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Project: picard (GitHub Link)
  • picard-master
    • .github
      • PULL_REQUEST_TEMPLATE.md
      • ISSUE_TEMPLATE.md
    • src
      • main
        • resources
          • picard
            • helpTemplates
              • common.html
              • generic.index.template.html
              • generic.template.html
              • picardDoc.css
            • analysis
              • insertSizeHistogram.R
              • gcBias.R
              • meanQualityByCycle.R
              • rnaSeqCoverage.R
              • baseDistributionByCycle.R
              • rrbsQc.R
              • qualityScoreDistribution.R
              • wgsHistogram.R
          • log4j2.xml
          • properties.templates
            • legacyParserProperties.properties
            • barclayParserProperties.properties
          • release_picard.sh
        • java
          • picard
            • fingerprint
              • CrosscheckReadGroupFingerprints.java
              • FingerprintResults.java
              • Fingerprint.java
              • ExtractFingerprint.java
              • HaplotypeMap.java
              • FingerprintIdDetails.java
              • ClusterCrosscheckMetrics.java
              • LocusResult.java
              • HaplotypeProbabilitiesFromSequence.java
              • HaplotypeProbabilitiesUsingLogLikelihoods.java
              • DiploidHaplotype.java
              • DiploidGenotype.java
              • CalculateFingerprintMetrics.java
              • Snp.java
              • CrosscheckFingerprints.java
              • FingerprintChecker.java
              • IdentifyContaminant.java
              • CappedHaplotypeProbabilities.java
              • HaplotypeProbabilitiesFromGenotypeLikelihoods.java
              • HaplotypeProbabilityOfNormalGivenTumor.java
              • MatchResults.java
              • CheckFingerprint.java
              • CrosscheckMetric.java
              • HaplotypeProbabilities.java
              • HaplotypeBlock.java
              • ClusteredCrosscheckMetric.java
              • FingerprintUtils.java
              • HaplotypeProbabilitiesFromContaminatorSequence.java
              • FingerprintMetrics.java
              • HaplotypeProbabilitiesFromGenotype.java
            • cmdline
              • CommandLineDefaults.java
              • CommandLineProgram.java
              • ClassFinder.java
              • argumentcollections
                • RequiredReferenceArgumentCollection.java
                • OutputArgumentCollection.java
                • OptionalReferenceArgumentCollection.java
                • IntervalArgumentCollection.java
                • ReferenceArgumentCollection.java
                • EmptyOutputArgumentCollection.java
                • RequiredOutputArgumentCollection.java
              • CommandLineSyntaxTranslater.java
              • PicardCommandLine.java
              • StandardOptionDefinitions.java
              • programgroups
                • VariantFilteringProgramGroup.java
                • GenotypingArraysProgramGroup.java
                • VariantEvaluationProgramGroup.java
                • DiagnosticsAndQCProgramGroup.java
                • Testing.java
                • BaseCallingProgramGroup.java
                • ReferenceProgramGroup.java
                • IntervalsManipulationProgramGroup.java
                • OtherProgramGroup.java
                • ReadDataManipulationProgramGroup.java
                • VariantManipulationProgramGroup.java
            • vcf
              • MendelianViolations
                • MendelianViolationDetector.java
                • FindMendelianViolations.java
                • MendelianViolationsByFamily.java
                • MendelianViolationMetrics.java
              • MakeVcfSampleNameMap.java
              • FixVcfHeader.java
              • GA4GHScheme.java
              • ByIntervalListVariantContextIterator.java
              • processor
                • VcfFileSegmentGenerator.java
                • VcfFileSegment.java
                • util
                  • PredicateFilterDecoratingClosableIterator.java
                • VariantAccumulatorExecutor.java
                • VariantIteratorProducer.java
                • VariantProcessor.java
              • AccumulateVariantCallingMetrics.java
              • GenotypeConcordanceSchemeFactory.java
              • GA4GHSchemeWithMissingAsHomRef.java
              • SplitVcfs.java
              • VcfToIntervalList.java
              • GenotypeConcordanceStates.java
              • UpdateVcfSequenceDictionary.java
              • GvcfMetricAccumulator.java
              • VcfUtils.java
              • GenotypeConcordanceDetailMetrics.java
              • MakeSitesOnlyVcf.java
              • VcfFormatConverter.java
              • CallingMetricAccumulator.java
              • GenotypeConcordanceStateCodes.java
              • GatherVcfs.java
              • GenotypeConcordanceScheme.java
              • CollectVariantCallingMetrics.java
              • MergeVcfs.java
              • GenotypeConcordance.java
              • PairedVariantSubContextIterator.java
              • LiftoverVcf.java
              • RenameSampleInVcf.java
              • GenotypeConcordanceContingencyMetrics.java
              • GenotypeConcordanceCounts.java
              • GenotypeConcordanceSummaryMetrics.java
              • filter
                • AlleleBalanceFilter.java
                • DepthFilter.java
                • FisherStrandFilter.java
                • FilterApplyingVariantIterator.java
                • GenotypeFilter.java
                • FilterVcf.java
                • GenotypeQualityFilter.java
                • QdFilter.java
                • VariantFilter.java
              • SortVcf.java
            • Test.java
            • PicardException.java
            • illumina
              • CollectIlluminaLaneMetrics.java
              • IlluminaPhasingMetrics.java
              • CollectIlluminaBasecallingMetrics.java
              • IlluminaLaneMetrics.java
              • NewIlluminaBasecallsConverter.java
              • quality
                • CollectHiSeqXPfFailMetrics.java
              • IlluminaBasecallsToSam.java
              • BasecallsConverter.java
              • CustomAdapterPair.java
              • CheckIlluminaDirectory.java
              • DistanceMetric.java
              • ClusterDataToSamConverter.java
              • MarkIlluminaAdapters.java
              • IlluminaBasecallingMetrics.java
              • ExtractIlluminaBarcodes.java
              • IlluminaBasecallsConverter.java
              • LanePhasingMetricsCollector.java
              • parser
                • ReadStructure.java
                • CycleIlluminaFileMap.java
                • ClusterData.java
                • PerTileCycleParser.java
                • IlluminaFileNotFoundException.java
                • IlluminaTextIterator.java
                • FilterParser.java
                • ReadData.java
                • IlluminaDataProvider.java
                • MultiTileParser.java
                • IlluminaData.java
                • IntensityChannel.java
                • MultiTileFileUtil.java
                • FourChannelIntensityData.java
                • IlluminaFileMap.java
                • ClusterIntensityFileReader.java
                • fakers
                  • BciFileFaker.java
                  • PosFileFaker.java
                  • BarcodeFileFaker.java
                  • MultiTileLocsFileFaker.java
                  • MultiTileBclFileFaker.java
                  • LocsFileFaker.java
                  • FileFaker.java
                  • FilterFileFaker.java
                  • BclFileFaker.java
                  • ClocsFileFaker.java
                • BaseIlluminaDataProvider.java
                • PerTileParser.java
                • IlluminaFileUtil.java
                • IlluminaParser.java
                • BclData.java
                • Tile.java
                • MultiTileLocsParser.java
                • Range.java
                • NewIlluminaDataProvider.java
                • IlluminaDataType.java
                • BarcodeParser.java
                • PerTileFileUtil.java
                • ReadType.java
                • TilePhasingValue.java
                • ParameterizedFileUtil.java
                • PerTileOrPerRunFileUtil.java
                • MultiTileBclFileUtil.java
                • MultiTileFilterParser.java
                • CbclData.java
                • readers
                  • BclReader.java
                  • BaseBclReader.java
                  • BclIndexReader.java
                  • ClocsFileReader.java
                  • EmpiricalPhasingMetricsOutReader.java
                  • PosFileReader.java
                  • BclQualityEvaluationStrategy.java
                  • FilterFileReader.java
                  • TileMetricsOutReader.java
                  • MMapBackedIteratorFactory.java
                  • BarcodeFileReader.java
                  • AbstractIlluminaPositionFileReader.java
                  • LocsFileReader.java
                  • CbclReader.java
                • OutputMapping.java
                • IlluminaDataProviderFactory.java
                • TileMetricsUtil.java
                • IlluminaMetricsCode.java
                • PerTilePerCycleFileUtil.java
                • TileIndex.java
                • TileTemplateRead.java
                • MultiTileBclParser.java
                • BclParser.java
                • PosParser.java
                • ReadDescriptor.java
              • IlluminaBasecallsToFastq.java
            • pedigree
              • PedFile.java
              • Sex.java
            • util
              • LiftoverUtils.java
              • DelimitedTextFileWithHeaderIterator.java
              • PropertyUtils.java
              • FifoBuffer.java
              • ReflectionUtil.java
              • CircularByteBuffer.java
              • help
                • HelpConstants.java
                • PicardHelpDoclet.java
                • PicardHelpDocWorkUnitHandler.java
              • AlleleSubsettingUtils.java
              • AsyncIterator.java
              • VariantType.java
              • BarcodeEditDistanceQuery.java
              • GraphUtils.java
              • ThreadPoolExecutorWithExceptions.java
              • LiftOverIntervalList.java
              • AdapterPair.java
              • BasicInputParser.java
              • RExecutor.java
              • BaitDesigner.java
              • IntervalListTools.java
              • QuerySortedReadPairIteratorUtil.java
              • Iterators.java
              • DbSnpBitSetUtil.java
              • BedToIntervalList.java
              • AtomicIterator.java
              • SequenceDictionaryUtils.java
              • ScatterIntervalsByNs.java
              • MathUtil.java
              • TabbedTextFileWithHeaderParser.java
              • IntervalList
                • IntervalListScatterer.java
                • IntervalListScattererWithoutSubdivision.java
                • IntervalListScattererByIntervalCount.java
                • IntervalListScattererWithoutSubdivisionWithOverflow.java
                • IntervalListScatter.java
                • IntervalListScattererWithSubdivision.java
                • IntervalListScattererByBaseCount.java
                • IntervalListScatterMode.java
              • SingleBarcodeDistanceMetric.java
              • ThreadPoolExecutorUtil.java
              • IlluminaUtil.java
              • ClippingUtility.java
              • AbstractInputParser.java
              • TabbedInputParser.java
              • CsvInputParser.java
              • IntervalListToBed.java
              • UnsignedTypeUtil.java
              • AdapterMarker.java
            • arrays
              • VerifyIDIntensityContaminationMetrics.java
              • MergePedIntoVcf.java
              • CreateVerifyIDIntensityContaminationMetricsFile.java
              • illumina
                • InfiniumEGTFile.java
                • Build37ExtendedIlluminaManifest.java
                • IlluminaManifest.java
                • InfiniumVcfFields.java
                • InfiniumDataFile.java
                • Build37ExtendedIlluminaManifestRecord.java
                • InfiniumTransformation.java
                • InfiniumFileTOC.java
                • IlluminaGenotype.java
                • IlluminaBPMLocusEntry.java
                • ArraysControlInfo.java
                • InfiniumGTCRecord.java
                • BpmToNormalizationManifestCsv.java
                • InfiniumNormalizationManifest.java
                • InfiniumGTCFile.java
                • IlluminaBPMFile.java
                • IlluminaAdpcFileWriter.java
                • CompareGtcFiles.java
                • IlluminaManifestRecord.java
              • GtcToVcf.java
              • CollectArraysVariantCallingMetrics.java
              • ZCallPedFile.java
              • ArraysCallingMetricAccumulator.java
              • CombineGenotypingArrayVcfs.java
              • VcfToAdpc.java
            • fastq
              • ReadNameEncoder.java
              • BamToBfqWriter.java
              • IlluminaReadNameEncoder.java
              • Casava18ReadNameEncoder.java
              • BamToBfq.java
            • analysis
              • TheoreticalSensitivity.java
              • CollectRawWgsMetrics.java
              • InsertSizeMetrics.java
              • AbstractWgsMetricsCollector.java
              • MeanQualityByCycle.java
              • GcBiasSummaryMetrics.java
              • RrbsMetricsCollector.java
              • replicates
                • CollectIndependentReplicateMetrics.java
                • IndependentReplicateMetric.java
              • ChimeraUtil.java
              • SinglePassSamProgram.java
              • GcBiasUtils.java
              • GcBiasDetailMetrics.java
              • BaseDistributionByCycleMetrics.java
              • GcBiasMetricsCollector.java
              • CollectAlignmentSummaryMetrics.java
              • FastWgsMetricsCollector.java
              • AdapterUtility.java
              • AlignmentSummaryMetricsCollector.java
              • directed
                • CollectTargetedPcrMetrics.java
                • HsMetricCollector.java
                • TargetedPcrMetrics.java
                • TargetMetrics.java
                • CollectHsMetrics.java
                • TargetMetricsCollector.java
                • PanelMetricsBase.java
                • InsertSizeMetricsCollector.java
                • HsMetrics.java
                • CollectTargetedMetrics.java
                • TargetedPcrMetricsCollector.java
                • TargetMetricsBase.java
                • RnaSeqMetricsCollector.java
              • RrbsSummaryMetrics.java
              • artifacts
                • ContextAccumulator.java
                • Transition.java
                • SequencingArtifactMetrics.java
                • ArtifactCounter.java
                • ErrorSummaryMetrics.java
                • CollectSequencingArtifactMetrics.java
                • ConvertSequencingArtifactToOxoG.java
              • MergeableMetricBase.java
              • CollectGcBiasMetrics.java
              • JumpingLibraryMetrics.java
              • CollectJumpingLibraryMetrics.java
              • RrbsCpgDetailMetrics.java
              • QualityScoreDistribution.java
              • CollectRrbsMetrics.java
              • TheoreticalSensitivityMetrics.java
              • CollectInsertSizeMetrics.java
              • CollectQualityYieldMetrics.java
              • CollectWgsMetrics.java
              • CounterManager.java
              • FingerprintingSummaryMetrics.java
              • AlignmentSummaryMetrics.java
              • CollectRnaSeqMetrics.java
              • WgsMetricsProcessor.java
              • WgsMetrics.java
              • RnaSeqMetrics.java
              • CollectBaseDistributionByCycle.java
              • CollectWgsMetricsWithNonZeroCoverage.java
              • CollectOxoGMetrics.java
              • CompareMetrics.java
              • FingerprintingDetailMetrics.java
              • WgsMetricsProcessorImpl.java
              • CollectMultipleMetrics.java
              • RrbsMetrics.java
              • MetricAccumulationLevel.java
            • reference
              • NormalizeFasta.java
              • NonNFastaSize.java
              • ExtractSequences.java
            • annotation
              • LocusFunction.java
              • RefFlatReader.java
              • AnnotationException.java
              • Gene.java
              • GeneAnnotationReader.java
            • sam
              • BuildBamIndex.java
              • CreateSequenceDictionary.java
              • MultiHitAlignedReadIterator.java
              • SamToFastq.java
              • FixMateInformation.java
              • markduplicates
                • ElcHashBasedDuplicatesFinder.java
                • UmiAwareMarkDuplicatesWithMateCigar.java
                • UmiUtil.java
                • MarkDuplicatesWithMateCigar.java
                • UmiGraph.java
                • MarkDuplicatesWithMateCigarIterator.java
                • EstimateLibraryComplexity.java
                • CollectDuplicateMetrics.java
                • util
                  • LibraryIdGenerator.java
                  • MemoryBasedReadEndsForMarkDuplicatesMap.java
                  • ReadEndsForMarkDuplicatesWithBarcodesCodec.java
                  • PhysicalLocationForMateCigar.java
                  • SamRecordWithOrdinalAndSetDuplicateReadFlag.java
                  • ReadEndsForMarkDuplicatesCodec.java
                  • RepresentativeReadIndexerCodec.java
                  • ReadEndsForMarkDuplicatesMap.java
                  • AbstractMarkDuplicatesCommandLineProgram.java
                  • ReadEndsForMarkDuplicatesWithBarcodes.java
                  • DiskBasedReadEndsForMarkDuplicatesMap.java
                  • PhysicalLocationForMateCigarSet.java
                  • ReadEnds.java
                  • ReadEndsForMarkDuplicates.java
                  • MarkQueue.java
                  • AbstractOpticalDuplicateFinderCommandLineProgram.java
                  • OpticalDuplicateFinder.java
                  • ReadEndsForMateCigar.java
                • ElcDuplicatesFinder.java
                • ElcIdenticalBasesDuplicatesFinder.java
                • MarkDuplicates.java
                • SimpleMarkDuplicatesWithMateCigar.java
                • UmiMetrics.java
                • UmiAwareDuplicateSetIterator.java
                • ElcDuplicatesFinderResolver.java
              • GatherBamFiles.java
              • DuplicationMetrics.java
              • ReplaceSamHeader.java
              • AddOATag.java
              • RevertSam.java
              • CheckTerminatorBlock.java
              • MergeSamFiles.java
              • SetNmMdAndUqTags.java
              • ReorderSam.java
              • AddCommentsToBam.java
              • SamFormatConverter.java
              • RevertOriginalBaseQualitiesAndAddMateCigar.java
              • CompareSAMs.java
              • BamIndexStats.java
              • BestEndMapqPrimaryAlignmentStrategy.java
              • SamComparisonMetric.java
              • CalculateReadGroupChecksum.java
              • CleanSam.java
              • SortSam.java
              • FilterSamReads.java
              • util
                • PrimaryAlignmentKey.java
                • SAMComparisonArgumentCollection.java
                • SamComparison.java
                • PhysicalLocationShort.java
                • PGTagArgumentCollection.java
                • ReadNameParser.java
                • RepresentativeReadIndexer.java
                • PhysicalLocation.java
                • PhysicalLocationInt.java
                • Pair.java
              • FastqToSam.java
              • BestMapqPrimaryAlignmentSelectionStrategy.java
              • ViewSam.java
              • SetNmAndUqTags.java
              • AddOrReplaceReadGroups.java
              • EarliestFragmentPrimaryAlignmentSelectionStrategy.java
              • PrimaryAlignmentSelectionStrategy.java
              • MergeBamAlignment.java
              • SamAlignmentMerger.java
              • SplitSamByLibrary.java
              • HitsForInsert.java
              • SplitSamByNumberOfReads.java
              • MostDistantPrimaryAlignmentSelectionStrategy.java
              • DownsampleSam.java
              • SamErrorMetric
                • CollectSamErrorMetrics.java
                • IndelErrorMetric.java
                • BaseErrorMetric.java
                • OverlappingErrorMetric.java
                • ReadBaseStratification.java
                • BaseCalculator.java
                • SimpleErrorCalculator.java
                • IndelErrorCalculator.java
                • ErrorType.java
                • BaseErrorCalculator.java
                • BaseErrorAggregation.java
                • ErrorMetric.java
                • OverlappingReadsErrorCalculator.java
              • ValidateSamFile.java
              • PositionBasedDownsampleSam.java
              • AbstractAlignmentMerger.java
              • SamToFastqWithTags.java
            • metrics
              • PerUnitMetricCollector.java
              • MultilevelMetrics.java
              • GcBiasMetrics.java
              • MultiLevelCollector.java
              • SAMRecordMultiLevelCollector.java
              • SAMRecordAndReference.java
              • SAMRecordAndReferenceMultiLevelCollector.java
            • filter
              • CountingFilter.java
              • CountingAdapterFilter.java
              • CountingDuplicateFilter.java
              • CountingMapQFilter.java
              • CountingPairedFilter.java
            • nio
              • GoogleStorageUtils.java
              • PathProvider.java
      • test
        • resources
          • failing.R
          • passing.R
          • testng.xml
        • java
          • picard
            • fingerprint
              • CheckFingerprintTest.java
              • ClusterCrosscheckMetricsTest.java
              • CrosscheckFingerprintsTest.java
              • CalculateFingerprintMetricsTest.java
              • HaplotypeProbabilitiesTest.java
              • FingerprintingTestUtils.java
              • CrosscheckReadGroupFingerprintsTest.java
              • FingerprintCheckerTest.java
              • HaplotypeProbabilityOfNormalGivenTumorTest.java
              • HaplotypeMapTest.java
            • cmdline
              • CommandLineProgramTest.java
              • PicardCommandLineTest.java
              • CommandLineProgramStartupErrorLogTest.java
            • vcf
              • MendelianViolations
                • FindMendelianViolationsTest.java
              • VcfToIntervalListTest.java
              • CallingMetricAccumulatorTest.java
              • FixVcfHeaderTest.java
              • SplitVcfsTest.java
              • MakeVcfSampleNameMapTest.java
              • processor
                • AccumulatorExecutorTest.java
                • VcfFileSegmentGeneratorTest.java
                • WidthLimitingDecoratorTest.java
                • ByWholeContigTest.java
                • ThreadsafeTest.java
              • VariantContextComparatorTest.java
              • GenotypeConcordanceGA4GHSchemeWithMissingTest.java
              • VcfTestUtils.java
              • AbstractVcfMergingClpTester.java
              • SortVcfsTest.java
              • GatherVcfsTest.java
              • AccumulateVariantCallingMetricsTest.java
              • VcfFormatConverterTest.java
              • GenotypeConcordanceGA4GHSchemeTest.java
              • ByIntervalListVariantContextIteratorTest.java
              • SamTestUtils.java
              • UpdateVcfSequenceDictionaryTest.java
              • MergeVcfsTest.java
              • GenotypeConcordanceTest.java
              • CollectVariantCallingMetricsTest.java
              • filter
                • TestFilterVcf.java
            • illumina
              • CollectIlluminaBasecallingMetricsTest.java
              • IlluminaBasecallsToSamAdapterClippingTest.java
              • IlluminaLaneMetricsCollectorTest.java
              • CheckIlluminaDirectoryTest.java
              • IlluminaBasecallsToSamTest.java
              • DistanceMetricTest.java
              • ExtractIlluminaBarcodesTest.java
              • ReadStructureTest.java
              • IlluminaBasecallsToFastqTest.java
              • parser
                • PerTilePerCycleParserTest.java
                • BclParserTest.java
                • IlluminaDataProviderTest.java
                • fakers
                  • BclFileFakerTest.java
                • IlluminaFileUtilTest.java
                • CycleIlluminaFileMapTest.java
                • IlluminaDataProviderFactoryTest.java
                • FilterParserTest.java
                • PosParserTest.java
                • PerTileParserTest.java
                • readers
                  • MMapBackedIteratorFactoryTest.java
                  • IlluminaFileUtilTest.java
                  • FilterFileReaderTest.java
                  • BclReaderTest.java
                  • ClocsFileReaderTest.java
                  • PosFileReaderTest.java
                  • LocsFileReaderTest.java
                  • AbstractIlluminaPositionFileReaderTest.java
                  • CbclReaderTest.java
                • TileMetricsUtilTest.java
                • BinTdUtil.java
            • IntelInflaterDeflaterLoadTest.java
            • pedigree
              • PedFileTest.java
            • util
              • QuerySortedReadPairIteratorUtilTest.java
              • MergingIteratorTest.java
              • UnsignedTypeUtilTest.java
              • MathUtilTest.java
              • AlleleSubsettingUtilsTest.java
              • BedToIntervalListTest.java
              • DelimitedTextFileWithHeaderIteratorTest.java
              • LiftoverUtilsTest.java
              • IlluminaUtilTest.java
              • GraphUtilsTest.java
              • IntervalListToBedTest.java
              • TextFileParsersTest.java
              • IntervalListToolsTest.java
              • ScatterIntervalsByNsTest.java
              • LiftoverVcfTest.java
              • MiscTest.java
              • IntervalListScattererTest.java
              • RExecutorTest.java
              • EditDistanceQueriesTest.java
              • TestNGUtil.java
              • FifoBufferTest.java
              • ClippingUtilityTest.java
              • TabbedTextFileWithHeaderParserTest.java
            • arrays
              • CollectArraysVariantCallingMetricsTest.java
              • MergePedIntoVcfTest.java
              • CreateVerifyIDIntensityContaminationMetricsFileTest.java
              • illumina
                • InfiniumVcfFieldsTest.java
                • IlluminaAdpcFileWriterTest.java
                • Build37ExtendedIlluminaManifestTest.java
                • VcfToAdpcTest.java
                • InfiniumDataFileTest.java
                • CombineGenotypingArrayVcfsTest.java
                • IlluminaManifestTest.java
                • InfiniumNormalizationManifestTest.java
              • GtcToVcfTest.java
            • fastq
              • BamToBfqTest.java
            • analysis
              • CollectAlignmentSummaryMetricsTest.java
              • MultiLevelCollectorTest.java
              • WgsMetricsProcessorImplTest.java
              • CollectQualityYieldMetricsTest.java
              • CollectWgsMetricsTest.java
              • replicates
                • CollectIndependentReplicatesMetricTest.java
              • CollectOxoGMetricsTest.java
              • FastWgsMetricsCollectorTest.java
              • CollectWgsMetricsWithNonZeroCoverageTest.java
              • directed
                • CollectTargetedMetricsTest.java
                • CollectHsMetricsTest.java
              • artifacts
                • TransitionTest.java
                • CollectSequencingArtifactMetricsTest.java
                • ConvertSequencingArtifactToOxoGTest.java
              • CompareMetricsTest.java
              • MergeableMetricBaseTest.java
              • CollectMultipleMetricsTest.java
              • CollectRnaSeqMetricsTest.java
              • CollectJumpingLibraryMetricsTest.java
              • CollectGcBiasMetricsTest.java
              • AdapterUtilityTest.java
              • AbstractWgsMetricsCollectorTest.java
              • CollectWgsMetricsTestUtils.java
              • CounterManagerTest.java
              • WgsMetricsTest.java
              • CollectInsertSizeMetricsTest.java
              • TheoreticalSensitivityTest.java
            • reference
              • NonNFastaSizeTest.java
            • TestDataProviders.java
            • sam
              • CompareSAMsTest.java
              • AbstractAlignmentMergerTest.java
              • RevertSamTest.java
              • markduplicates
                • MarkDuplicatesSetSizeHistogramTester.java
                • MarkDuplicatesSetSizeHistogramTest.java
                • MarkDuplicatesWithMateCigarTest.java
                • MarkDuplicateWithMissingReadTwoBarcodeTest.java
                • UmiUtilTest.java
                • CollectDuplicateMetricsTest.java
                • SimpleMarkDuplicatesWithMateCigarTest.java
                • QuerySortedMarkDuplicatesTester.java
                • MarkDuplicatesTest.java
                • AbstractMarkDuplicatesCommandLineProgramTester.java
                • MarkDuplicatesTestQueryNameSorted.java
                • BySumOfBaseQAndInOriginalOrderMDTester.java
                • util
                  • OpticalDuplicateFinderTest.java
                • MarkDuplicatesTagRepresentativeReadIndexTester.java
                • MarkDuplicatesTester.java
                • UmiAwareMarkDuplicatesWithMateCigarTester.java
                • MarkDuplicateWithMissingReadOneBarcodeTest.java
                • MarkDuplicateWithMissingSampleBarcodeTest.java
                • MarkDuplicateWithMissingBarcodeTest.java
                • ElcHashBasedDuplicatesFinderTest.java
                • MarkDuplicatesTagRepresentativeReadIndexTest.java
                • AsIsMarkDuplicatesTest.java
                • CollectDuplicateMetricsTester.java
                • AsIsCollectDuplicateMetricsTest.java
                • SimpleMarkDuplicatesWithMateCigarTester.java
                • ElcIdenticalBasesDuplicatesFinderTest.java
                • MarkDuplicatesWithMateCigarTester.java
                • UmiAwareMarkDuplicatesWithMateCigarTest.java
                • EstimateLibraryComplexityTest.java
                • AbstractMarkDuplicatesCommandLineProgramTest.java
              • ViewSamTest.java
              • AddOATagTest.java
              • CleanSamTest.java
              • ReorderSamTest.java
              • PipedDataTest.java
              • MergeBamAlignmentTest.java
              • SplitSamByNumberOfReadsTest.java
              • SamToFastqTest.java
              • SortSamTest.java
              • util
                • PrimaryAlignmentKeyTest.java
                • ReadNameParserTests.java
                • SamTestUtil.java
                • SamComparisonTest.java
              • SamToFastqWithTagsTest.java
              • FixMateInformationTest.java
              • FastqToSamTest.java
              • SetNmMdAndUqTagsTest.java
              • ValidateSamFileTest.java
              • DownsampleSamTest.java
              • SamFormatConverterTest.java
              • FilterSamReadsTest.java
              • SplitSamByLibraryTest.java
              • PositionBasedDownsampleSamTest.java
              • DuplicationMetricsTest.java
              • AddCommentsToBamTest.java
              • GatherBamFilesTest.java
              • testers
                • SamFileTester.java
                • CleanSamTester.java
                • ValidateSamTester.java
              • SamErrorMetric
                • BaseErrorCalculationTest.java
                • BaseErrorAggregationTest.java
                • CollectSamErrorMetricsTest.java
                • ReadBaseStratificationTest.java
              • MergeSamFilesTest.java
              • CreateSequenceDictionaryTest.java
            • metrics
              • CollectRrbsMetricsTest.java
              • MetricBaseTest.java
    • build.xml
    • gradle
      • wrapper
        • gradle-wrapper.properties
    • testdata
      • picard
        • fingerprint
          • NA12891_to_NA12892.txt
          • NA12891.with_swapped_NON_REF.g.vcf
          • NA12891andNA12892_part3.vcf
          • DuplicateKey.txt
          • NA12891.vcf
          • reference.dict
          • reference.fasta
          • NA12891andNA12892.vcf
          • NA12891.vcf.gz
          • haplotypeMap.vcf
          • NA12892.g.vcf
          • aligned_queryname_sorted.sam
          • NA12891.g.vcf
          • reference.fasta.fai
          • NA12891andNA12892_part1.vcf
          • NA12891.fp.vcf
          • expectedFingerprint_small.vcf
          • too_few_fields.txt
          • fingerprinting_detail_metrics.example
          • NA12891andNA12892_part2.vcf
          • reference.shifted.for.crams.fasta.fai
          • NA12892_to_NA12891.txt
          • NA12891.not.over.fingerprints.r1.sam
          • fingerprinting_summary_metrics.example
          • Homo_sapiens_assembly19.haplotype_database.subset.shifted.for.crams.txt
          • haplotypeMap_small.vcf
          • reference.shifted.for.crams.fasta
          • testSample_small.vcf
          • emptyNA12892.vcf
          • too_many_fields.txt
          • NA12891.no.fp.sites.and.NA12892.vcf
          • NA12891.no.fp.sites.vcf
          • NA12892.vcf
          • haplotypeMap.txt
          • NotThere_to_NA12891.txt
          • NA12892.fp.vcf
          • Homo_sapiens_assembly19.haplotype_database.subset.txt
          • reference.shifted.for.crams.dict
          • NA12891_named_NA12892.vcf
        • vcf
          • vcfFormatTest.scrambled.vcf
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp.genotype_concordance_detail_metrics
          • CEUTrio-random-scatter-0.vcf
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq.genotype_concordance_contingency_metrics
          • CEUTrio-random-scatter-3.vcf.idx
          • CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff.genotype_concordance_detail_metrics
          • NIST.selected.vcf
          • NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff.genotype_concordance_summary_metrics
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff.genotype_concordance_detail_metrics
          • CEUTrio_plus_FAKE.vcf.idx
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows.genotype_concordance_summary_metrics
          • CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff.genotype_concordance_detail_metrics
          • spanningDeletionCallset_vs_spanningDeletionTruth.genotype_concordance_contingency_metrics
          • CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff.vcf
          • spanningDeletionCallset_vs_spanningDeletionTruth.vcf
          • CEUTrio-snps_first_line_diff.vcf
          • CEUTrio-merged-indels-snps.vcf
          • CEUTrio-random-scatter-0.vcf.idx
          • NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff.vcf
          • CEUTrio-indels-scrambled.1.vcf
          • mergeTest.emptyShard.variant_calling_summary_metrics
          • CEUTrio-snps-scrambled.2.vcf
          • mini.dbsnp.vcf.idx
          • CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff.vcf
          • CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff.vcf
          • CEUTrio-random-scatter-1.vcf.idx
          • CEUTrio-merged-indels-snps.vcf.idx
          • CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff.genotype_concordance_contingency_metrics
          • NA12878.ped
          • CEUTrio-random-scatter-4.vcf
          • allHomRef.vcf
          • empty.vcf
          • CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff.genotype_concordance_detail_metrics
          • CEUTrio-snps-scrambled.1.vcf
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff.genotype_concordance_summary_metrics
          • CEUTrio-random-scatter-4.vcf.idx
          • CEUTrio-indels-no-contigs.vcf
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq.genotype_concordance_summary_metrics
          • CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff.genotype_concordance_summary_metrics
          • empty.vcf.idx
          • NIST_subset_3sites.vcf
          • normalize_alleles_truth.vcf
          • vcfFormatTest.bcf.idx
          • NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff.genotype_concordance_detail_metrics
          • CEUTrio-snps_last_line_diff.vcf
          • spanningDeletionCallset_vs_spanningDeletionTruth.genotype_concordance_summary_metrics
          • CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff.genotype_concordance_summary_metrics
          • small_m2_more_variants.vcf
          • CEUTrio-indels-bad-samples.vcf.idx
          • CEUTrio-random-scatter-5.vcf
          • chunking
            • multi_allelic_at_10M.vcf
            • multi_allelic_at_10M.vcf.idx
          • vcfFormatTest.bad_dict.vcf
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows.vcf
          • GatherVcf
            • shard1.vcf
            • shard3.vcf
            • input.vcf
            • shard2_bad.vcf
            • shard2.vcf
          • CEUTrio_plus_FAKE.vcf
          • CEUTrio-indels-bad-samples.vcf
          • mini_gvcf.vcf.idx
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq.genotype_concordance_detail_metrics
          • mergeTest.shard2.variant_calling_detail_metrics
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp.genotype_concordance_contingency_metrics
          • NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff.genotype_concordance_contingency_metrics
          • spanningDeletionTruth.vcf
          • CEUTrio-snps.vcf.idx
          • mergeTest.shard1.variant_calling_detail_metrics
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp.vcf
          • FixVcfHeaderTest
            • header_with_extra_sample.vcf
            • input.vcf
            • header.vcf
            • output.vcf
          • CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff.genotype_concordance_summary_metrics
          • normalize_no_calls_call.vcf
          • vcf_with_filtered_calls.vcf
          • CEUTrio-random-scatter-2.vcf
          • spanningDeletionCallset.vcf
          • normalize_alleles_call.vcf
          • CEUTrio-random-scatter-2.vcf.idx
          • CEUTrio-indels.vcf.idx
          • CEUTrio-random-scatter-3.vcf
          • IntervalListChr1Small.interval_list
          • normalize_no_calls_truth.vcf
          • CEUTrio-snps.vcf
          • CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff.genotype_concordance_detail_metrics
          • CEUTrio-indels-dissimilar-contigs.vcf
          • CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff.genotype_concordance_summary_metrics
          • MakeVcfSampleNameMap
            • NA12878.vcf
            • NA12891.vcf
            • NA12892.vcf
            • expected.sample_map
          • noSeqDict.vcf
          • CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff.genotype_concordance_contingency_metrics
          • mini_gvcf.vcf
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq.vcf
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff.genotype_concordance_contingency_metrics
          • NIST.selected.vcf.idx
          • mergeTest.shard2.variant_calling_summary_metrics
          • vcfFormatTest.vcf.idx
          • IntervalList1PerChrom.interval_list
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows.genotype_concordance_detail_metrics
          • spanningDeletionCallset_vs_spanningDeletionTruth.genotype_concordance_detail_metrics
          • CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff.genotype_concordance_contingency_metrics
          • LiftOver
            • vcfWithFlippedAllelesNegativeChain.lift.vcf
            • test.positive.over.chain
            • testLiftoverFailingVariants.vcf
            • testLiftoverUsingMissingContig.vcf
            • testLiftoverMismatchingSnps.vcf
            • dummy.reference.fasta.fai
            • vcfWithFlippedAlleles.reject.vcf
            • vcfWithMixed.reject.vcf
            • vcfWithMixed.lift.vcf
            • dummy.reference.dict
            • test.over.chain
            • testLiftoverMultiallelicIndels.vcf
            • dummy.two.block.reference.fasta
            • testLiftoverMixedVariants.vcf
            • vcfWithFlippedAllelesNegativeChain.reject.vcf
            • test.over.badContig.chain
            • dummy.two.block.reference.dict
            • testLiftoverBiallelicIndels.vcf
            • vcfWithFlippedAlleles.lift.vcf
            • dummy.reference.fasta
            • test.two.block.over.chain
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp.genotype_concordance_summary_metrics
          • CEUTrio-snps_del_line.vcf
          • CEUTrio-random-scatter-5.vcf.idx
          • filter
            • testFilteringNoSeqDictionary.vcf
            • testFilteringSitesOnly.vcf
            • testFiltering.vcf
          • mini.vcf.idx
          • CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff.genotype_concordance_contingency_metrics
          • CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff.vcf
          • mergeTest.shard1.variant_calling_summary_metrics
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff.vcf
          • CEUTrio-indels-dissimilar-contigs.vcf.idx
          • CEUTrio-indels.vcf
          • vcfFormatTest.bcf
          • mergeTest.emptyShard.variant_calling_detail_metrics
          • CEUTrio-random-scatter-1.vcf
          • vcfFormatTest.vcf
          • CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows.genotype_concordance_contingency_metrics
        • illumina
          • readerTests
            • s_3_2102.clocs
            • bcl_failing2.bcl
            • bcl_tooLong.bcl
            • s_1_1101_pos.txt
            • s_1_1102_pos.txt
            • pos_failing1_pos.txt
            • s_1_7.locs
            • tile_1101.filter
            • s_1_6.locs
            • s_2_1101_pos.txt
            • pf_passing.filter
            • s_3_2103.clocs
            • tile_1102.filter
            • s_1_10.locs
            • s_1_1104_pos.txt
            • s_1_2106.clocs
            • pf_badVersionBytes.filter
            • pf_badOpeningBytes.filter
            • s_3_2104.clocs
            • s_2_1101.clocs
            • bcl_failing.bcl
            • bcl_passing.bcl
            • pf_failing2.filter
            • s_1_9.locs
            • pf_tooLarge.filter
            • s_1_8.locs
            • s_1_1103_pos.txt
            • pf_tooShort.filter
            • cbcls
              • tile_1101.filter
              • C3.1
                • L001_1.cbcl
              • C2.1
                • L001_1.cbcl
              • C1.1
                • L001_1.cbcl
            • pf_failing1.filter
            • bcl_tooShort.bcl
            • s_3_2105.clocs
            • binary_passing.bin
          • parserTests
            • filterParser
              • L001
                • s_1_0001.filter
                • s_1_0003.filter
                • s_1_0002.filter
                • s_1_0004.filter
            • posParser
              • s_1_1_pos.txt
              • s_9_3202_pos.txt
              • s_1_2_pos.txt
              • s_9_3201_pos.txt
              • s_1_3_pos.txt
          • CollectIlluminaBasecallingMetrics
            • 125T125T
              • Data
                • Intensities
                  • L001
                    • s_1_1101.clocs
                  • BaseCalls
                    • L001
                      • C205.1
                        • s_1_1101.bcl
                      • C152.1
                        • s_1_1101.bcl
                      • C161.1
                        • s_1_1101.bcl
                      • C101.1
                        • s_1_1101.bcl
                      • C114.1
                        • s_1_1101.bcl
                      • C118.1
                        • s_1_1101.bcl
                      • C22.1
                        • s_1_1101.bcl
                      • C146.1
                        • s_1_1101.bcl
                      • C149.1
                        • s_1_1101.bcl
                      • C243.1
                        • s_1_1101.bcl
                      • C68.1
                        • s_1_1101.bcl
                      • C38.1
                        • s_1_1101.bcl
                      • C201.1
                        • s_1_1101.bcl
                      • C140.1
                        • s_1_1101.bcl
                      • C160.1
                        • s_1_1101.bcl
                      • C236.1
                        • s_1_1101.bcl
                      • C113.1
                        • s_1_1101.bcl
                      • C80.1
                        • s_1_1101.bcl
                      • C156.1
                        • s_1_1101.bcl
                      • C51.1
                        • s_1_1101.bcl
                      • C103.1
                        • s_1_1101.bcl
                      • C115.1
                        • s_1_1101.bcl
                      • C164.1
                        • s_1_1101.bcl
                      • C171.1
                        • s_1_1101.bcl
                      • C23.1
                        • s_1_1101.bcl
                      • C73.1
                        • s_1_1101.bcl
                      • C246.1
                        • s_1_1101.bcl
                      • C123.1
                        • s_1_1101.bcl
                      • C60.1
                        • s_1_1101.bcl
                      • C91.1
                        • s_1_1101.bcl
                      • C220.1
                        • s_1_1101.bcl
                      • C125.1
                        • s_1_1101.bcl
                      • C200.1
                        • s_1_1101.bcl
                      • C57.1
                        • s_1_1101.bcl
                      • C159.1
                        • s_1_1101.bcl
                      • C224.1
                        • s_1_1101.bcl
                      • C196.1
                        • s_1_1101.bcl
                      • C97.1
                        • s_1_1101.bcl
                      • C124.1
                        • s_1_1101.bcl
                      • C7.1
                        • s_1_1101.bcl
                      • C151.1
                        • s_1_1101.bcl
                      • C214.1
                        • s_1_1101.bcl
                      • C54.1
                        • s_1_1101.bcl
                      • C130.1
                        • s_1_1101.bcl
                      • C25.1
                        • s_1_1101.bcl
                      • C59.1
                        • s_1_1101.bcl
                      • C61.1
                        • s_1_1101.bcl
                      • C138.1
                        • s_1_1101.bcl
                      • C79.1
                        • s_1_1101.bcl
                      • C139.1
                        • s_1_1101.bcl
                      • C105.1
                        • s_1_1101.bcl
                      • C128.1
                        • s_1_1101.bcl
                      • C4.1
                        • s_1_1101.bcl
                      • C137.1
                        • s_1_1101.bcl
                      • C67.1
                        • s_1_1101.bcl
                      • C209.1
                        • s_1_1101.bcl
                      • C6.1
                        • s_1_1101.bcl
                      • C218.1
                        • s_1_1101.bcl
                      • C49.1
                        • s_1_1101.bcl
                      • C40.1
                        • s_1_1101.bcl
                      • C157.1
                        • s_1_1101.bcl
                      • C121.1
                        • s_1_1101.bcl
                      • C50.1
                        • s_1_1101.bcl
                      • C81.1
                        • s_1_1101.bcl
                      • C231.1
                        • s_1_1101.bcl
                      • C75.1
                        • s_1_1101.bcl
                      • C32.1
                        • s_1_1101.bcl
                      • C192.1
                        • s_1_1101.bcl
                      • C70.1
                        • s_1_1101.bcl
                      • C240.1
                        • s_1_1101.bcl
                      • C33.1
                        • s_1_1101.bcl
                      • C136.1
                        • s_1_1101.bcl
                      • C182.1
                        • s_1_1101.bcl
                      • C62.1
                        • s_1_1101.bcl
                      • s_1_1101.filter
                      • C142.1
                        • s_1_1101.bcl
                      • C69.1
                        • s_1_1101.bcl
                      • C187.1
                        • s_1_1101.bcl
                      • C85.1
                        • s_1_1101.bcl
                      • C30.1
                        • s_1_1101.bcl
                      • C19.1
                        • s_1_1101.bcl
                      • C3.1
                        • s_1_1101.bcl
                      • C119.1
                        • s_1_1101.bcl
                      • C46.1
                        • s_1_1101.bcl
                      • C39.1
                        • s_1_1101.bcl
                      • C14.1
                        • s_1_1101.bcl
                      • C42.1
                        • s_1_1101.bcl
                      • C9.1
                        • s_1_1101.bcl
                      • C82.1
                        • s_1_1101.bcl
                      • C150.1
                        • s_1_1101.bcl
                      • C223.1
                        • s_1_1101.bcl
                      • C166.1
                        • s_1_1101.bcl
                      • C107.1
                        • s_1_1101.bcl
                      • C55.1
                        • s_1_1101.bcl
                      • C247.1
                        • s_1_1101.bcl
                      • C87.1
                        • s_1_1101.bcl
                      • C77.1
                        • s_1_1101.bcl
                      • C177.1
                        • s_1_1101.bcl
                      • C249.1
                        • s_1_1101.bcl
                      • C183.1
                        • s_1_1101.bcl
                      • C34.1
                        • s_1_1101.bcl
                      • C207.1
                        • s_1_1101.bcl
                      • C100.1
                        • s_1_1101.bcl
                      • C12.1
                        • s_1_1101.bcl
                      • C47.1
                        • s_1_1101.bcl
                      • C195.1
                        • s_1_1101.bcl
                      • C232.1
                        • s_1_1101.bcl
                      • C129.1
                        • s_1_1101.bcl
                      • C222.1
                        • s_1_1101.bcl
                      • C65.1
                        • s_1_1101.bcl
                      • C239.1
                        • s_1_1101.bcl
                      • C180.1
                        • s_1_1101.bcl
                      • C88.1
                        • s_1_1101.bcl
                      • C64.1
                        • s_1_1101.bcl
                      • C76.1
                        • s_1_1101.bcl
                      • C74.1
                        • s_1_1101.bcl
                      • C27.1
                        • s_1_1101.bcl
                      • C72.1
                        • s_1_1101.bcl
                      • C235.1
                        • s_1_1101.bcl
                      • C230.1
                        • s_1_1101.bcl
                      • C71.1
                        • s_1_1101.bcl
                      • C134.1
                        • s_1_1101.bcl
                      • C245.1
                        • s_1_1101.bcl
                      • C208.1
                        • s_1_1101.bcl
                      • C194.1
                        • s_1_1101.bcl
                      • C202.1
                        • s_1_1101.bcl
                      • C122.1
                        • s_1_1101.bcl
                      • C167.1
                        • s_1_1101.bcl
                      • C238.1
                        • s_1_1101.bcl
                      • C191.1
                        • s_1_1101.bcl
                      • C86.1
                        • s_1_1101.bcl
                      • C229.1
                        • s_1_1101.bcl
                      • C211.1
                        • s_1_1101.bcl
                      • C10.1
                        • s_1_1101.bcl
                      • C237.1
                        • s_1_1101.bcl
                      • C31.1
                        • s_1_1101.bcl
                      • C37.1
                        • s_1_1101.bcl
                      • C131.1
                        • s_1_1101.bcl
                      • C168.1
                        • s_1_1101.bcl
                      • C217.1
                        • s_1_1101.bcl
                      • C99.1
                        • s_1_1101.bcl
                      • C41.1
                        • s_1_1101.bcl
                      • C162.1
                        • s_1_1101.bcl
                      • C165.1
                        • s_1_1101.bcl
                      • C203.1
                        • s_1_1101.bcl
                      • C112.1
                        • s_1_1101.bcl
                      • C170.1
                        • s_1_1101.bcl
                      • C63.1
                        • s_1_1101.bcl
                      • C78.1
                        • s_1_1101.bcl
                      • C133.1
                        • s_1_1101.bcl
                      • C8.1
                        • s_1_1101.bcl
                      • C18.1
                        • s_1_1101.bcl
                      • C95.1
                        • s_1_1101.bcl
                      • C5.1
                        • s_1_1101.bcl
                      • C24.1
                        • s_1_1101.bcl
                      • C84.1
                        • s_1_1101.bcl
                      • C155.1
                        • s_1_1101.bcl
                      • C94.1
                        • s_1_1101.bcl
                      • C176.1
                        • s_1_1101.bcl
                      • C108.1
                        • s_1_1101.bcl
                      • C169.1
                        • s_1_1101.bcl
                      • C153.1
                        • s_1_1101.bcl
                      • C226.1
                        • s_1_1101.bcl
                      • C148.1
                        • s_1_1101.bcl
                      • C48.1
                        • s_1_1101.bcl
                      • C104.1
                        • s_1_1101.bcl
                      • C197.1
                        • s_1_1101.bcl
                      • C35.1
                        • s_1_1101.bcl
                      • C2.1
                        • s_1_1101.bcl
                      • C163.1
                        • s_1_1101.bcl
                      • C184.1
                        • s_1_1101.bcl
                      • C28.1
                        • s_1_1101.bcl
                      • C145.1
                        • s_1_1101.bcl
                      • C189.1
                        • s_1_1101.bcl
                      • C83.1
                        • s_1_1101.bcl
                      • C233.1
                        • s_1_1101.bcl
                      • C234.1
                        • s_1_1101.bcl
                      • C102.1
                        • s_1_1101.bcl
                      • C154.1
                        • s_1_1101.bcl
                      • C178.1
                        • s_1_1101.bcl
                      • C216.1
                        • s_1_1101.bcl
                      • C15.1
                        • s_1_1101.bcl
                      • C227.1
                        • s_1_1101.bcl
                      • C206.1
                        • s_1_1101.bcl
                      • C198.1
                        • s_1_1101.bcl
                      • C44.1
                        • s_1_1101.bcl
                      • C244.1
                        • s_1_1101.bcl
                      • C132.1
                        • s_1_1101.bcl
                      • C89.1
                        • s_1_1101.bcl
                      • C248.1
                        • s_1_1101.bcl
                      • C141.1
                        • s_1_1101.bcl
                      • C144.1
                        • s_1_1101.bcl
                      • C185.1
                        • s_1_1101.bcl
                      • C45.1
                        • s_1_1101.bcl
                      • C1.1
                        • s_1_1101.bcl
                      • C20.1
                        • s_1_1101.bcl
                      • C36.1
                        • s_1_1101.bcl
                      • C13.1
                        • s_1_1101.bcl
                      • C210.1
                        • s_1_1101.bcl
                      • C215.1
                        • s_1_1101.bcl
                      • C190.1
                        • s_1_1101.bcl
                      • C126.1
                        • s_1_1101.bcl
                      • C127.1
                        • s_1_1101.bcl
                      • C250.1
                        • s_1_1101.bcl
                      • C52.1
                        • s_1_1101.bcl
                      • C56.1
                        • s_1_1101.bcl
                      • C96.1
                        • s_1_1101.bcl
                      • C199.1
                        • s_1_1101.bcl
                      • C143.1
                        • s_1_1101.bcl
                      • C106.1
                        • s_1_1101.bcl
                      • C109.1
                        • s_1_1101.bcl
                      • C135.1
                        • s_1_1101.bcl
                      • C43.1
                        • s_1_1101.bcl
                      • C193.1
                        • s_1_1101.bcl
                      • C228.1
                        • s_1_1101.bcl
                      • C92.1
                        • s_1_1101.bcl
                      • C17.1
                        • s_1_1101.bcl
                      • C26.1
                        • s_1_1101.bcl
                      • C147.1
                        • s_1_1101.bcl
                      • C110.1
                        • s_1_1101.bcl
                      • C204.1
                        • s_1_1101.bcl
                      • C21.1
                        • s_1_1101.bcl
                      • C11.1
                        • s_1_1101.bcl
                      • C120.1
                        • s_1_1101.bcl
                      • C188.1
                        • s_1_1101.bcl
                      • C219.1
                        • s_1_1101.bcl
                      • C111.1
                        • s_1_1101.bcl
                      • C172.1
                        • s_1_1101.bcl
                      • C58.1
                        • s_1_1101.bcl
                      • C98.1
                        • s_1_1101.bcl
                      • C90.1
                        • s_1_1101.bcl
                      • C242.1
                        • s_1_1101.bcl
                      • C29.1
                        • s_1_1101.bcl
                      • C93.1
                        • s_1_1101.bcl
                      • C241.1
                        • s_1_1101.bcl
                      • C212.1
                        • s_1_1101.bcl
                      • C158.1
                        • s_1_1101.bcl
                      • C117.1
                        • s_1_1101.bcl
                      • C66.1
                        • s_1_1101.bcl
                      • C181.1
                        • s_1_1101.bcl
                      • C174.1
                        • s_1_1101.bcl
                      • C116.1
                        • s_1_1101.bcl
                      • C225.1
                        • s_1_1101.bcl
                      • C179.1
                        • s_1_1101.bcl
                      • C175.1
                        • s_1_1101.bcl
                      • C186.1
                        • s_1_1101.bcl
                      • C53.1
                        • s_1_1101.bcl
                      • C213.1
                        • s_1_1101.bcl
                      • C173.1
                        • s_1_1101.bcl
                      • C16.1
                        • s_1_1101.bcl
                      • C221.1
                        • s_1_1101.bcl
            • 25T8B25T
              • Data
                • Intensities
                  • L001
                    • s_1_1101.clocs
                  • BaseCalls
                    • L001
                      • C22.1
                        • s_1_1101.bcl
                      • C38.1
                        • s_1_1101.bcl
                      • C51.1
                        • s_1_1101.bcl
                      • C23.1
                        • s_1_1101.bcl
                      • C57.1
                        • s_1_1101.bcl
                      • C7.1
                        • s_1_1101.bcl
                      • C54.1
                        • s_1_1101.bcl
                      • C25.1
                        • s_1_1101.bcl
                      • C4.1
                        • s_1_1101.bcl
                      • C6.1
                        • s_1_1101.bcl
                      • C49.1
                        • s_1_1101.bcl
                      • C40.1
                        • s_1_1101.bcl
                      • C50.1
                        • s_1_1101.bcl
                      • C32.1
                        • s_1_1101.bcl
                      • C33.1
                        • s_1_1101.bcl
                      • s_1_1101.filter
                      • C30.1
                        • s_1_1101.bcl
                      • C19.1
                        • s_1_1101.bcl
                      • C3.1
                        • s_1_1101.bcl
                      • C46.1
                        • s_1_1101.bcl
                      • C39.1
                        • s_1_1101.bcl
                      • C14.1
                        • s_1_1101.bcl
                      • C42.1
                        • s_1_1101.bcl
                      • C9.1
                        • s_1_1101.bcl
                      • C55.1
                        • s_1_1101.bcl
                      • C34.1
                        • s_1_1101.bcl
                      • C12.1
                        • s_1_1101.bcl
                      • C47.1
                        • s_1_1101.bcl
                      • C27.1
                        • s_1_1101.bcl
                      • C10.1
                        • s_1_1101.bcl
                      • C31.1
                        • s_1_1101.bcl
                      • C37.1
                        • s_1_1101.bcl
                      • C41.1
                        • s_1_1101.bcl
                      • C8.1
                        • s_1_1101.bcl
                      • C18.1
                        • s_1_1101.bcl
                      • C5.1
                        • s_1_1101.bcl
                      • C24.1
                        • s_1_1101.bcl
                      • C48.1
                        • s_1_1101.bcl
                      • C35.1
                        • s_1_1101.bcl
                      • C2.1
                        • s_1_1101.bcl
                      • C28.1
                        • s_1_1101.bcl
                      • C15.1
                        • s_1_1101.bcl
                      • C44.1
                        • s_1_1101.bcl
                      • C45.1
                        • s_1_1101.bcl
                      • C1.1
                        • s_1_1101.bcl
                      • C20.1
                        • s_1_1101.bcl
                      • C36.1
                        • s_1_1101.bcl
                      • C13.1
                        • s_1_1101.bcl
                      • C52.1
                        • s_1_1101.bcl
                      • C56.1
                        • s_1_1101.bcl
                      • C43.1
                        • s_1_1101.bcl
                      • C17.1
                        • s_1_1101.bcl
                      • C26.1
                        • s_1_1101.bcl
                      • C21.1
                        • s_1_1101.bcl
                      • C11.1
                        • s_1_1101.bcl
                      • C58.1
                        • s_1_1101.bcl
                      • C29.1
                        • s_1_1101.bcl
                      • C53.1
                        • s_1_1101.bcl
                      • C16.1
                        • s_1_1101.bcl
                    • s_1_1101_barcode.txt.gz
                    • barcodeData.1
              • barcodes_dir
                • s_1_1101_barcode.txt.gz
          • CollectIlluminaLaneMetrics
            • .gitignore
          • mark_illumina_adapters_test.sam
          • 125T125T
            • Data
              • Intensities
                • L001
                  • s_1_1101.clocs
                • BaseCalls
                  • L001
                    • C205.1
                      • s_1_1101.bcl
                    • C152.1
                      • s_1_1101.bcl
                    • C161.1
                      • s_1_1101.bcl
                    • C101.1
                      • s_1_1101.bcl
                    • C114.1
                      • s_1_1101.bcl
                    • C118.1
                      • s_1_1101.bcl
                    • C22.1
                      • s_1_1101.bcl
                    • C146.1
                      • s_1_1101.bcl
                    • C149.1
                      • s_1_1101.bcl
                    • C243.1
                      • s_1_1101.bcl
                    • C68.1
                      • s_1_1101.bcl
                    • C38.1
                      • s_1_1101.bcl
                    • C201.1
                      • s_1_1101.bcl
                    • C140.1
                      • s_1_1101.bcl
                    • C160.1
                      • s_1_1101.bcl
                    • C236.1
                      • s_1_1101.bcl
                    • C113.1
                      • s_1_1101.bcl
                    • C80.1
                      • s_1_1101.bcl
                    • C156.1
                      • s_1_1101.bcl
                    • C51.1
                      • s_1_1101.bcl
                    • C103.1
                      • s_1_1101.bcl
                    • C115.1
                      • s_1_1101.bcl
                    • C164.1
                      • s_1_1101.bcl
                    • C171.1
                      • s_1_1101.bcl
                    • C23.1
                      • s_1_1101.bcl
                    • C73.1
                      • s_1_1101.bcl
                    • C246.1
                      • s_1_1101.bcl
                    • C123.1
                      • s_1_1101.bcl
                    • C60.1
                      • s_1_1101.bcl
                    • C91.1
                      • s_1_1101.bcl
                    • C220.1
                      • s_1_1101.bcl
                    • C125.1
                      • s_1_1101.bcl
                    • C200.1
                      • s_1_1101.bcl
                    • C57.1
                      • s_1_1101.bcl
                    • C159.1
                      • s_1_1101.bcl
                    • C224.1
                      • s_1_1101.bcl
                    • C196.1
                      • s_1_1101.bcl
                    • C97.1
                      • s_1_1101.bcl
                    • C124.1
                      • s_1_1101.bcl
                    • C7.1
                      • s_1_1101.bcl
                    • C151.1
                      • s_1_1101.bcl
                    • C214.1
                      • s_1_1101.bcl
                    • C54.1
                      • s_1_1101.bcl
                    • C130.1
                      • s_1_1101.bcl
                    • C25.1
                      • s_1_1101.bcl
                    • C59.1
                      • s_1_1101.bcl
                    • C61.1
                      • s_1_1101.bcl
                    • C138.1
                      • s_1_1101.bcl
                    • C79.1
                      • s_1_1101.bcl
                    • C139.1
                      • s_1_1101.bcl
                    • C105.1
                      • s_1_1101.bcl
                    • C128.1
                      • s_1_1101.bcl
                    • C4.1
                      • s_1_1101.bcl
                    • C137.1
                      • s_1_1101.bcl
                    • C67.1
                      • s_1_1101.bcl
                    • C209.1
                      • s_1_1101.bcl
                    • C6.1
                      • s_1_1101.bcl
                    • C218.1
                      • s_1_1101.bcl
                    • C49.1
                      • s_1_1101.bcl
                    • C40.1
                      • s_1_1101.bcl
                    • C157.1
                      • s_1_1101.bcl
                    • C121.1
                      • s_1_1101.bcl
                    • C50.1
                      • s_1_1101.bcl
                    • C81.1
                      • s_1_1101.bcl
                    • C231.1
                      • s_1_1101.bcl
                    • C75.1
                      • s_1_1101.bcl
                    • C32.1
                      • s_1_1101.bcl
                    • C192.1
                      • s_1_1101.bcl
                    • C70.1
                      • s_1_1101.bcl
                    • C240.1
                      • s_1_1101.bcl
                    • C33.1
                      • s_1_1101.bcl
                    • C136.1
                      • s_1_1101.bcl
                    • C182.1
                      • s_1_1101.bcl
                    • C62.1
                      • s_1_1101.bcl
                    • s_1_1101.filter
                    • C142.1
                      • s_1_1101.bcl
                    • C69.1
                      • s_1_1101.bcl
                    • C187.1
                      • s_1_1101.bcl
                    • C85.1
                      • s_1_1101.bcl
                    • C30.1
                      • s_1_1101.bcl
                    • C19.1
                      • s_1_1101.bcl
                    • C3.1
                      • s_1_1101.bcl
                    • C119.1
                      • s_1_1101.bcl
                    • C46.1
                      • s_1_1101.bcl
                    • C39.1
                      • s_1_1101.bcl
                    • C14.1
                      • s_1_1101.bcl
                    • C42.1
                      • s_1_1101.bcl
                    • C9.1
                      • s_1_1101.bcl
                    • C82.1
                      • s_1_1101.bcl
                    • C150.1
                      • s_1_1101.bcl
                    • C223.1
                      • s_1_1101.bcl
                    • C166.1
                      • s_1_1101.bcl
                    • C107.1
                      • s_1_1101.bcl
                    • C55.1
                      • s_1_1101.bcl
                    • C247.1
                      • s_1_1101.bcl
                    • C87.1
                      • s_1_1101.bcl
                    • C77.1
                      • s_1_1101.bcl
                    • C177.1
                      • s_1_1101.bcl
                    • C249.1
                      • s_1_1101.bcl
                    • C183.1
                      • s_1_1101.bcl
                    • C34.1
                      • s_1_1101.bcl
                    • C207.1
                      • s_1_1101.bcl
                    • C100.1
                      • s_1_1101.bcl
                    • C12.1
                      • s_1_1101.bcl
                    • C47.1
                      • s_1_1101.bcl
                    • C195.1
                      • s_1_1101.bcl
                    • C232.1
                      • s_1_1101.bcl
                    • C129.1
                      • s_1_1101.bcl
                    • C222.1
                      • s_1_1101.bcl
                    • C65.1
                      • s_1_1101.bcl
                    • C239.1
                      • s_1_1101.bcl
                    • C180.1
                      • s_1_1101.bcl
                    • C88.1
                      • s_1_1101.bcl
                    • C64.1
                      • s_1_1101.bcl
                    • C76.1
                      • s_1_1101.bcl
                    • C74.1
                      • s_1_1101.bcl
                    • C27.1
                      • s_1_1101.bcl
                    • C72.1
                      • s_1_1101.bcl
                    • C235.1
                      • s_1_1101.bcl
                    • C230.1
                      • s_1_1101.bcl
                    • C71.1
                      • s_1_1101.bcl
                    • C134.1
                      • s_1_1101.bcl
                    • C245.1
                      • s_1_1101.bcl
                    • C208.1
                      • s_1_1101.bcl
                    • C194.1
                      • s_1_1101.bcl
                    • C202.1
                      • s_1_1101.bcl
                    • C122.1
                      • s_1_1101.bcl
                    • C167.1
                      • s_1_1101.bcl
                    • C238.1
                      • s_1_1101.bcl
                    • C191.1
                      • s_1_1101.bcl
                    • C86.1
                      • s_1_1101.bcl
                    • C229.1
                      • s_1_1101.bcl
                    • C211.1
                      • s_1_1101.bcl
                    • C10.1
                      • s_1_1101.bcl
                    • C237.1
                      • s_1_1101.bcl
                    • C31.1
                      • s_1_1101.bcl
                    • C37.1
                      • s_1_1101.bcl
                    • C131.1
                      • s_1_1101.bcl
                    • C168.1
                      • s_1_1101.bcl
                    • C217.1
                      • s_1_1101.bcl
                    • C99.1
                      • s_1_1101.bcl
                    • C41.1
                      • s_1_1101.bcl
                    • C162.1
                      • s_1_1101.bcl
                    • C165.1
                      • s_1_1101.bcl
                    • C203.1
                      • s_1_1101.bcl
                    • C112.1
                      • s_1_1101.bcl
                    • C170.1
                      • s_1_1101.bcl
                    • C63.1
                      • s_1_1101.bcl
                    • C78.1
                      • s_1_1101.bcl
                    • C133.1
                      • s_1_1101.bcl
                    • C8.1
                      • s_1_1101.bcl
                    • C18.1
                      • s_1_1101.bcl
                    • C95.1
                      • s_1_1101.bcl
                    • C5.1
                      • s_1_1101.bcl
                    • C24.1
                      • s_1_1101.bcl
                    • C84.1
                      • s_1_1101.bcl
                    • C155.1
                      • s_1_1101.bcl
                    • C94.1
                      • s_1_1101.bcl
                    • C176.1
                      • s_1_1101.bcl
                    • C108.1
                      • s_1_1101.bcl
                    • C169.1
                      • s_1_1101.bcl
                    • C153.1
                      • s_1_1101.bcl
                    • C226.1
                      • s_1_1101.bcl
                    • C148.1
                      • s_1_1101.bcl
                    • C48.1
                      • s_1_1101.bcl
                    • C104.1
                      • s_1_1101.bcl
                    • C197.1
                      • s_1_1101.bcl
                    • C35.1
                      • s_1_1101.bcl
                    • C2.1
                      • s_1_1101.bcl
                    • C163.1
                      • s_1_1101.bcl
                    • C184.1
                      • s_1_1101.bcl
                    • C28.1
                      • s_1_1101.bcl
                    • C145.1
                      • s_1_1101.bcl
                    • C189.1
                      • s_1_1101.bcl
                    • C83.1
                      • s_1_1101.bcl
                    • C233.1
                      • s_1_1101.bcl
                    • C234.1
                      • s_1_1101.bcl
                    • C102.1
                      • s_1_1101.bcl
                    • C154.1
                      • s_1_1101.bcl
                    • C178.1
                      • s_1_1101.bcl
                    • C216.1
                      • s_1_1101.bcl
                    • C15.1
                      • s_1_1101.bcl
                    • C227.1
                      • s_1_1101.bcl
                    • C206.1
                      • s_1_1101.bcl
                    • C198.1
                      • s_1_1101.bcl
                    • C44.1
                      • s_1_1101.bcl
                    • C244.1
                      • s_1_1101.bcl
                    • C132.1
                      • s_1_1101.bcl
                    • C89.1
                      • s_1_1101.bcl
                    • C248.1
                      • s_1_1101.bcl
                    • C141.1
                      • s_1_1101.bcl
                    • C144.1
                      • s_1_1101.bcl
                    • C185.1
                      • s_1_1101.bcl
                    • C45.1
                      • s_1_1101.bcl
                    • C1.1
                      • s_1_1101.bcl
                    • C20.1
                      • s_1_1101.bcl
                    • C36.1
                      • s_1_1101.bcl
                    • C13.1
                      • s_1_1101.bcl
                    • C210.1
                      • s_1_1101.bcl
                    • C215.1
                      • s_1_1101.bcl
                    • C190.1
                      • s_1_1101.bcl
                    • C126.1
                      • s_1_1101.bcl
                    • C127.1
                      • s_1_1101.bcl
                    • C250.1
                      • s_1_1101.bcl
                    • C52.1
                      • s_1_1101.bcl
                    • C56.1
                      • s_1_1101.bcl
                    • C96.1
                      • s_1_1101.bcl
                    • C199.1
                      • s_1_1101.bcl
                    • C143.1
                      • s_1_1101.bcl
                    • C106.1
                      • s_1_1101.bcl
                    • C109.1
                      • s_1_1101.bcl
                    • C135.1
                      • s_1_1101.bcl
                    • C43.1
                      • s_1_1101.bcl
                    • C193.1
                      • s_1_1101.bcl
                    • C228.1
                      • s_1_1101.bcl
                    • C92.1
                      • s_1_1101.bcl
                    • C17.1
                      • s_1_1101.bcl
                    • C26.1
                      • s_1_1101.bcl
                    • C147.1
                      • s_1_1101.bcl
                    • C110.1
                      • s_1_1101.bcl
                    • C204.1
                      • s_1_1101.bcl
                    • C21.1
                      • s_1_1101.bcl
                    • C11.1
                      • s_1_1101.bcl
                    • C120.1
                      • s_1_1101.bcl
                    • C188.1
                      • s_1_1101.bcl
                    • C219.1
                      • s_1_1101.bcl
                    • C111.1
                      • s_1_1101.bcl
                    • C172.1
                      • s_1_1101.bcl
                    • C58.1
                      • s_1_1101.bcl
                    • C98.1
                      • s_1_1101.bcl
                    • C90.1
                      • s_1_1101.bcl
                    • C242.1
                      • s_1_1101.bcl
                    • C29.1
                      • s_1_1101.bcl
                    • C93.1
                      • s_1_1101.bcl
                    • C241.1
                      • s_1_1101.bcl
                    • C212.1
                      • s_1_1101.bcl
                    • C158.1
                      • s_1_1101.bcl
                    • C117.1
                      • s_1_1101.bcl
                    • C66.1
                      • s_1_1101.bcl
                    • C181.1
                      • s_1_1101.bcl
                    • C174.1
                      • s_1_1101.bcl
                    • C116.1
                      • s_1_1101.bcl
                    • C225.1
                      • s_1_1101.bcl
                    • C179.1
                      • s_1_1101.bcl
                    • C175.1
                      • s_1_1101.bcl
                    • C186.1
                      • s_1_1101.bcl
                    • C53.1
                      • s_1_1101.bcl
                    • C213.1
                      • s_1_1101.bcl
                    • C173.1
                      • s_1_1101.bcl
                    • C16.1
                      • s_1_1101.bcl
                    • C221.1
                      • s_1_1101.bcl
                  • L002
                    • C205.1
                      • s_2_1101.bcl
                    • C152.1
                      • s_2_1101.bcl
                    • C161.1
                      • s_2_1101.bcl
                    • C101.1
                      • s_2_1101.bcl
                    • C114.1
                      • s_2_1101.bcl
                    • C118.1
                      • s_2_1101.bcl
                    • C22.1
                      • s_2_1101.bcl
                    • C146.1
                      • s_2_1101.bcl
                    • C149.1
                      • s_2_1101.bcl
                    • C243.1
                      • s_2_1101.bcl
                    • C68.1
                      • s_2_1101.bcl
                    • C38.1
                      • s_2_1101.bcl
                    • C201.1
                      • s_2_1101.bcl
                    • C140.1
                      • s_2_1101.bcl
                    • C160.1
                      • s_2_1101.bcl
                    • C236.1
                      • s_2_1101.bcl
                    • C113.1
                      • s_2_1101.bcl
                    • C80.1
                      • s_2_1101.bcl
                    • C156.1
                      • s_2_1101.bcl
                    • C51.1
                      • s_2_1101.bcl
                    • C103.1
                      • s_2_1101.bcl
                    • C115.1
                      • s_2_1101.bcl
                    • C164.1
                      • s_2_1101.bcl
                    • C171.1
                      • s_2_1101.bcl
                    • C23.1
                      • s_2_1101.bcl
                    • C73.1
                      • s_2_1101.bcl
                    • C246.1
                      • s_2_1101.bcl
                    • C123.1
                      • s_2_1101.bcl
                    • C60.1
                      • s_2_1101.bcl
                    • C91.1
                      • s_2_1101.bcl
                    • C220.1
                      • s_2_1101.bcl
                    • C125.1
                      • s_2_1101.bcl
                    • C200.1
                      • s_2_1101.bcl
                    • C57.1
                      • s_2_1101.bcl
                    • C159.1
                      • s_2_1101.bcl
                    • C224.1
                      • s_2_1101.bcl
                    • C196.1
                      • s_2_1101.bcl
                    • C97.1
                      • s_2_1101.bcl
                    • C124.1
                      • s_2_1101.bcl
                    • C7.1
                      • s_2_1101.bcl
                    • C151.1
                      • s_2_1101.bcl
                    • C214.1
                      • s_2_1101.bcl
                    • C54.1
                      • s_2_1101.bcl
                    • C130.1
                      • s_2_1101.bcl
                    • C25.1
                      • s_2_1101.bcl
                    • C59.1
                      • s_2_1101.bcl
                    • C61.1
                      • s_2_1101.bcl
                    • C138.1
                      • s_2_1101.bcl
                    • C79.1
                      • s_2_1101.bcl
                    • C139.1
                      • s_2_1101.bcl
                    • C105.1
                      • s_2_1101.bcl
                    • C128.1
                      • s_2_1101.bcl
                    • C4.1
                      • s_2_1101.bcl
                    • C137.1
                      • s_2_1101.bcl
                    • C67.1
                      • s_2_1101.bcl
                    • C209.1
                      • s_2_1101.bcl
                    • C6.1
                      • s_2_1101.bcl
                    • C218.1
                      • s_2_1101.bcl
                    • C49.1
                      • s_2_1101.bcl
                    • C40.1
                      • s_2_1101.bcl
                    • C157.1
                      • s_2_1101.bcl
                    • C121.1
                      • s_2_1101.bcl
                    • C50.1
                      • s_2_1101.bcl
                    • C81.1
                      • s_2_1101.bcl
                    • C231.1
                      • s_2_1101.bcl
                    • C75.1
                      • s_2_1101.bcl
                    • C32.1
                      • s_2_1101.bcl
                    • C192.1
                      • s_2_1101.bcl
                    • C70.1
                      • s_2_1101.bcl
                    • C240.1
                      • s_2_1101.bcl
                    • C33.1
                      • s_2_1101.bcl
                    • C136.1
                      • s_2_1101.bcl
                    • C182.1
                      • s_2_1101.bcl
                    • C62.1
                      • s_2_1101.bcl
                    • C142.1
                      • s_2_1101.bcl
                    • C69.1
                      • s_2_1101.bcl
                    • C187.1
                      • s_2_1101.bcl
                    • C85.1
                      • s_2_1101.bcl
                    • C30.1
                      • s_2_1101.bcl
                    • C19.1
                      • s_2_1101.bcl
                    • C3.1
                      • s_2_1101.bcl
                    • C119.1
                      • s_2_1101.bcl
                    • C46.1
                      • s_2_1101.bcl
                    • C39.1
                      • s_2_1101.bcl
                    • C14.1
                      • s_2_1101.bcl
                    • C42.1
                      • s_2_1101.bcl
                    • C9.1
                      • s_2_1101.bcl
                    • C82.1
                      • s_2_1101.bcl
                    • C150.1
                      • s_2_1101.bcl
                    • C223.1
                      • s_2_1101.bcl
                    • C166.1
                      • s_2_1101.bcl
                    • C107.1
                      • s_2_1101.bcl
                    • C55.1
                      • s_2_1101.bcl
                    • C247.1
                      • s_2_1101.bcl
                    • C87.1
                      • s_2_1101.bcl
                    • C77.1
                      • s_2_1101.bcl
                    • C177.1
                      • s_2_1101.bcl
                    • C249.1
                      • s_2_1101.bcl
                    • C183.1
                      • s_2_1101.bcl
                    • C34.1
                      • s_2_1101.bcl
                    • C207.1
                      • s_2_1101.bcl
                    • C100.1
                      • s_2_1101.bcl
                    • C12.1
                      • s_2_1101.bcl
                    • C47.1
                      • s_2_1101.bcl
                    • C195.1
                      • s_2_1101.bcl
                    • C232.1
                      • s_2_1101.bcl
                    • C129.1
                      • s_2_1101.bcl
                    • C222.1
                      • s_2_1101.bcl
                    • C65.1
                      • s_2_1101.bcl
                    • C239.1
                      • s_2_1101.bcl
                    • C180.1
                      • s_2_1101.bcl
                    • C88.1
                      • s_2_1101.bcl
                    • C64.1
                      • s_2_1101.bcl
                    • C76.1
                      • s_2_1101.bcl
                    • C74.1
                      • s_2_1101.bcl
                    • C27.1
                      • s_2_1101.bcl
                    • C72.1
                      • s_2_1101.bcl
                    • C235.1
                      • s_2_1101.bcl
                    • C230.1
                      • s_2_1101.bcl
                    • C71.1
                      • s_2_1101.bcl
                    • C134.1
                      • s_2_1101.bcl
                    • C245.1
                      • s_2_1101.bcl
                    • C208.1
                      • s_2_1101.bcl
                    • C194.1
                      • s_2_1101.bcl
                    • C202.1
                      • s_2_1101.bcl
                    • C122.1
                      • s_2_1101.bcl
                    • C167.1
                      • s_2_1101.bcl
                    • C238.1
                      • s_2_1101.bcl
                    • C191.1
                      • s_2_1101.bcl
                    • C86.1
                      • s_2_1101.bcl
                    • C229.1
                      • s_2_1101.bcl
                    • C211.1
                      • s_2_1101.bcl
                    • C10.1
                      • s_2_1101.bcl
                    • C237.1
                      • s_2_1101.bcl
                    • C31.1
                      • s_2_1101.bcl
                    • C37.1
                      • s_2_1101.bcl
                    • C131.1
                      • s_2_1101.bcl
                    • C168.1
                      • s_2_1101.bcl
                    • C217.1
                      • s_2_1101.bcl
                    • C99.1
                      • s_2_1101.bcl
                    • C41.1
                      • s_2_1101.bcl
                    • C162.1
                      • s_2_1101.bcl
                    • C165.1
                      • s_2_1101.bcl
                    • C203.1
                      • s_2_1101.bcl
                    • C112.1
                      • s_2_1101.bcl
                    • C170.1
                      • s_2_1101.bcl
                    • C63.1
                      • s_2_1101.bcl
                    • C78.1
                      • s_2_1101.bcl
                    • C133.1
                      • s_2_1101.bcl
                    • C8.1
                      • s_2_1101.bcl
                    • C18.1
                      • s_2_1101.bcl
                    • C95.1
                      • s_2_1101.bcl
                    • C5.1
                      • s_2_1101.bcl
                    • C24.1
                      • s_2_1101.bcl
                    • C84.1
                      • s_2_1101.bcl
                    • C155.1
                      • s_2_1101.bcl
                    • C94.1
                      • s_2_1101.bcl
                    • C176.1
                      • s_2_1101.bcl
                    • C108.1
                      • s_2_1101.bcl
                    • C169.1
                      • s_2_1101.bcl
                    • C153.1
                      • s_2_1101.bcl
                    • C226.1
                      • s_2_1101.bcl
                    • C148.1
                      • s_2_1101.bcl
                    • C48.1
                      • s_2_1101.bcl
                    • C104.1
                      • s_2_1101.bcl
                    • C197.1
                      • s_2_1101.bcl
                    • C35.1
                      • s_2_1101.bcl
                    • C2.1
                      • s_2_1101.bcl
                    • C163.1
                      • s_2_1101.bcl
                    • C184.1
                      • s_2_1101.bcl
                    • C28.1
                      • s_2_1101.bcl
                    • C145.1
                      • s_2_1101.bcl
                    • C189.1
                      • s_2_1101.bcl
                    • C83.1
                      • s_2_1101.bcl
                    • C233.1
                      • s_2_1101.bcl
                    • C234.1
                      • s_2_1101.bcl
                    • C102.1
                      • s_2_1101.bcl
                    • C154.1
                      • s_2_1101.bcl
                    • C178.1
                      • s_2_1101.bcl
                    • C216.1
                      • s_2_1101.bcl
                    • C15.1
                      • s_2_1101.bcl
                    • C227.1
                      • s_2_1101.bcl
                    • C206.1
                      • s_2_1101.bcl
                    • C198.1
                      • s_2_1101.bcl
                    • C44.1
                      • s_2_1101.bcl
                    • C244.1
                      • s_2_1101.bcl
                    • C132.1
                      • s_2_1101.bcl
                    • C89.1
                      • s_2_1101.bcl
                    • C248.1
                      • s_2_1101.bcl
                    • C141.1
                      • s_2_1101.bcl
                    • C144.1
                      • s_2_1101.bcl
                    • C185.1
                      • s_2_1101.bcl
                    • C45.1
                      • s_2_1101.bcl
                    • C1.1
                      • s_2_1101.bcl
                    • C20.1
                      • s_2_1101.bcl
                    • C36.1
                      • s_2_1101.bcl
                    • C13.1
                      • s_2_1101.bcl
                    • C210.1
                      • s_2_1101.bcl
                    • C215.1
                      • s_2_1101.bcl
                    • C190.1
                      • s_2_1101.bcl
                    • C126.1
                      • s_2_1101.bcl
                    • C127.1
                      • s_2_1101.bcl
                    • C250.1
                      • s_2_1101.bcl
                    • C52.1
                      • s_2_1101.bcl
                    • C56.1
                      • s_2_1101.bcl
                    • C96.1
                      • s_2_1101.bcl
                    • C199.1
                      • s_2_1101.bcl
                    • C143.1
                      • s_2_1101.bcl
                    • C106.1
                      • s_2_1101.bcl
                    • C109.1
                      • s_2_1101.bcl
                    • C135.1
                      • s_2_1101.bcl
                    • C43.1
                      • s_2_1101.bcl
                    • C193.1
                      • s_2_1101.bcl
                    • C228.1
                      • s_2_1101.bcl
                    • C92.1
                      • s_2_1101.bcl
                    • C17.1
                      • s_2_1101.bcl
                    • C26.1
                      • s_2_1101.bcl
                    • C147.1
                      • s_2_1101.bcl
                    • C110.1
                      • s_2_1101.bcl
                    • C204.1
                      • s_2_1101.bcl
                    • C21.1
                      • s_2_1101.bcl
                    • C11.1
                      • s_2_1101.bcl
                    • C120.1
                      • s_2_1101.bcl
                    • C188.1
                      • s_2_1101.bcl
                    • C219.1
                      • s_2_1101.bcl
                    • C111.1
                      • s_2_1101.bcl
                    • C172.1
                      • s_2_1101.bcl
                    • C58.1
                      • s_2_1101.bcl
                    • C98.1
                      • s_2_1101.bcl
                    • s_2_1101.filter
                    • C90.1
                      • s_2_1101.bcl
                    • C242.1
                      • s_2_1101.bcl
                    • C29.1
                      • s_2_1101.bcl
                    • C93.1
                      • s_2_1101.bcl
                    • C241.1
                      • s_2_1101.bcl
                    • C212.1
                      • s_2_1101.bcl
                    • C158.1
                      • s_2_1101.bcl
                    • C117.1
                      • s_2_1101.bcl
                    • C66.1
                      • s_2_1101.bcl
                    • C181.1
                      • s_2_1101.bcl
                    • C174.1
                      • s_2_1101.bcl
                    • C116.1
                      • s_2_1101.bcl
                    • C225.1
                      • s_2_1101.bcl
                    • C179.1
                      • s_2_1101.bcl
                    • C175.1
                      • s_2_1101.bcl
                    • C186.1
                      • s_2_1101.bcl
                    • C53.1
                      • s_2_1101.bcl
                    • C213.1
                      • s_2_1101.bcl
                    • C173.1
                      • s_2_1101.bcl
                    • C16.1
                      • s_2_1101.bcl
                    • C221.1
                      • s_2_1101.bcl
                • L002
                  • s_2_1101.clocs
          • 151T8B8B151T_cbcl
            • sams
              • GCTATAGTCCAGCAGC.sam
              • TTGCGGCCGGTTTAAC.sam
              • 1102.CACCTAGTACTCGAGT.sam
              • 1102.TTGCGGCCGGTTTAAC.sam
              • 1102.CCCCGCTTTTGCGTGT.sam
              • 1102.NN.sam
              • CACCTAGTACTCGAGT.sam
              • library_double.params
              • 1102.GCTATAGTCCAGCAGC.sam
              • NN.sam
              • CCCCGCTTTTGCGTGT.sam
            • fastq
              • NN.barcode_2.fastq
              • GCTATAGTCCAGCAGC.barcode_1.fastq
              • GCTATAGTCCAGCAGC.barcode_2.fastq
              • TTGCGGCCGGTTTAAC.1.fastq
              • NN.1.fastq
              • barcode_double.params
              • TTGCGGCCGGTTTAAC.2.fastq
              • GCTATAGTCCAGCAGC.1.fastq
              • NN.2.fastq
              • CCCCGCTTTTGCGTGT.1.fastq
              • CACCTAGTACTCGAGT.barcode_2.fastq
              • CACCTAGTACTCGAGT.barcode_1.fastq
              • CCCCGCTTTTGCGTGT.2.fastq
              • TTGCGGCCGGTTTAAC.barcode_2.fastq
              • NN.barcode_1.fastq
              • GCTATAGTCCAGCAGC.2.fastq
              • CCCCGCTTTTGCGTGT.barcode_1.fastq
              • CACCTAGTACTCGAGT.2.fastq
              • CCCCGCTTTTGCGTGT.barcode_2.fastq
              • TTGCGGCCGGTTTAAC.barcode_1.fastq
              • CACCTAGTACTCGAGT.1.fastq
            • Data
              • Intensities
                • BaseCalls
                  • L001
                    • C205.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C152.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C161.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C101.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C114.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C317.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C305.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C282.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C118.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C300.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C22.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C146.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C149.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C243.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C68.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C38.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C288.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C253.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C270.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C201.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C140.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C160.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C236.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C113.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C80.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C156.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C51.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C103.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C115.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C164.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C171.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C284.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C23.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C73.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C246.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C123.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C60.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C297.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C91.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C220.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C125.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C200.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C57.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C159.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C224.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C196.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C267.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C97.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C260.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C124.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C7.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C151.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C214.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C252.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C293.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C54.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C130.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C25.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C59.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C61.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C138.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C79.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C139.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C105.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C128.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C308.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C4.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C137.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C67.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C209.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C312.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C6.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C218.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C49.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C40.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C157.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C121.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C292.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C50.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C81.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C314.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C289.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C231.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C286.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C75.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C32.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C261.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C192.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C258.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C70.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C240.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C275.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C285.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C262.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C33.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C136.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C182.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C62.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C264.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • s_1_1101.filter
                    • C142.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C69.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C187.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C85.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C30.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C19.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C3.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C119.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C46.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C39.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C14.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C42.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C9.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C82.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C150.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C223.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C166.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C107.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C55.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C255.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C247.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C87.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C77.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C273.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C177.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C249.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C183.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C34.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C304.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C296.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C207.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C100.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C12.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C306.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C47.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C195.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C232.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C129.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C222.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C65.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C239.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C180.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C88.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C64.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C76.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C290.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C74.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C27.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C271.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C295.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C72.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C235.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C230.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C71.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C134.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C245.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C307.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C259.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C208.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C283.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C318.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C313.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C194.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C202.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C122.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C167.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C291.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C238.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C191.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C86.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C298.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C229.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C211.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C10.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C268.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C237.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C31.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C37.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C131.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C168.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C217.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C99.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C41.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C162.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C299.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C165.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C203.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C112.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C278.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C170.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C63.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C78.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C133.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C8.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C18.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C95.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C294.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C5.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C24.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C84.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C155.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C94.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C176.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C108.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C169.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C265.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C153.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C226.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C301.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C148.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C251.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C48.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C104.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C197.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C35.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C2.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C280.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C163.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C287.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C184.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C28.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C145.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C189.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C83.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C233.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C234.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C102.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C154.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C178.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C216.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C15.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C227.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C206.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C198.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C44.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C266.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C310.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C309.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C276.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C311.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C244.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C132.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C89.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C248.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C141.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C144.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C303.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C185.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C45.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C1.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C20.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C36.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C13.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C210.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C215.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C190.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C257.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C126.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C279.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C127.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C250.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C52.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C56.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C96.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C199.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C281.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C143.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C106.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C269.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C109.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C135.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C43.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C302.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C193.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C228.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C274.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C92.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C17.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C26.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C272.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C147.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C110.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C204.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C21.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C11.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C277.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C120.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C188.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C219.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C256.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C111.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C172.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C58.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C98.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C90.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C242.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C29.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C315.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C263.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C93.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C254.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C241.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C212.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C158.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C117.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C66.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C181.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C174.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C116.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C225.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C179.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • s_1_1102.filter
                    • C316.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C175.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C186.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C53.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C213.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C173.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C16.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                    • C221.1
                      • L001_1.cbcl
                      • L001_2.cbcl
                  • s_1_1102_barcode.txt.gz
                  • s_1_1101_barcode.txt.gz
                  • barcodeData.1
          • 25T8B25T
            • sams
              • TTGTCTAT.sam
              • CAACTCTC.sam
              • AACAATGG.sam
              • AAAAGAAG.sam
              • ACTAAGAC.sam
              • AAAAAAAA.sam
              • CAATAGAC.sam
              • nonBarcodedWithTagPerMolecularIndex4M4M.sam
              • ACAGGTAT.sam
              • ATTATCAA.sam
              • N.sam
              • GCCTAGCC.sam
              • GTAACATC.sam
              • nonBarcodedDescriptionNonBI.sam
              • GCCGTCGA.sam
              • nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam
              • TCTGCAAG.sam
              • GAAAAAAA.sam
              • CCATGCGT.sam
              • GAAGGAAG.sam
              • CTATGCGC.sam
              • ACTGTATC.sam
              • nonBarcodedWithMolecularIndex4M4M.sam
              • TATCAGCC.sam
              • TCCGTCTA.sam
              • TCGCTAGA.sam
              • GACCTAAC.sam
              • CTATGCGT.sam
              • GAACGAT..sam
              • CTAACTCG.sam
              • library.params
              • ACTGTACC.sam
              • CCAACATT.sam
              • CAGCGGTA.sam
              • AGCATGGA.sam
              • AGAAAAGA.sam
              • CAGCGGAT.sam
              • CGCCTTCC.sam
              • CCAGCACC.sam
              • TATCCAGG.sam
              • ACAAAATT.sam
              • TATCTCGG.sam
              • TGTAATCA.sam
              • CAATAGTC.sam
              • AACGCATT.sam
              • TATCCATG.sam
              • TAAGCACA.sam
              • TATCTGCC.sam
              • ACGAAATC.sam
              • GTCCACAG.sam
              • ACCAGTTG.sam
              • nonBarcoded.sam
              • multiplexed_positive_rgtags.params
              • AGGTAAGG.sam
              • AGGTCGCA.sam
              • TGCTGCTG.sam
              • ATTCCTCT.sam
              • ACAGTTGA.sam
              • GACCAGGA.sam
              • GACCGTTG.sam
              • CTGTAATC.sam
              • TACCGTCT.sam
              • TGTAACTC.sam
              • CGCTATGT.sam
              • nonBarcodedWithMolecularIndex8M.sam
              • nonBarcodedTileSubset.sam
              • TGCAAGTA.sam
              • GACCAGGC.sam
              • CTGCGGAT.sam
              • GATATCCA.sam
              • TAGCGGTA.sam
            • fastq_with_4M4M
              • ATTATCAA.barcode_1.fastq
              • GTAACATC.1.fastq
              • CCAGCACC.1.fastq
              • GCCTAGCC.index_2.fastq
              • TATCCAGG.index_1.fastq
              • CTGTAATC.1.fastq
              • AAAAGAAG.index_2.fastq
              • N.barcode_1.fastq
              • GCCTAGCC.2.fastq
              • TCTGCAAG.index_1.fastq
              • ACAAAATT.barcode_1.fastq
              • ACTAAGAC.index_1.fastq
              • TAAGCACA.index_2.fastq
              • CAGCGGAT.2.fastq
              • ACTGTACC.2.fastq
              • ACTGTATC.1.fastq
              • GACCAGGC.barcode_1.fastq
              • TATCCATG.index_2.fastq
              • GACCGTTG.index_2.fastq
              • GAAAAAAA.index_2.fastq
              • GAACGAT..index_2.fastq
              • CCAACATT.barcode_1.fastq
              • TCCGTCTA.2.fastq
              • ATTATCAA.index_2.fastq
              • ACAGGTAT.barcode_1.fastq
              • CTGCGGAT.2.fastq
              • CAGCGGTA.2.fastq
              • ACTGTATC.barcode_1.fastq
              • CCAGCACC.2.fastq
              • ATTCCTCT.index_2.fastq
              • TGCAAGTA.index_1.fastq
              • AGCATGGA.1.fastq
              • AAAAGAAG.index_1.fastq
              • TGCTGCTG.barcode_1.fastq
              • CAGCGGAT.1.fastq
              • CAATAGAC.barcode_1.fastq
              • TAAGCACA.barcode_1.fastq
              • CTATGCGT.index_2.fastq
              • ACAGTTGA.index_1.fastq
              • TTGTCTAT.1.fastq
              • ACAAAATT.1.fastq
              • ATTCCTCT.index_1.fastq
              • ATTCCTCT.barcode_1.fastq
              • GTAACATC.index_2.fastq
              • GAAAAAAA.barcode_1.fastq
              • CCAGCACC.barcode_1.fastq
              • CTGCGGAT.index_1.fastq
              • TAAGCACA.2.fastq
              • ACTGTACC.barcode_1.fastq
              • ACAGTTGA.index_2.fastq
              • GACCAGGA.index_1.fastq
              • CTGCGGAT.1.fastq
              • ACAGTTGA.barcode_1.fastq
              • CAATAGAC.index_1.fastq
              • CGCCTTCC.index_2.fastq
              • GAACGAT..2.fastq
              • AACAATGG.barcode_1.fastq
              • TATCCAGG.2.fastq
              • TCTGCAAG.2.fastq
              • AGAAAAGA.index_1.fastq
              • GATATCCA.index_2.fastq
              • CAACTCTC.index_1.fastq
              • AGAAAAGA.barcode_1.fastq
              • CTATGCGC.index_1.fastq
              • TATCCATG.barcode_1.fastq
              • AGGTCGCA.index_1.fastq
              • AACGCATT.barcode_1.fastq
              • GCCTAGCC.barcode_1.fastq
              • GCCGTCGA.barcode_1.fastq