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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
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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
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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