/src/utils/Contexts/ContextJaccard.cpp
quast_libs/bedtools/src/utils/Contexts/ContextJaccard.h
quast_libs/bedtools/src/utils/Contexts/ContextMap.cpp
quast_libs/bedtools/src/utils/Contexts/ContextMap.h
quast_libs/bedtools/src/utils/Contexts/ContextMerge.cpp
quast_libs/bedtools/src/utils/Contexts/ContextMerge.h
quast_libs/bedtools/src/utils/Contexts/ContextSample.cpp
quast_libs/bedtools/src/utils/Contexts/ContextSample.h
quast_libs/bedtools/src/utils/Contexts/ContextSpacing.cpp
quast_libs/bedtools/src/utils/Contexts/ContextSpacing.h
quast_libs/bedtools/src/utils/Contexts/ContextSubtract.cpp
quast_libs/bedtools/src/utils/Contexts/ContextSubtract.h
quast_libs/bedtools/src/utils/Contexts/Makefile
quast_libs/bedtools/src/utils/Fasta/Fasta.cpp
quast_libs/bedtools/src/utils/Fasta/Fasta.h
quast_libs/bedtools/src/utils/Fasta/LargeFileSupport.h
quast_libs/bedtools/src/utils/Fasta/Makefile
quast_libs/bedtools/src/utils/Fasta/split.cpp
quast_libs/bedtools/src/utils/Fasta/split.h
quast_libs/bedtools/src/utils/FileRecordTools/FileRecordMergeMgr.cpp
quast_libs/bedtools/src/utils/FileRecordTools/FileRecordMergeMgr.h
quast_libs/bedtools/src/utils/FileRecordTools/FileRecordMgr.cpp
quast_libs/bedtools/src/utils/FileRecordTools/FileRecordMgr.h
quast_libs/bedtools/src/utils/FileRecordTools/Makefile
quast_libs/bedtools/src/utils/FileRecordTools/FileReaders/BamFileReader.cpp
quast_libs/bedtools/src/utils/FileRecordTools/FileReaders/BamFileReader.h
quast_libs/bedtools/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp
quast_libs/bedtools/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.h
quast_libs/bedtools/src/utils/FileRecordTools/FileReaders/FileReader.cpp
quast_libs/bedtools/src/utils/FileRecordTools/FileReaders/FileReader.h
quast_libs/bedtools/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp
quast_libs/bedtools/src/utils/FileRecordTools/FileReaders/InputStreamMgr.h
quast_libs/bedtools/src/utils/FileRecordTools/FileReaders/Makefile
quast_libs/bedtools/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp
quast_libs/bedtools/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h
quast_libs/bedtools/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp
quast_libs/bedtools/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/BamRecord.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/BamRecord.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/Bed12Interval.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/Bed12Interval.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/Bed3Interval.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/Bed3Interval.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/Bed4Interval.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/Bed4Interval.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/Bed5Interval.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/Bed5Interval.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/Bed6Interval.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/Bed6Interval.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/BedGraphInterval.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/BedGraphInterval.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/BedPlusInterval.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/BedPlusInterval.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/BlockMgr.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/BlockMgr.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/EmptyRecord.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/EmptyRecord.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/GffPlusRecord.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/GffPlusRecord.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/GffRecord.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/GffRecord.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/Makefile
quast_libs/bedtools/src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/NoPosPlusRecord.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/PlusFields.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/PlusFields.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/Record.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/Record.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/RecordKeyList.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/RecordKeyList.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/RecordKeyVector.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/RecordKeyVector.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/RecordList.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/RecordList.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/RecordMgr.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/RecordMgr.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/StrandQueue.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/StrandQueue.h
quast_libs/bedtools/src/utils/FileRecordTools/Records/VcfRecord.cpp
quast_libs/bedtools/src/utils/FileRecordTools/Records/VcfRecord.h
quast_libs/bedtools/src/utils/GenomeFile/GenomeFile.cpp
quast_libs/bedtools/src/utils/GenomeFile/GenomeFile.h
quast_libs/bedtools/src/utils/GenomeFile/Makefile
quast_libs/bedtools/src/utils/GenomeFile/NewGenomeFile.cpp
quast_libs/bedtools/src/utils/GenomeFile/NewGenomeFile.h
quast_libs/bedtools/src/utils/KeyListOps/KeyListOps.cpp
quast_libs/bedtools/src/utils/KeyListOps/KeyListOps.h
quast_libs/bedtools/src/utils/KeyListOps/KeyListOpsMethods.cpp
quast_libs/bedtools/src/utils/KeyListOps/KeyListOpsMethods.h
quast_libs/bedtools/src/utils/KeyListOps/Makefile
quast_libs/bedtools/src/utils/NewChromsweep/CloseSweep.cpp
quast_libs/bedtools/src/utils/NewChromsweep/CloseSweep.h
quast_libs/bedtools/src/utils/NewChromsweep/Makefile
quast_libs/bedtools/src/utils/NewChromsweep/NewChromsweep.cpp
quast_libs/bedtools/src/utils/NewChromsweep/NewChromsweep.h
quast_libs/bedtools/src/utils/Point/Point.h
quast_libs/bedtools/src/utils/RecordOutputMgr/Makefile
quast_libs/bedtools/src/utils/RecordOutputMgr/RecordOutputMgr.cpp
quast_libs/bedtools/src/utils/RecordOutputMgr/RecordOutputMgr.h
quast_libs/bedtools/src/utils/ToolBase/Makefile
quast_libs/bedtools/src/utils/ToolBase/ToolBase.cpp
quast_libs/bedtools/src/utils/ToolBase/ToolBase.h
quast_libs/bedtools/src/utils/VectorOps/Makefile
quast_libs/bedtools/src/utils/VectorOps/VectorOps.cpp
quast_libs/bedtools/src/utils/VectorOps/VectorOps.h
quast_libs/bedtools/src/utils/bedFile/Makefile
quast_libs/bedtools/src/utils/bedFile/bedFile.cpp
quast_libs/bedtools/src/utils/bedFile/bedFile.h
quast_libs/bedtools/src/utils/bedFilePE/Makefile
quast_libs/bedtools/src/utils/bedFilePE/bedFilePE.cpp
quast_libs/bedtools/src/utils/bedFilePE/bedFilePE.h
quast_libs/bedtools/src/utils/bedGraphFile/Makefile
quast_libs/bedtools/src/utils/bedGraphFile/bedGraphFile.cpp
quast_libs/bedtools/src/utils/bedGraphFile/bedGraphFile.h
quast_libs/bedtools/src/utils/chromsweep/Makefile
quast_libs/bedtools/src/utils/chromsweep/chromsweep.cpp
quast_libs/bedtools/src/utils/chromsweep/chromsweep.h
quast_libs/bedtools/src/utils/driver/BedtoolsDriver.cpp
quast_libs/bedtools/src/utils/driver/BedtoolsDriver.h
quast_libs/bedtools/src/utils/driver/Makefile
quast_libs/bedtools/src/utils/fileType/FileRecordTypeChecker.cpp
quast_libs/bedtools/src/utils/fileType/FileRecordTypeChecker.h
quast_libs/bedtools/src/utils/fileType/Makefile
quast_libs/bedtools/src/utils/fileType/fileType.cpp
quast_libs/bedtools/src/utils/fileType/fileType.h
quast_libs/bedtools/src/utils/general/BTlist.h
quast_libs/bedtools/src/utils/general/BedtoolsTypes.h
quast_libs/bedtools/src/utils/general/CommonHelp.cpp
quast_libs/bedtools/src/utils/general/CommonHelp.h
quast_libs/bedtools/src/utils/general/CompressionTools.cpp
quast_libs/bedtools/src/utils/general/CompressionTools.h
quast_libs/bedtools/src/utils/general/ErrorMsg.cpp
quast_libs/bedtools/src/utils/general/ErrorMsg.h
quast_libs/bedtools/src/utils/general/FreeList.h
quast_libs/bedtools/src/utils/general/InflateStreamBuf.h
quast_libs/bedtools/src/utils/general/Makefile
quast_libs/bedtools/src/utils/general/ParseTools.cpp
quast_libs/bedtools/src/utils/general/ParseTools.h
quast_libs/bedtools/src/utils/general/PushBackStreamBuf.cpp
quast_libs/bedtools/src/utils/general/PushBackStreamBuf.h
quast_libs/bedtools/src/utils/general/QuickString.cpp
quast_libs/bedtools/src/utils/general/QuickString.h
quast_libs/bedtools/src/utils/general/Tokenizer.cpp
quast_libs/bedtools/src/utils/general/Tokenizer.h
quast_libs/bedtools/src/utils/gzstream/COPYING.LIB
quast_libs/bedtools/src/utils/gzstream/Makefile
quast_libs/bedtools/src/utils/gzstream/README
quast_libs/bedtools/src/utils/gzstream/gzstream.C
quast_libs/bedtools/src/utils/gzstream/gzstream.h
quast_libs/bedtools/src/utils/gzstream/version
quast_libs/bedtools/src/utils/lineFileUtilities/lineFileUtilities.h
quast_libs/bedtools/src/utils/sequenceUtilities/Makefile
quast_libs/bedtools/src/utils/sequenceUtilities/sequenceUtils.cpp
quast_libs/bedtools/src/utils/sequenceUtilities/sequenceUtils.h
quast_libs/bedtools/src/utils/stringUtilities/stringUtilities.h
quast_libs/bedtools/src/utils/tabFile/Makefile
quast_libs/bedtools/src/utils/tabFile/tabFile.cpp
quast_libs/bedtools/src/utils/tabFile/tabFile.h
quast_libs/bedtools/src/utils/version/Makefile
quast_libs/bedtools/src/utils/version/version.cpp
quast_libs/bedtools/src/utils/version/version.h
quast_libs/bedtools/src/utils/version/version_git.h
quast_libs/bedtools/src/utils/version/version_release.txt
quast_libs/bedtools/src/windowBed/Makefile
quast_libs/bedtools/src/windowBed/windowBed.cpp
quast_libs/bedtools/src/windowBed/windowBed.h
quast_libs/bedtools/src/windowBed/windowMain.cpp
quast_libs/bedtools/src/windowMaker/Makefile
quast_libs/bedtools/src/windowMaker/windowMaker.cpp
quast_libs/bedtools/src/windowMaker/windowMaker.h
quast_libs/bedtools/src/windowMaker/windowMakerMain.cpp
quast_libs/busco/BuscoAnalysis.py
quast_libs/busco/BuscoConfig.py
quast_libs/busco/GeneSetAnalysis.py
quast_libs/busco/GenomeAnalysis.py
quast_libs/busco/TranscriptomeAnalysis.py
quast_libs/busco/__init__.py
quast_libs/busco/_version.py
quast_libs/busco/busco.py
quast_libs/busco/config.ini.default
quast_libs/busco/hmmsearch
quast_libs/busco/pipebricks/PipeConfig.py
quast_libs/busco/pipebricks/PipeHelper.py
quast_libs/busco/pipebricks/PipeLogger.py
quast_libs/busco/pipebricks/Toolset.py
quast_libs/busco/pipebricks/__init__.py
quast_libs/bwa/.gitignore
quast_libs/bwa/.travis.yml
quast_libs/bwa/COPYING
quast_libs/bwa/ChangeLog
quast_libs/bwa/Makefile
quast_libs/bwa/NEWS.md
quast_libs/bwa/QSufSort.c
quast_libs/bwa/QSufSort.h
quast_libs/bwa/QSufSort.o
quast_libs/bwa/README-alt.md
quast_libs/bwa/README.md
quast_libs/bwa/bamlite.c
quast_libs/bwa/bamlite.h
quast_libs/bwa/bamlite.o
quast_libs/bwa/bntseq.c
quast_libs/bwa/bntseq.h
quast_libs/bwa/bntseq.o
quast_libs/bwa/bwa
quast_libs/bwa/bwa.1
quast_libs/bwa/bwa.c
quast_libs/bwa/bwa.h
quast_libs/bwa/bwa.o
quast_libs/bwa/bwamem.c
quast_libs/bwa/bwamem.h
quast_libs/bwa/bwamem.o
quast_libs/bwa/bwamem_extra.c
quast_libs/bwa/bwamem_extra.o
quast_libs/bwa/bwamem_pair.c
quast_libs/bwa/bwamem_pair.o
quast_libs/bwa/bwape.c
quast_libs/bwa/bwape.o
quast_libs/bwa/bwase.c
quast_libs/bwa/bwase.h
quast_libs/bwa/bwase.o
quast_libs/bwa/bwaseqio.c
quast_libs/bwa/bwaseqio.o
quast_libs/bwa/bwashm.c
quast_libs/bwa/bwashm.o
quast_libs/bwa/bwt.c
quast_libs/bwa/bwt.h
quast_libs/bwa/bwt.o
quast_libs/bwa/bwt_gen.c
quast_libs/bwa/bwt_gen.o
quast_libs/bwa/bwt_lite.c
quast_libs/bwa/bwt_lite.h
quast_libs/bwa/bwt_lite.o
quast_libs/bwa/bwtaln.c
quast_libs/bwa/bwtaln.h
quast_libs/bwa/bwtaln.o
quast_libs/bwa/bwtgap.c
quast_libs/bwa/bwtgap.h
quast_libs/bwa/bwtgap.o
quast_libs/bwa/bwtindex.c
quast_libs/bwa/bwtindex.o
quast_libs/bwa/bwtsw2.h
quast_libs/bwa/bwtsw2_aux.c
quast_libs/bwa/bwtsw2_aux.o
quast_libs/bwa/bwtsw2_chain.c
quast_libs/bwa/bwtsw2_chain.o
quast_libs/bwa/bwtsw2_core.c
quast_libs/bwa/bwtsw2_core.o
quast_libs/bwa/bwtsw2_main.c
quast_libs/bwa/bwtsw2_main.o
quast_libs/bwa/bwtsw2_pair.c
quast_libs/bwa/bwtsw2_pair.o
quast_libs/bwa/example.c
quast_libs/bwa/fastmap.c
quast_libs/bwa/fastmap.o
quast_libs/bwa/is.c
quast_libs/bwa/is.o
quast_libs/bwa/kbtree.h
quast_libs/bwa/khash.h
quast_libs/bwa/kopen.c
quast_libs/bwa/kopen.o
quast_libs/bwa/kseq.h
quast_libs/bwa/ksort.h
quast_libs/bwa/kstring.c
quast_libs/bwa/kstring.h
quast_libs/bwa/kstring.o
quast_libs/bwa/ksw.c
quast_libs/bwa/ksw.h
quast_libs/bwa/ksw.o
quast_libs/bwa/kthread.c
quast_libs/bwa/kthread.o
quast_libs/bwa/kvec.h
quast_libs/bwa/libbwa.a
quast_libs/bwa/main.c
quast_libs/bwa/main.o
quast_libs/bwa/make.err
quast_libs/bwa/make.log
quast_libs/bwa/malloc_wrap.c
quast_libs/bwa/malloc_wrap.h
quast_libs/bwa/malloc_wrap.o
quast_libs/bwa/maxk.c
quast_libs/bwa/maxk.o
quast_libs/bwa/pemerge.c
quast_libs/bwa/pemerge.o
quast_libs/bwa/qualfa2fq.pl
quast_libs/bwa/rle.c
quast_libs/bwa/rle.h
quast_libs/bwa/rle.o
quast_libs/bwa/rope.c
quast_libs/bwa/rope.h
quast_libs/bwa/rope.o
quast_libs/bwa/utils.c
quast_libs/bwa/utils.h
quast_libs/bwa/utils.o
quast_libs/bwa/xa2multi.pl
quast_libs/bwa/bwakit/README.md
quast_libs/bwa/bwakit/bwa-postalt.js
quast_libs/bwa/bwakit/run-HLA
quast_libs/bwa/bwakit/run-bwamem
quast_libs/bwa/bwakit/run-gen-ref
quast_libs/bwa/bwakit/typeHLA-selctg.js
quast_libs/bwa/bwakit/typeHLA.js
quast_libs/bwa/bwakit/typeHLA.sh
quast_libs/ca_utils/__init__.py
quast_libs/ca_utils/align_contigs.py
quast_libs/ca_utils/analyze_contigs.py
quast_libs/ca_utils/analyze_misassemblies.py
quast_libs/ca_utils/best_set_selection.py
quast_libs/ca_utils/misc.py
quast_libs/ca_utils/save_results.py
quast_libs/glimmer/COPYRIGHT
quast_libs/glimmer/LICENSE
quast_libs/glimmer/README.first
quast_libs/glimmer/version_update
quast_libs/glimmer/src/context.h
quast_libs/glimmer/src/delcher.h
quast_libs/glimmer/src/gene.h
quast_libs/glimmer/src/glimmerhmm.c
quast_libs/glimmer/src/graph.c
quast_libs/glimmer/src/graph.h
quast_libs/glimmer/src/icm.h
quast_libs/glimmer/src/makefile
quast_libs/glimmer/src/oc1.h
quast_libs/glimmer/src/sites.c
quast_libs/glimmer/src/sites.h
quast_libs/glimmer/src/strarray.h
quast_libs/glimmer/src/tree_util_prob.c
quast_libs/glimmer/src/util.c
quast_libs/glimmer/trained/arabidopsis/acc.dt
quast_libs/glimmer/trained/arabidopsis/acc1.mar
quast_libs/glimmer/trained/arabidopsis/acc2
quast_libs/glimmer/trained/arabidopsis/acc4
quast_libs/glimmer/trained/arabidopsis/acc5
quast_libs/glimmer/trained/arabidopsis/acc6
quast_libs/glimmer/trained/arabidopsis/all.hexfreq
quast_libs/glimmer/trained/arabidopsis/atg.dt
quast_libs/glimmer/trained/arabidopsis/atg.markov
quast_libs/glimmer/trained/arabidopsis/coding_0_100.model
quast_libs/glimmer/trained/arabidopsis/config.file
quast_libs/glimmer/trained/arabidopsis/don.dt
quast_libs/glimmer/trained/arabidopsis/don1.mar
quast_libs/glimmer/trained/arabidopsis/don2
quast_libs/glimmer/trained/arabidopsis/don4
quast_libs/glimmer/trained/arabidopsis/don5
quast_libs/glimmer/trained/arabidopsis/don6
quast_libs/glimmer/trained/arabidopsis/exon.distr
quast_libs/glimmer/trained/arabidopsis/exon.hexfreq
quast_libs/glimmer/trained/arabidopsis/exonno.distr
quast_libs/glimmer/trained/arabidopsis/exons.dat
quast_libs/glimmer/trained/arabidopsis/false.acc
quast_libs/glimmer/trained/arabidopsis/false.atg
quast_libs/glimmer/trained/arabidopsis/false.don
quast_libs/glimmer/trained/arabidopsis/false.stop
quast_libs/glimmer/trained/arabidopsis/genelist
quast_libs/glimmer/trained/arabidopsis/noncoding_0_100.model
quast_libs/glimmer/trained/arabidopsis/outex
quast_libs/glimmer/trained/arabidopsis/outin
quast_libs/glimmer/trained/arabidopsis/score_ex.acc
quast_libs/glimmer/trained/arabidopsis/score_ex.don
quast_libs/glimmer/trained/arabidopsis/score_in.acc
quast_libs/glimmer/trained/arabidopsis/score_in.don
quast_libs/glimmer/trained/arabidopsis/seqs
quast_libs/glimmer/trained/arabidopsis/stop.dt
quast_libs/glimmer/trained/arabidopsis/stop.markov
quast_libs/glimmer/trained/arabidopsis/train_0_100.cfg
quast_libs/html_saver/__init__.py
quast_libs/html_saver/glossary.json
quast_libs/html_saver/html_saver.py
quast_libs/html_saver/icarus_menu_templ.html
quast_libs/html_saver/json_saver.py
quast_libs/html_saver/template.html
quast_libs/html_saver/viewers_template.html
quast_libs/html_saver/static/common.css
quast_libs/html_saver/static/d3.js
quast_libs/html_saver/static/dragtable.js
quast_libs/html_saver/static/icarus.css
quast_libs/html_saver/static/ie_html5.js
quast_libs/html_saver/static/jquery-1.7.2.min.js
quast_libs/html_saver/static/jquery-1.8.2.js
quast_libs/html_saver/static/jquery-1.8.2.min.js
quast_libs/html_saver/static/jquery-ui.js
quast_libs/html_saver/static/jquery.css
quast_libs/html_saver/static/report.css
quast_libs/html_saver/static/bootstrap/bootstrap-tooltip-5px-lower.min.js
quast_libs/html_saver/static/bootstrap/bootstrap-tooltip-vlad.js
quast_libs/html_saver/static/bootstrap/bootstrap.css
quast_libs/html_saver/static/bootstrap/bootstrap.min.css
quast_libs/html_saver/static/bootstrap/bootstrap.min.js
quast_libs/html_saver/static/flot/API.txt
quast_libs/html_saver/static/flot/FAQ.txt
quast_libs/html_saver/static/flot/LICENSE.txt
quast_libs/html_saver/static/flot/Makefile
quast_libs/html_saver/static/flot/NEWS.txt
quast_libs/html_saver/static/flot/PLUGINS.txt
quast_libs/html_saver/static/flot/README.txt
quast_libs/html_saver/static/flot/excanvas.js
quast_libs/html_saver/static/flot/excanvas.min.js
quast_libs/html_saver/static/flot/jquery.colorhelpers.js
quast_libs/html_saver/static/flot/jquery.colorhelpers.min.js
quast_libs/html_saver/static/flot/jquery.flot.crosshair.js
quast_libs/html_saver/static/flot/jquery.flot.crosshair.min.js
quast_libs/html_saver/static/flot/jquery.flot.dashes.js
quast_libs/html_saver/static/flot/jquery.flot.fillbetween.js
quast_libs/html_saver/static/flot/jquery.flot.fillbetween.min.js
quast_libs/html_saver/static/flot/jquery.flot.image.js
quast_libs/html_saver/static/flot/jquery.flot.image.min.js
quast_libs/html_saver/static/flot/jquery.flot.js
quast_libs/html_saver/static/flot/jquery.flot.min.js
quast_libs/html_saver/static/flot/jquery.flot.navigate.js
quast_libs/html_saver/static/flot/jquery.flot.navigate.min.js
quast_libs/html_saver/static/flot/jquery.flot.pie.js
quast_libs/html_saver/static/flot/jquery.flot.pie.min.js
quast_libs/html_saver/static/flot/jquery.flot.resize.js
quast_libs/html_saver/static/flot/jquery.flot.resize.min.js
quast_libs/html_saver/static/flot/jquery.flot.selection.js
quast_libs/html_saver/static/flot/jquery.flot.selection.min.js
quast_libs/html_saver/static/flot/jquery.flot.stack.js
quast_libs/html_saver/static/flot/jquery.flot.stack.min.js
quast_libs/html_saver/static/flot/jquery.flot.symbol.js
quast_libs/html_saver/static/flot/jquery.flot.symbol.min.js
quast_libs/html_saver/static/flot/jquery.flot.threshold.js
quast_libs/html_saver/static/flot/jquery.flot.threshold.min.js
quast_libs/html_saver/static/flot/jquery.flot.tickrotor.js
quast_libs/html_saver/static/flot/jquery.js
quast_libs/html_saver/static/flot/jquery.min.js
quast_libs/html_saver/static/img/draggable.png
quast_libs/html_saver/static/img/draggable_16p.png
quast_libs/html_saver/static/img/favicon.ico
quast_libs/html_saver/static/img/icon_plot.png
quast_libs/html_saver/static/img/quast_logo.png
quast_libs/html_saver/static/img/quast_logo_black.png
quast_libs/html_saver/static/img/semi-transparent-10px.png
quast_libs/html_saver/static/img/semi-transparent-10px.pxm
quast_libs/html_saver/static/scripts/build_icarus.js
quast_libs/html_saver/static/scripts/build_report.js
quast_libs/html_saver/static/scripts/build_report_common.js
quast_libs/html_saver/static/scripts/build_report_meta.js
quast_libs/html_saver/static/scripts/build_total_report.js
quast_libs/html_saver/static/scripts/build_total_report_common.js
quast_libs/html_saver/static/scripts/build_total_report_meta.js
quast_libs/html_saver/static/scripts/display_icarus.js
quast_libs/html_saver/static/scripts/draw_cumulative_plot.js
quast_libs/html_saver/static/scripts/draw_frc_plot.js
quast_libs/html_saver/static/scripts/draw_gc_plot.js
quast_libs/html_saver/static/scripts/draw_genes_plot.js
quast_libs/html_saver/static/scripts/draw_meta_misassembl_plot.js
quast_libs/html_saver/static/scripts/draw_metasummary_plot.js
quast_libs/html_saver/static/scripts/draw_nx_plot.js
quast_libs/html_saver/static/scripts/hsvToRgb.js
quast_libs/html_saver/static/scripts/icarus_interface.js
quast_libs/html_saver/static/scripts/icarus_utils.js
quast_libs/html_saver/static/scripts/lighter_darker.js
quast_libs/html_saver/static/scripts/utils.js
quast_libs/kronatools/LICENSE.txt
quast_libs/kronatools/img/favicon.ico
quast_libs/kronatools/img/favicon.uri
quast_libs/kronatools/img/hidden.png
quast_libs/kronatools/img/hidden.uri
quast_libs/kronatools/img/loading.gif
quast_libs/kronatools/img/loading.uri
quast_libs/kronatools/img/logo-small.png
quast_libs/kronatools/img/logo-small.uri
quast_libs/kronatools/lib/KronaTools.pm
quast_libs/kronatools/scripts/ImportText.pl
quast_libs/kronatools/src/krona-2.0.js
quast_libs/minimap2/LICENSE.txt
quast_libs/minimap2/MANIFEST.in
quast_libs/minimap2/Makefile
quast_libs/minimap2/NEWS.md
quast_libs/minimap2/README.md
quast_libs/minimap2/align.c
quast_libs/minimap2/bseq.c
quast_libs/minimap2/bseq.h
quast_libs/minimap2/chain.c
quast_libs/minimap2/esterr.c
quast_libs/minimap2/example.c
quast_libs/minimap2/format.c
quast_libs/minimap2/getopt.c
quast_libs/minimap2/getopt.h
quast_libs/minimap2/hit.c
quast_libs/minimap2/index.c
quast_libs/minimap2/kalloc.c
quast_libs/minimap2/kalloc.h
quast_libs/minimap2/kdq.h
quast_libs/minimap2/khash.h
quast_libs/minimap2/kseq.h
quast_libs/minimap2/ksort.h
quast_libs/minimap2/ksw2.h
quast_libs/minimap2/ksw2_dispatch.c
quast_libs/minimap2/ksw2_extd2_sse.c
quast_libs/minimap2/ksw2_exts2_sse.c
quast_libs/minimap2/ksw2_extz2_sse.c
quast_libs/minimap2/ksw2_ll_sse.c
quast_libs/minimap2/kthread.c
quast_libs/minimap2/kthread.h
quast_libs/minimap2/kvec.h
quast_libs/minimap2/main.c
quast_libs/minimap2/map.c
quast_libs/minimap2/minimap.h
quast_libs/minimap2/minimap2.1
quast_libs/minimap2/misc.c
quast_libs/minimap2/mmpriv.h
quast_libs/minimap2/options.c
quast_libs/minimap2/pe.c
quast_libs/minimap2/sdust.c
quast_libs/minimap2/sdust.h
quast_libs/minimap2/setup.py
quast_libs/minimap2/sketch.c
quast_libs/minimap2/misc/README.md
quast_libs/minimap2/misc/paftools.js
quast_libs/minimap2/python/README.rst
quast_libs/minimap2/python/cmappy.h
quast_libs/minimap2/python/cmappy.pxd
quast_libs/minimap2/python/mappy.pyx
quast_libs/minimap2/python/minimap2.py
quast_libs/minimap2/sse2neon/emmintrin.h
quast_libs/ra_utils/__init__.py
quast_libs/ra_utils/argparse.py
quast_libs/ra_utils/misc.py
quast_libs/ra_utils/vcfToBedpe.py
quast_libs/sambamba/sambamba_linux
quast_libs/sambamba/sambamba_osx
quast_libs/site_packages/__init__.py
quast_libs/site_packages/_bz2.py
quast_libs/site_packages/_compression.py
quast_libs/site_packages/bz2.py
quast_libs/site_packages/ordered_dict.py
quast_libs/site_packages/jsontemplate/__init__.py
quast_libs/site_packages/jsontemplate/jsontemplate.py
test_data/contigs_1.fasta
test_data/contigs_2.fasta
test_data/genes.bed
test_data/genes.gff
test_data/genes.ncbi
test_data/genes.txt
test_data/meta_contigs_1.fasta
test_data/meta_contigs_2.fasta
test_data/meta_ref_1.fasta
test_data/meta_ref_2.fasta
test_data/meta_ref_3.fasta
test_data/operons.bed
test_data/operons.gff
test_data/operons.txt
test_data/reads1.fastq.gz
test_data/reads2.fastq.gz
test_data/reference.fasta.gz