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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