[med-svn] [picard-tools] branch master updated (42a89b7 -> bd3256e)
Andreas Tille
tille at debian.org
Sun Feb 21 18:51:49 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository picard-tools.
from 42a89b7 Introduced EDAM annotation
new 268564c Care for xz compression right inside d/watch
new c9f5b97 Imported Upstream version 2.1.0+dfsg
new 77fac7d New upstream version
new 4234434 Merge
new 47e74c7 Add error in build process as TODO item
new bd3256e Cleanup d/changelog after unsuccessful merge
The 6 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.gitignore | 5 +-
.travis.yml | 9 +-
README.md | 9 +-
build.sbt | 8 +-
build.xml | 38 +-
debian/changelog | 15 +-
debian/control | 19 +-
debian/rules | 3 -
debian/watch | 2 +-
src/java/picard/analysis/AdapterUtility.java | 117 +++
.../analysis/AlignmentSummaryMetricsCollector.java | 132 ++-
.../analysis/BaseDistributionByCycleMetrics.java | 24 +
src/java/picard/analysis/ChimeraUtil.java | 79 ++
.../analysis/CollectAlignmentSummaryMetrics.java | 55 +-
.../analysis/CollectBaseDistributionByCycle.java | 62 +-
src/java/picard/analysis/CollectGcBiasMetrics.java | 61 +-
.../picard/analysis/CollectInsertSizeMetrics.java | 43 +-
.../analysis/CollectJumpingLibraryMetrics.java | 28 +-
.../picard/analysis/CollectMultipleMetrics.java | 88 +-
src/java/picard/analysis/CollectOxoGMetrics.java | 49 +-
.../analysis/CollectQualityYieldMetrics.java | 141 +--
src/java/picard/analysis/CollectRawWgsMetrics.java | 67 +-
src/java/picard/analysis/CollectRrbsMetrics.java | 49 +-
src/java/picard/analysis/CollectWgsMetrics.java | 203 ++--
.../analysis/CollectWgsMetricsFromQuerySorted.java | 331 +++++--
.../CollectWgsMetricsFromSampledSites.java | 25 +
src/java/picard/analysis/CompareMetrics.java | 41 +-
.../analysis/FingerprintingDetailMetrics.java | 70 ++
.../analysis/FingerprintingSummaryMetrics.java | 79 ++
.../picard/analysis/GcBiasMetricsCollector.java | 27 +
src/java/picard/analysis/GcBiasSummaryMetrics.java | 9 +
src/java/picard/analysis/MeanQualityByCycle.java | 23 +-
.../picard/analysis/QualityScoreDistribution.java | 25 +-
src/java/picard/analysis/SinglePassSamProgram.java | 24 +
.../picard/analysis/TheoreticalSensitivity.java | 188 ++++
.../picard/analysis/artifacts/ArtifactCounter.java | 75 +-
.../CollectSequencingArtifactMetrics.java | 89 +-
.../analysis/artifacts/ContextAccumulator.java | 70 +-
.../artifacts/ConvertSequencingArtifactToOxoG.java | 34 +-
.../artifacts/SequencingArtifactMetrics.java | 33 +-
src/java/picard/analysis/artifacts/Transition.java | 42 +-
.../analysis/directed/CalculateHsMetrics.java | 63 +-
...lculateHsMetrics.java => CollectHsMetrics.java} | 27 +-
.../analysis/directed/CollectTargetedMetrics.java | 34 +-
.../directed/CollectTargetedPcrMetrics.java | 38 +-
.../analysis/directed/HsMetricCollector.java | 35 +-
src/java/picard/analysis/directed/HsMetrics.java | 66 +-
.../directed/InsertSizeMetricsCollector.java | 118 ++-
.../analysis/directed/RnaSeqMetricsCollector.java | 16 +-
.../analysis/directed/TargetMetricsCollector.java | 609 ++++++++----
.../analysis/directed/TargetedPcrMetrics.java | 41 +-
.../directed/TargetedPcrMetricsCollector.java | 36 +-
src/java/picard/cmdline/CommandLineParser.java | 57 +-
src/java/picard/cmdline/Option.java | 14 +
src/java/picard/cmdline/programgroups/Alpha.java | 13 +
src/java/picard/fastq/BamToBfq.java | 19 +-
.../CountingDuplicateFilter.java} | 20 +-
src/java/picard/filter/CountingFilter.java | 67 ++
.../CountingMapQFilter.java} | 24 +-
.../CountingPairedFilter.java} | 20 +-
src/java/picard/fingerprint/CheckFingerprint.java | 228 +++++
.../CrosscheckReadGroupFingerprints.java | 312 ++++++
src/java/picard/fingerprint/DiploidGenotype.java | 109 +++
.../DiploidHaplotype.java} | 22 +-
src/java/picard/fingerprint/Fingerprint.java | 100 ++
.../picard/fingerprint/FingerprintChecker.java | 635 ++++++++++++
.../FingerprintResults.java} | 40 +-
src/java/picard/fingerprint/GenotypeReader.java | 167 ++++
src/java/picard/fingerprint/HaplotypeBlock.java | 169 ++++
src/java/picard/fingerprint/HaplotypeMap.java | 388 ++++++++
.../picard/fingerprint/HaplotypeProbabilities.java | 241 +++++
...otypeProbabilitiesFromContaminatorSequence.java | 129 +++
.../HaplotypeProbabilitiesFromGenotype.java | 72 ++
...lotypeProbabilitiesFromGenotypeLikelihoods.java | 90 ++
.../HaplotypeProbabilitiesFromSequence.java | 126 +++
.../HaplotypeProbabilitiesUsingLogLikelihoods.java | 145 +++
.../HaplotypeProbabilityOfNormalGivenTumor.java | 101 ++
src/java/picard/fingerprint/LocusResult.java | 77 ++
src/java/picard/fingerprint/MatchResults.java | 96 ++
src/java/picard/fingerprint/Snp.java | 120 +++
.../picard/illumina/ClusterDataToSamConverter.java | 59 +-
.../CollectIlluminaBasecallingMetrics.java | 2 +-
.../illumina/CollectIlluminaLaneMetrics.java | 51 +-
.../picard/illumina/ExtractIlluminaBarcodes.java | 53 +-
.../illumina/IlluminaBasecallsConverter.java | 6 +-
.../picard/illumina/IlluminaBasecallsToFastq.java | 156 +--
.../picard/illumina/IlluminaBasecallsToSam.java | 31 +-
src/java/picard/illumina/MarkIlluminaAdapters.java | 4 +-
src/java/picard/illumina/parser/ReadStructure.java | 58 +-
src/java/picard/illumina/parser/ReadType.java | 9 +-
src/java/picard/illumina/parser/Tile.java | 15 +-
.../picard/illumina/parser/TileMetricsUtil.java | 37 +-
src/java/picard/reference/ExtractSequences.java | 25 +-
src/java/picard/reference/NonNFastaSize.java | 128 +++
src/java/picard/reference/NormalizeFasta.java | 26 +-
src/java/picard/sam/AddCommentsToBam.java | 23 +-
src/java/picard/sam/AddOrReplaceReadGroups.java | 30 +-
src/java/picard/sam/BamIndexStats.java | 21 +-
src/java/picard/sam/BuildBamIndex.java | 19 +-
.../picard/sam/CalculateReadGroupChecksum.java | 19 +-
src/java/picard/sam/CompareSAMs.java | 22 +-
src/java/picard/sam/CreateSequenceDictionary.java | 20 +-
src/java/picard/sam/DownsampleSam.java | 35 +-
src/java/picard/sam/FastqToSam.java | 27 +-
src/java/picard/sam/FilterSamReads.java | 21 +-
src/java/picard/sam/FixMateInformation.java | 31 +-
src/java/picard/sam/GatherBamFiles.java | 28 +-
src/java/picard/sam/MergeBamAlignment.java | 26 +-
src/java/picard/sam/MergeSamFiles.java | 62 +-
.../picard/sam/PositionBasedDownsampleSam.java | 17 +-
src/java/picard/sam/ReplaceSamHeader.java | 22 +-
src/java/picard/sam/RevertSam.java | 18 +-
src/java/picard/sam/SamToFastq.java | 93 +-
src/java/picard/sam/SortSam.java | 18 +-
src/java/picard/sam/ValidateSamFile.java | 44 +-
.../markduplicates/EstimateLibraryComplexity.java | 105 +-
.../picard/sam/markduplicates/MarkDuplicates.java | 106 +-
.../MarkDuplicatesWithMateCigar.java | 28 +-
.../MarkDuplicatesWithMateCigarIterator.java | 2 +-
.../AbstractMarkDuplicatesCommandLineProgram.java | 46 +-
.../util/OpticalDuplicateFinder.java | 205 ++--
.../util/PhysicalLocationForMateCigar.java | 27 +-
.../picard/sam/markduplicates/util/ReadEnds.java | 28 +-
.../util/ReadEndsForMarkDuplicatesCodec.java | 4 +-
src/java/picard/sam/util/PhysicalLocation.java | 117 +--
src/java/picard/sam/util/PhysicalLocationInt.java | 37 +
.../util/PhysicalLocationShort.java} | 29 +-
src/java/picard/sam/util/ReadNameParser.java | 193 ++++
src/java/picard/sam/util/ReadNameParsingUtils.java | 83 --
src/java/picard/util/BedToIntervalList.java | 49 +-
src/java/picard/util/IlluminaUtil.java | 19 +-
src/java/picard/util/IntervalListToBed.java | 90 ++
src/java/picard/util/IntervalListTools.java | 34 +-
src/java/picard/util/LiftOverIntervalList.java | 21 +-
src/java/picard/util/MathUtil.java | 32 +
src/java/picard/util/ScatterIntervalsByNs.java | 18 +-
src/java/picard/vcf/CallingMetricAccumulator.java | 202 ++--
.../picard/vcf/CollectVariantCallingMetrics.java | 61 +-
src/java/picard/vcf/GenotypeConcordance.java | 51 +-
src/java/picard/vcf/GvcfMetricAccumulator.java | 64 ++
src/java/picard/vcf/LiftoverVcf.java | 49 +-
src/java/picard/vcf/RenameSampleInVcf.java | 17 +-
src/java/picard/vcf/SortVcf.java | 23 +-
src/java/picard/vcf/SplitVcfs.java | 21 +-
src/java/picard/vcf/VcfFormatConverter.java | 22 +-
src/scripts/picard/analysis/insertSizeHistogram.R | 8 +-
src/scripts/release_picard.sh | 8 +-
.../CollectAlignmentSummaryMetricsTest.java | 24 +-
.../picard/analysis/CollectGcBiasMetricsTest.java | 34 +-
.../analysis/CollectMultipleMetricsTest.java | 19 +-
.../analysis/CollectQualityYieldMetricsTest.java | 75 ++
.../CollectWgsMetricsFromQuerySortedTest.java | 51 +-
.../CollectWgsMetricsFromSampledSitesTest.java | 10 +-
.../picard/analysis/CollectWgsMetricsTest.java | 174 ++++
.../analysis/TheoreticalSensitivityTest.java | 231 +++++
.../CollectSequencingArtifactMetricsTest.java | 9 +-
.../analysis/directed/CollectHsMetricsTest.java | 83 ++
.../directed/CollectTargetedMetricsTest.java | 17 +-
.../picard/fingerprint/FingerprintCheckerTest.java | 29 +
.../java/picard/fingerprint/HaplotypeMapTest.java | 102 ++
.../fingerprint/HaplotypeProbabilitiesTest.java | 188 ++++
...HaplotypeProbabilityOfNormalGivenTumorTest.java | 56 ++
.../illumina/ExtractIlluminaBarcodesTest.java | 17 +
.../illumina/IlluminaBasecallsToFastqTest.java | 29 +-
.../illumina/IlluminaBasecallsToSamTest.java | 51 +-
.../java/picard/illumina/ReadStructureTest.java | 106 +-
.../java/picard/reference/NonNFastaSizeTest.java | 87 ++
.../java/picard/sam/FixMateInformationTest.java | 65 ++
.../EstimateLibraryComplexityTest.java | 121 +++
.../MarkDuplicateWithMissingBarcodeTest.java | 33 +
...MarkDuplicateWithMissingReadOneBarcodeTest.java | 22 +
...MarkDuplicateWithMissingReadTwoBarcodeTest.java | 21 +
.../MarkDuplicateWithMissingSampleBarcodeTest.java | 21 +
.../SimpleMarkDuplicatesWithMateCigar.java | 15 +-
.../util/OpticalDuplicateFinderTest.java | 171 +++-
.../java/picard/sam/util/ReadNameParserTests.java | 142 +++
.../java/picard/util/BedToIntervalListTest.java | 1 +
.../java/picard/util/IntervalListToBedTest.java | 43 +
.../picard/vcf/CallingMetricAccumulatorTest.java | 78 ++
.../vcf/CollectVariantCallingMetricsTest.java | 122 ++-
src/tests/java/picard/vcf/LiftoverVcfTest.java | 32 +
src/tests/java/picard/vcf/TestFilterVcf.java | 14 +-
.../Solexa332667_BaseQ.histo | 31 +
.../Solexa332667_DepthDist.histo | 501 ++++++++++
.../test_25103070136.targeted_pcr_metrics | 1013 ++++++++++++++++++++
.../test_NexPond-359781.hsMetrics | 1013 ++++++++++++++++++++
.../test_Solexa-316269_sampled.wgs_metrics | 263 +++++
.../test_Solexa-332667.wgs_metrics | 263 +++++
.../with_context.bait_bias_detail_metrics | 240 ++---
.../with_context.bait_bias_summary_metrics | 26 +-
.../with_context.pre_adapter_detail_metrics | 240 ++---
.../with_context.pre_adapter_summary_metrics | 28 +-
.../directed/CollectHsMetrics/chrM.interval_list | 3 +
.../directed/CollectHsMetrics/lowbaseq.sam | 14 +
.../analysis/directed/CollectHsMetrics/lowmapq.sam | 14 +
.../directed/CollectHsMetrics/overlapping.sam | 14 +
testdata/picard/fingerprint/haplotypeMap.txt | 73 ++
.../{fastq => fastq_with_4M}/AAAAAAAA.1.fastq | 0
.../{fastq => fastq_with_4M}/AAAAAAAA.2.fastq | 0
.../AAAAAAAA.barcode_1.fastq | 0
.../AAAAAAAA.index_1.fastq} | 0
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.../AAAAGAAG.barcode_1.fastq | 0
.../AAAAGAAG.index_1.fastq} | 0
.../{fastq => fastq_with_4M}/AACAATGG.1.fastq | 0
.../25T8B25T/fastq_with_4M/AACAATGG.2.fastq | 16 +
.../AACAATGG.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/AACAATGG.index_1.fastq | 16 +
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.../25T8B25T/fastq_with_4M/AACGCATT.2.fastq | 28 +
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.../25T8B25T/fastq_with_4M/ACAGTTGA.2.fastq | 8 +
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.../25T8B25T/fastq_with_4M/ACTAAGAC.index_1.fastq | 16 +
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.../25T8B25T/fastq_with_4M/ACTGTATC.2.fastq | 16 +
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.../25T8B25T/fastq_with_4M/ACTGTATC.index_1.fastq | 16 +
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.../AGAAAAGA.index_1.fastq} | 0
.../{fastq => fastq_with_4M}/AGCATGGA.1.fastq | 0
.../25T8B25T/fastq_with_4M/AGCATGGA.2.fastq | 12 +
.../AGCATGGA.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/AGCATGGA.index_1.fastq | 12 +
.../{fastq => fastq_with_4M}/AGGTAAGG.1.fastq | 0
.../25T8B25T/fastq_with_4M/AGGTAAGG.2.fastq | 16 +
.../AGGTAAGG.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/AGGTAAGG.index_1.fastq | 16 +
.../{fastq => fastq_with_4M}/AGGTCGCA.1.fastq | 0
.../25T8B25T/fastq_with_4M/AGGTCGCA.2.fastq | 16 +
.../AGGTCGCA.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/AGGTCGCA.index_1.fastq | 16 +
.../{fastq => fastq_with_4M}/ATTATCAA.1.fastq | 0
.../25T8B25T/fastq_with_4M/ATTATCAA.2.fastq | 20 +
.../ATTATCAA.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/ATTATCAA.index_1.fastq | 20 +
.../{fastq => fastq_with_4M}/ATTCCTCT.1.fastq | 0
.../25T8B25T/fastq_with_4M/ATTCCTCT.2.fastq | 16 +
.../ATTCCTCT.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/ATTCCTCT.index_1.fastq | 16 +
.../{fastq => fastq_with_4M}/CAACTCTC.1.fastq | 0
.../25T8B25T/fastq_with_4M/CAACTCTC.2.fastq | 20 +
.../CAACTCTC.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/CAACTCTC.index_1.fastq | 20 +
.../{fastq => fastq_with_4M}/CAATAGAC.1.fastq | 0
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.../CAATAGAC.index_1.fastq} | 0
.../{fastq => fastq_with_4M}/CAATAGTC.1.fastq | 0
.../25T8B25T/fastq_with_4M/CAATAGTC.2.fastq | 28 +
.../CAATAGTC.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/CAATAGTC.index_1.fastq | 28 +
.../{fastq => fastq_with_4M}/CAGCGGAT.1.fastq | 0
.../{fastq => fastq_with_4M}/CAGCGGAT.2.fastq | 0
.../CAGCGGAT.barcode_1.fastq | 0
.../CAGCGGAT.index_1.fastq} | 0
.../{fastq => fastq_with_4M}/CAGCGGTA.1.fastq | 0
.../25T8B25T/fastq_with_4M/CAGCGGTA.2.fastq | 20 +
.../CAGCGGTA.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/CAGCGGTA.index_1.fastq | 20 +
.../{fastq => fastq_with_4M}/CCAACATT.1.fastq | 0
.../25T8B25T/fastq_with_4M/CCAACATT.2.fastq | 28 +
.../CCAACATT.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/CCAACATT.index_1.fastq | 28 +
.../{fastq => fastq_with_4M}/CCAGCACC.1.fastq | 0
.../25T8B25T/fastq_with_4M/CCAGCACC.2.fastq | 12 +
.../CCAGCACC.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/CCAGCACC.index_1.fastq | 12 +
.../{fastq => fastq_with_4M}/CCATGCGT.1.fastq | 0
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.../CCATGCGT.index_1.fastq} | 0
.../{fastq => fastq_with_4M}/CGCCTTCC.1.fastq | 0
.../25T8B25T/fastq_with_4M/CGCCTTCC.2.fastq | 8 +
.../CGCCTTCC.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/CGCCTTCC.index_1.fastq | 8 +
.../{fastq => fastq_with_4M}/CGCTATGT.1.fastq | 0
.../25T8B25T/fastq_with_4M/CGCTATGT.2.fastq | 20 +
.../CGCTATGT.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/CGCTATGT.index_1.fastq | 20 +
.../{fastq => fastq_with_4M}/CTAACTCG.1.fastq | 0
.../25T8B25T/fastq_with_4M/CTAACTCG.2.fastq | 16 +
.../CTAACTCG.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/CTAACTCG.index_1.fastq | 16 +
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.../25T8B25T/fastq_with_4M/CTATGCGT.index_1.fastq | 28 +
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.../25T8B25T/fastq_with_4M/CTGCGGAT.index_1.fastq | 12 +
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.../25T8B25T/fastq_with_4M/CTGTAATC.2.fastq | 24 +
.../CTGTAATC.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/CTGTAATC.index_1.fastq | 24 +
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.../25T8B25T/fastq_with_4M/GAAGGAAG.index_1.fastq | 12 +
.../{fastq => fastq_with_4M}/GACCAGGA.1.fastq | 0
.../25T8B25T/fastq_with_4M/GACCAGGA.2.fastq | 28 +
.../GACCAGGA.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/GACCAGGA.index_1.fastq | 28 +
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.../25T8B25T/fastq_with_4M/GACCGTTG.2.fastq | 16 +
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.../25T8B25T/fastq_with_4M/GACCGTTG.index_1.fastq | 16 +
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.../25T8B25T/fastq_with_4M/GACCTAAC.index_1.fastq | 4 +
.../{fastq => fastq_with_4M}/GATATCCA.1.fastq | 0
.../25T8B25T/fastq_with_4M/GATATCCA.2.fastq | 12 +
.../GATATCCA.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/GATATCCA.index_1.fastq | 12 +
.../{fastq => fastq_with_4M}/GCCGTCGA.1.fastq | 0
.../25T8B25T/fastq_with_4M/GCCGTCGA.2.fastq | 20 +
.../GCCGTCGA.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/GCCGTCGA.index_1.fastq | 20 +
.../{fastq => fastq_with_4M}/GCCTAGCC.1.fastq | 0
.../25T8B25T/fastq_with_4M/GCCTAGCC.2.fastq | 20 +
.../GCCTAGCC.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/GCCTAGCC.index_1.fastq | 20 +
.../{fastq => fastq_with_4M}/GTAACATC.1.fastq | 0
.../25T8B25T/fastq_with_4M/GTAACATC.2.fastq | 8 +
.../GTAACATC.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/GTAACATC.index_1.fastq | 8 +
.../{fastq => fastq_with_4M}/GTCCACAG.1.fastq | 0
.../25T8B25T/fastq_with_4M/GTCCACAG.2.fastq | 8 +
.../GTCCACAG.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/GTCCACAG.index_1.fastq | 8 +
.../25T8B25T/{fastq => fastq_with_4M}/N.1.fastq | 0
.../illumina/25T8B25T/fastq_with_4M/N.2.fastq | 64 ++
.../{fastq => fastq_with_4M}/N.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/N.index_1.fastq | 64 ++
.../{fastq => fastq_with_4M}/TAAGCACA.1.fastq | 0
.../25T8B25T/fastq_with_4M/TAAGCACA.2.fastq | 8 +
.../TAAGCACA.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/TAAGCACA.index_1.fastq | 8 +
.../{fastq => fastq_with_4M}/TACCGTCT.1.fastq | 0
.../{fastq => fastq_with_4M}/TACCGTCT.2.fastq | 0
.../TACCGTCT.barcode_1.fastq | 0
.../TACCGTCT.index_1.fastq} | 0
.../{fastq => fastq_with_4M}/TAGCGGTA.1.fastq | 0
.../{fastq => fastq_with_4M}/TAGCGGTA.2.fastq | 0
.../TAGCGGTA.barcode_1.fastq | 0
.../TAGCGGTA.index_1.fastq} | 0
.../{fastq => fastq_with_4M}/TATCAGCC.1.fastq | 0
.../{fastq => fastq_with_4M}/TATCAGCC.2.fastq | 0
.../TATCAGCC.barcode_1.fastq | 0
.../TATCAGCC.index_1.fastq} | 0
.../{fastq => fastq_with_4M}/TATCCAGG.1.fastq | 0
.../25T8B25T/fastq_with_4M/TATCCAGG.2.fastq | 16 +
.../TATCCAGG.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/TATCCAGG.index_1.fastq | 16 +
.../{fastq => fastq_with_4M}/TATCCATG.1.fastq | 0
.../{fastq => fastq_with_4M}/TATCCATG.2.fastq | 0
.../TATCCATG.barcode_1.fastq | 0
.../TATCCATG.index_1.fastq} | 0
.../{fastq => fastq_with_4M}/TATCTCGG.1.fastq | 0
.../{fastq => fastq_with_4M}/TATCTCGG.2.fastq | 0
.../TATCTCGG.barcode_1.fastq | 0
.../TATCTCGG.index_1.fastq} | 0
.../{fastq => fastq_with_4M}/TATCTGCC.1.fastq | 0
.../25T8B25T/fastq_with_4M/TATCTGCC.2.fastq | 28 +
.../TATCTGCC.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/TATCTGCC.index_1.fastq | 28 +
.../{fastq => fastq_with_4M}/TCCGTCTA.1.fastq | 0
.../{fastq => fastq_with_4M}/TCCGTCTA.2.fastq | 0
.../TCCGTCTA.barcode_1.fastq | 0
.../TCCGTCTA.index_1.fastq} | 0
.../{fastq => fastq_with_4M}/TCGCTAGA.1.fastq | 0
.../25T8B25T/fastq_with_4M/TCGCTAGA.2.fastq | 20 +
.../TCGCTAGA.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/TCGCTAGA.index_1.fastq | 20 +
.../{fastq => fastq_with_4M}/TCTGCAAG.1.fastq | 0
.../25T8B25T/fastq_with_4M/TCTGCAAG.2.fastq | 4 +
.../TCTGCAAG.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/TCTGCAAG.index_1.fastq | 4 +
.../{fastq => fastq_with_4M}/TGCAAGTA.1.fastq | 0
.../25T8B25T/fastq_with_4M/TGCAAGTA.2.fastq | 8 +
.../TGCAAGTA.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/TGCAAGTA.index_1.fastq | 8 +
.../{fastq => fastq_with_4M}/TGCTGCTG.1.fastq | 0
.../25T8B25T/fastq_with_4M/TGCTGCTG.2.fastq | 16 +
.../TGCTGCTG.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/TGCTGCTG.index_1.fastq | 16 +
.../{fastq => fastq_with_4M}/TGTAACTC.1.fastq | 0
.../25T8B25T/fastq_with_4M/TGTAACTC.2.fastq | 4 +
.../TGTAACTC.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/TGTAACTC.index_1.fastq | 4 +
.../{fastq => fastq_with_4M}/TGTAATCA.1.fastq | 0
.../25T8B25T/fastq_with_4M/TGTAATCA.2.fastq | 12 +
.../TGTAATCA.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/TGTAATCA.index_1.fastq | 12 +
.../{fastq => fastq_with_4M}/TTGTCTAT.1.fastq | 0
.../25T8B25T/fastq_with_4M/TTGTCTAT.2.fastq | 16 +
.../TTGTCTAT.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/TTGTCTAT.index_1.fastq | 16 +
.../25T8B25T/fastq_with_4M/mp_barcode.params | 62 ++
.../{fastq => fastq_with_4M4M}/AAAAGAAG.1.fastq | 0
.../{fastq => fastq_with_4M4M}/AAAAGAAG.2.fastq | 0
.../AAAAGAAG.barcode_1.fastq | 0
.../AAAAGAAG.index_1.fastq} | 0
.../AAAAGAAG.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/AACAATGG.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/AACAATGG.2.fastq | 16 +
.../AACAATGG.barcode_1.fastq | 0
.../fastq_with_4M4M/AACAATGG.index_1.fastq | 16 +
.../fastq_with_4M4M/AACAATGG.index_2.fastq | 16 +
.../{fastq => fastq_with_4M4M}/AACGCATT.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/AACGCATT.2.fastq | 28 +
.../AACGCATT.barcode_1.fastq | 0
.../fastq_with_4M4M/AACGCATT.index_1.fastq | 28 +
.../fastq_with_4M4M/AACGCATT.index_2.fastq | 28 +
.../{fastq => fastq_with_4M4M}/ACAAAATT.1.fastq | 0
.../{fastq => fastq_with_4M4M}/ACAAAATT.2.fastq | 0
.../ACAAAATT.barcode_1.fastq | 0
.../ACAAAATT.index_1.fastq} | 0
.../ACAAAATT.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/ACAGGTAT.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/ACAGGTAT.2.fastq | 16 +
.../ACAGGTAT.barcode_1.fastq | 0
.../fastq_with_4M4M/ACAGGTAT.index_1.fastq | 16 +
.../fastq_with_4M4M/ACAGGTAT.index_2.fastq | 16 +
.../{fastq => fastq_with_4M4M}/ACAGTTGA.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/ACAGTTGA.2.fastq | 8 +
.../ACAGTTGA.barcode_1.fastq | 0
.../fastq_with_4M4M/ACAGTTGA.index_1.fastq | 8 +
.../fastq_with_4M4M/ACAGTTGA.index_2.fastq | 8 +
.../{fastq => fastq_with_4M4M}/ACCAGTTG.1.fastq | 0
.../{fastq => fastq_with_4M4M}/ACCAGTTG.2.fastq | 0
.../ACCAGTTG.barcode_1.fastq | 0
.../ACCAGTTG.index_1.fastq} | 0
.../ACCAGTTG.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/ACGAAATC.1.fastq | 0
.../{fastq => fastq_with_4M4M}/ACGAAATC.2.fastq | 0
.../ACGAAATC.barcode_1.fastq | 0
.../ACGAAATC.index_1.fastq} | 0
.../ACGAAATC.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/ACTAAGAC.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/ACTAAGAC.2.fastq | 16 +
.../ACTAAGAC.barcode_1.fastq | 0
.../fastq_with_4M4M/ACTAAGAC.index_1.fastq | 16 +
.../fastq_with_4M4M/ACTAAGAC.index_2.fastq | 16 +
.../{fastq => fastq_with_4M4M}/ACTGTACC.1.fastq | 0
.../{fastq => fastq_with_4M4M}/ACTGTACC.2.fastq | 0
.../ACTGTACC.barcode_1.fastq | 0
.../ACTGTACC.index_1.fastq} | 0
.../ACTGTACC.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/ACTGTATC.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/ACTGTATC.2.fastq | 16 +
.../ACTGTATC.barcode_1.fastq | 0
.../fastq_with_4M4M/ACTGTATC.index_1.fastq | 16 +
.../fastq_with_4M4M/ACTGTATC.index_2.fastq | 16 +
.../{fastq => fastq_with_4M4M}/AGAAAAGA.1.fastq | 0
.../{fastq => fastq_with_4M4M}/AGAAAAGA.2.fastq | 0
.../AGAAAAGA.barcode_1.fastq | 0
.../AGAAAAGA.index_1.fastq} | 0
.../AGAAAAGA.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/AGCATGGA.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/AGCATGGA.2.fastq | 12 +
.../AGCATGGA.barcode_1.fastq | 0
.../fastq_with_4M4M/AGCATGGA.index_1.fastq | 12 +
.../fastq_with_4M4M/AGCATGGA.index_2.fastq | 12 +
.../{fastq => fastq_with_4M4M}/AGGTAAGG.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/AGGTAAGG.2.fastq | 16 +
.../AGGTAAGG.barcode_1.fastq | 0
.../fastq_with_4M4M/AGGTAAGG.index_1.fastq | 16 +
.../fastq_with_4M4M/AGGTAAGG.index_2.fastq | 16 +
.../{fastq => fastq_with_4M4M}/AGGTCGCA.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/AGGTCGCA.2.fastq | 16 +
.../AGGTCGCA.barcode_1.fastq | 0
.../fastq_with_4M4M/AGGTCGCA.index_1.fastq | 16 +
.../fastq_with_4M4M/AGGTCGCA.index_2.fastq | 16 +
.../{fastq => fastq_with_4M4M}/ATTATCAA.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/ATTATCAA.2.fastq | 20 +
.../ATTATCAA.barcode_1.fastq | 0
.../fastq_with_4M4M/ATTATCAA.index_1.fastq | 20 +
.../fastq_with_4M4M/ATTATCAA.index_2.fastq | 20 +
.../{fastq => fastq_with_4M4M}/ATTCCTCT.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/ATTCCTCT.2.fastq | 16 +
.../ATTCCTCT.barcode_1.fastq | 0
.../fastq_with_4M4M/ATTCCTCT.index_1.fastq | 16 +
.../fastq_with_4M4M/ATTCCTCT.index_2.fastq | 16 +
.../{fastq => fastq_with_4M4M}/CAACTCTC.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/CAACTCTC.2.fastq | 20 +
.../CAACTCTC.barcode_1.fastq | 0
.../fastq_with_4M4M/CAACTCTC.index_1.fastq | 20 +
.../fastq_with_4M4M/CAACTCTC.index_2.fastq | 20 +
.../{fastq => fastq_with_4M4M}/CAATAGAC.1.fastq | 0
.../{fastq => fastq_with_4M4M}/CAATAGAC.2.fastq | 0
.../CAATAGAC.barcode_1.fastq | 0
.../CAATAGAC.index_1.fastq} | 0
.../CAATAGAC.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/CAATAGTC.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/CAATAGTC.2.fastq | 28 +
.../CAATAGTC.barcode_1.fastq | 0
.../fastq_with_4M4M/CAATAGTC.index_1.fastq | 28 +
.../fastq_with_4M4M/CAATAGTC.index_2.fastq | 28 +
.../{fastq => fastq_with_4M4M}/CAGCGGAT.1.fastq | 0
.../{fastq => fastq_with_4M4M}/CAGCGGAT.2.fastq | 0
.../CAGCGGAT.barcode_1.fastq | 0
.../CAGCGGAT.index_1.fastq} | 0
.../CAGCGGAT.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/CAGCGGTA.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/CAGCGGTA.2.fastq | 20 +
.../CAGCGGTA.barcode_1.fastq | 0
.../fastq_with_4M4M/CAGCGGTA.index_1.fastq | 20 +
.../fastq_with_4M4M/CAGCGGTA.index_2.fastq | 20 +
.../{fastq => fastq_with_4M4M}/CCAACATT.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/CCAACATT.2.fastq | 28 +
.../CCAACATT.barcode_1.fastq | 0
.../fastq_with_4M4M/CCAACATT.index_1.fastq | 28 +
.../fastq_with_4M4M/CCAACATT.index_2.fastq | 28 +
.../{fastq => fastq_with_4M4M}/CCAGCACC.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/CCAGCACC.2.fastq | 12 +
.../CCAGCACC.barcode_1.fastq | 0
.../fastq_with_4M4M/CCAGCACC.index_1.fastq | 12 +
.../fastq_with_4M4M/CCAGCACC.index_2.fastq | 12 +
.../{fastq => fastq_with_4M4M}/CCATGCGT.1.fastq | 0
.../{fastq => fastq_with_4M4M}/CCATGCGT.2.fastq | 0
.../CCATGCGT.barcode_1.fastq | 0
.../CCATGCGT.index_1.fastq} | 0
.../CCATGCGT.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/CGCCTTCC.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/CGCCTTCC.2.fastq | 8 +
.../CGCCTTCC.barcode_1.fastq | 0
.../fastq_with_4M4M/CGCCTTCC.index_1.fastq | 8 +
.../fastq_with_4M4M/CGCCTTCC.index_2.fastq | 8 +
.../{fastq => fastq_with_4M4M}/CGCTATGT.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/CGCTATGT.2.fastq | 20 +
.../CGCTATGT.barcode_1.fastq | 0
.../fastq_with_4M4M/CGCTATGT.index_1.fastq | 20 +
.../fastq_with_4M4M/CGCTATGT.index_2.fastq | 20 +
.../{fastq => fastq_with_4M4M}/CTAACTCG.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/CTAACTCG.2.fastq | 16 +
.../CTAACTCG.barcode_1.fastq | 0
.../fastq_with_4M4M/CTAACTCG.index_1.fastq | 16 +
.../fastq_with_4M4M/CTAACTCG.index_2.fastq | 16 +
.../{fastq => fastq_with_4M4M}/CTATGCGC.1.fastq | 0
.../{fastq => fastq_with_4M4M}/CTATGCGC.2.fastq | 0
.../CTATGCGC.barcode_1.fastq | 0
.../CTATGCGC.index_1.fastq} | 0
.../CTATGCGC.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/CTATGCGT.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/CTATGCGT.2.fastq | 28 +
.../CTATGCGT.barcode_1.fastq | 0
.../fastq_with_4M4M/CTATGCGT.index_1.fastq | 28 +
.../fastq_with_4M4M/CTATGCGT.index_2.fastq | 28 +
.../{fastq => fastq_with_4M4M}/CTGCGGAT.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/CTGCGGAT.2.fastq | 12 +
.../CTGCGGAT.barcode_1.fastq | 0
.../fastq_with_4M4M/CTGCGGAT.index_1.fastq | 12 +
.../fastq_with_4M4M/CTGCGGAT.index_2.fastq | 12 +
.../{fastq => fastq_with_4M4M}/CTGTAATC.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/CTGTAATC.2.fastq | 24 +
.../CTGTAATC.barcode_1.fastq | 0
.../fastq_with_4M4M/CTGTAATC.index_1.fastq | 24 +
.../fastq_with_4M4M/CTGTAATC.index_2.fastq | 24 +
.../{fastq => fastq_with_4M4M}/GAAAAAAA.1.fastq | 0
.../{fastq => fastq_with_4M4M}/GAAAAAAA.2.fastq | 0
.../GAAAAAAA.barcode_1.fastq | 0
.../GAAAAAAA.index_1.fastq} | 0
.../GAAAAAAA.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/GAACGAT..1.fastq | 0
.../{fastq => fastq_with_4M4M}/GAACGAT..2.fastq | 0
.../GAACGAT..barcode_1.fastq | 0
.../GAACGAT..index_1.fastq} | 0
.../GAACGAT..index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/GAAGGAAG.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/GAAGGAAG.2.fastq | 12 +
.../GAAGGAAG.barcode_1.fastq | 0
.../fastq_with_4M4M/GAAGGAAG.index_1.fastq | 12 +
.../fastq_with_4M4M/GAAGGAAG.index_2.fastq | 12 +
.../{fastq => fastq_with_4M4M}/GACCAGGA.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/GACCAGGA.2.fastq | 28 +
.../GACCAGGA.barcode_1.fastq | 0
.../fastq_with_4M4M/GACCAGGA.index_1.fastq | 28 +
.../fastq_with_4M4M/GACCAGGA.index_2.fastq | 28 +
.../{fastq => fastq_with_4M4M}/GACCAGGC.1.fastq | 0
.../{fastq => fastq_with_4M4M}/GACCAGGC.2.fastq | 0
.../GACCAGGC.barcode_1.fastq | 0
.../GACCAGGC.index_1.fastq} | 0
.../GACCAGGC.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/GACCGTTG.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/GACCGTTG.2.fastq | 16 +
.../GACCGTTG.barcode_1.fastq | 0
.../fastq_with_4M4M/GACCGTTG.index_1.fastq | 16 +
.../fastq_with_4M4M/GACCGTTG.index_2.fastq | 16 +
.../{fastq => fastq_with_4M4M}/GACCTAAC.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/GACCTAAC.2.fastq | 4 +
.../GACCTAAC.barcode_1.fastq | 0
.../fastq_with_4M4M/GACCTAAC.index_1.fastq | 4 +
.../fastq_with_4M4M/GACCTAAC.index_2.fastq | 4 +
.../{fastq => fastq_with_4M4M}/GATATCCA.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/GATATCCA.2.fastq | 12 +
.../GATATCCA.barcode_1.fastq | 0
.../fastq_with_4M4M/GATATCCA.index_1.fastq | 12 +
.../fastq_with_4M4M/GATATCCA.index_2.fastq | 12 +
.../{fastq => fastq_with_4M4M}/GCCGTCGA.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/GCCGTCGA.2.fastq | 20 +
.../GCCGTCGA.barcode_1.fastq | 0
.../fastq_with_4M4M/GCCGTCGA.index_1.fastq | 20 +
.../fastq_with_4M4M/GCCGTCGA.index_2.fastq | 20 +
.../{fastq => fastq_with_4M4M}/GCCTAGCC.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/GCCTAGCC.2.fastq | 20 +
.../GCCTAGCC.barcode_1.fastq | 0
.../fastq_with_4M4M/GCCTAGCC.index_1.fastq | 20 +
.../fastq_with_4M4M/GCCTAGCC.index_2.fastq | 20 +
.../{fastq => fastq_with_4M4M}/GTAACATC.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/GTAACATC.2.fastq | 8 +
.../GTAACATC.barcode_1.fastq | 0
.../fastq_with_4M4M/GTAACATC.index_1.fastq | 8 +
.../fastq_with_4M4M/GTAACATC.index_2.fastq | 8 +
.../{fastq => fastq_with_4M4M}/GTCCACAG.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/GTCCACAG.2.fastq | 8 +
.../GTCCACAG.barcode_1.fastq | 0
.../fastq_with_4M4M/GTCCACAG.index_1.fastq | 8 +
.../fastq_with_4M4M/GTCCACAG.index_2.fastq | 8 +
.../25T8B25T/{fastq => fastq_with_4M4M}/N.1.fastq | 0
.../illumina/25T8B25T/fastq_with_4M4M/N.2.fastq | 64 ++
.../{fastq => fastq_with_4M4M}/N.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M4M/N.index_1.fastq | 64 ++
.../25T8B25T/fastq_with_4M4M/N.index_2.fastq | 64 ++
.../{fastq => fastq_with_4M4M}/TAAGCACA.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/TAAGCACA.2.fastq | 8 +
.../TAAGCACA.barcode_1.fastq | 0
.../fastq_with_4M4M/TAAGCACA.index_1.fastq | 8 +
.../fastq_with_4M4M/TAAGCACA.index_2.fastq | 8 +
.../{fastq => fastq_with_4M4M}/TACCGTCT.1.fastq | 0
.../{fastq => fastq_with_4M4M}/TACCGTCT.2.fastq | 0
.../TACCGTCT.barcode_1.fastq | 0
.../TACCGTCT.index_1.fastq} | 0
.../TACCGTCT.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/TAGCGGTA.1.fastq | 0
.../{fastq => fastq_with_4M4M}/TAGCGGTA.2.fastq | 0
.../TAGCGGTA.barcode_1.fastq | 0
.../TAGCGGTA.index_1.fastq} | 0
.../TAGCGGTA.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/TATCAGCC.1.fastq | 0
.../{fastq => fastq_with_4M4M}/TATCAGCC.2.fastq | 0
.../TATCAGCC.barcode_1.fastq | 0
.../TATCAGCC.index_1.fastq} | 0
.../TATCAGCC.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/TATCCAGG.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/TATCCAGG.2.fastq | 16 +
.../TATCCAGG.barcode_1.fastq | 0
.../fastq_with_4M4M/TATCCAGG.index_1.fastq | 16 +
.../fastq_with_4M4M/TATCCAGG.index_2.fastq | 16 +
.../{fastq => fastq_with_4M4M}/TATCCATG.1.fastq | 0
.../{fastq => fastq_with_4M4M}/TATCCATG.2.fastq | 0
.../TATCCATG.barcode_1.fastq | 0
.../TATCCATG.index_1.fastq} | 0
.../TATCCATG.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/TATCTCGG.1.fastq | 0
.../{fastq => fastq_with_4M4M}/TATCTCGG.2.fastq | 0
.../TATCTCGG.barcode_1.fastq | 0
.../TATCTCGG.index_1.fastq} | 0
.../TATCTCGG.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/TATCTGCC.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/TATCTGCC.2.fastq | 28 +
.../TATCTGCC.barcode_1.fastq | 0
.../fastq_with_4M4M/TATCTGCC.index_1.fastq | 28 +
.../fastq_with_4M4M/TATCTGCC.index_2.fastq | 28 +
.../{fastq => fastq_with_4M4M}/TCCGTCTA.1.fastq | 0
.../{fastq => fastq_with_4M4M}/TCCGTCTA.2.fastq | 0
.../TCCGTCTA.barcode_1.fastq | 0
.../TCCGTCTA.index_1.fastq} | 0
.../TCCGTCTA.index_2.fastq} | 0
.../{fastq => fastq_with_4M4M}/TCGCTAGA.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/TCGCTAGA.2.fastq | 20 +
.../TCGCTAGA.barcode_1.fastq | 0
.../fastq_with_4M4M/TCGCTAGA.index_1.fastq | 20 +
.../fastq_with_4M4M/TCGCTAGA.index_2.fastq | 20 +
.../{fastq => fastq_with_4M4M}/TCTGCAAG.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/TCTGCAAG.2.fastq | 4 +
.../TCTGCAAG.barcode_1.fastq | 0
.../fastq_with_4M4M/TCTGCAAG.index_1.fastq | 4 +
.../fastq_with_4M4M/TCTGCAAG.index_2.fastq | 4 +
.../{fastq => fastq_with_4M4M}/TGCAAGTA.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/TGCAAGTA.2.fastq | 8 +
.../TGCAAGTA.barcode_1.fastq | 0
.../fastq_with_4M4M/TGCAAGTA.index_1.fastq | 8 +
.../fastq_with_4M4M/TGCAAGTA.index_2.fastq | 8 +
.../{fastq => fastq_with_4M4M}/TGCTGCTG.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/TGCTGCTG.2.fastq | 16 +
.../TGCTGCTG.barcode_1.fastq | 0
.../fastq_with_4M4M/TGCTGCTG.index_1.fastq | 16 +
.../fastq_with_4M4M/TGCTGCTG.index_2.fastq | 16 +
.../{fastq => fastq_with_4M4M}/TGTAACTC.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/TGTAACTC.2.fastq | 4 +
.../TGTAACTC.barcode_1.fastq | 0
.../fastq_with_4M4M/TGTAACTC.index_1.fastq | 4 +
.../fastq_with_4M4M/TGTAACTC.index_2.fastq | 4 +
.../{fastq => fastq_with_4M4M}/TGTAATCA.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/TGTAATCA.2.fastq | 12 +
.../TGTAATCA.barcode_1.fastq | 0
.../fastq_with_4M4M/TGTAATCA.index_1.fastq | 12 +
.../fastq_with_4M4M/TGTAATCA.index_2.fastq | 12 +
.../{fastq => fastq_with_4M4M}/TTGTCTAT.1.fastq | 0
.../25T8B25T/fastq_with_4M4M/TTGTCTAT.2.fastq | 16 +
.../TTGTCTAT.barcode_1.fastq | 0
.../fastq_with_4M4M/TTGTCTAT.index_1.fastq | 16 +
.../fastq_with_4M4M/TTGTCTAT.index_2.fastq | 16 +
.../25T8B25T/fastq_with_4M4M/mp_barcode.params | 62 ++
.../sams/nonBarcodedWithMolecularIndex4M4M.sam | 182 ++++
.../sams/nonBarcodedWithMolecularIndex8M.sam | 182 ++++
.../25T8B25T/{sams => sams_with_4M}/AAAAAAAA.sam | 0
.../25T8B25T/{sams => sams_with_4M}/AAAAGAAG.sam | 0
.../illumina/25T8B25T/sams_with_4M/AACAATGG.sam | 10 +
.../illumina/25T8B25T/sams_with_4M/AACGCATT.sam | 16 +
.../25T8B25T/{sams => sams_with_4M}/ACAAAATT.sam | 0
.../illumina/25T8B25T/sams_with_4M/ACAGGTAT.sam | 10 +
.../illumina/25T8B25T/sams_with_4M/ACAGTTGA.sam | 6 +
.../25T8B25T/{sams => sams_with_4M}/ACCAGTTG.sam | 0
.../25T8B25T/{sams => sams_with_4M}/ACGAAATC.sam | 0
.../illumina/25T8B25T/sams_with_4M/ACTAAGAC.sam | 10 +
.../25T8B25T/{sams => sams_with_4M}/ACTGTACC.sam | 0
.../illumina/25T8B25T/sams_with_4M/ACTGTATC.sam | 10 +
.../25T8B25T/{sams => sams_with_4M}/AGAAAAGA.sam | 0
.../illumina/25T8B25T/sams_with_4M/AGCATGGA.sam | 8 +
.../illumina/25T8B25T/sams_with_4M/AGGTAAGG.sam | 10 +
.../illumina/25T8B25T/sams_with_4M/AGGTCGCA.sam | 10 +
.../illumina/25T8B25T/sams_with_4M/ATTATCAA.sam | 12 +
.../illumina/25T8B25T/sams_with_4M/ATTCCTCT.sam | 10 +
.../illumina/25T8B25T/sams_with_4M/CAACTCTC.sam | 12 +
.../25T8B25T/{sams => sams_with_4M}/CAATAGAC.sam | 0
.../illumina/25T8B25T/sams_with_4M/CAATAGTC.sam | 16 +
.../25T8B25T/{sams => sams_with_4M}/CAGCGGAT.sam | 0
.../illumina/25T8B25T/sams_with_4M/CAGCGGTA.sam | 12 +
.../illumina/25T8B25T/sams_with_4M/CCAACATT.sam | 16 +
.../illumina/25T8B25T/sams_with_4M/CCAGCACC.sam | 8 +
.../25T8B25T/{sams => sams_with_4M}/CCATGCGT.sam | 0
.../illumina/25T8B25T/sams_with_4M/CGCCTTCC.sam | 6 +
.../illumina/25T8B25T/sams_with_4M/CGCTATGT.sam | 12 +
.../illumina/25T8B25T/sams_with_4M/CTAACTCG.sam | 10 +
.../25T8B25T/{sams => sams_with_4M}/CTATGCGC.sam | 0
.../illumina/25T8B25T/sams_with_4M/CTATGCGT.sam | 16 +
.../illumina/25T8B25T/sams_with_4M/CTGCGGAT.sam | 8 +
.../illumina/25T8B25T/sams_with_4M/CTGTAATC.sam | 14 +
.../25T8B25T/{sams => sams_with_4M}/GAAAAAAA.sam | 0
.../25T8B25T/{sams => sams_with_4M}/GAACGAT..sam | 0
.../illumina/25T8B25T/sams_with_4M/GAAGGAAG.sam | 8 +
.../illumina/25T8B25T/sams_with_4M/GACCAGGA.sam | 16 +
.../25T8B25T/{sams => sams_with_4M}/GACCAGGC.sam | 0
.../illumina/25T8B25T/sams_with_4M/GACCGTTG.sam | 10 +
.../illumina/25T8B25T/sams_with_4M/GACCTAAC.sam | 4 +
.../illumina/25T8B25T/sams_with_4M/GATATCCA.sam | 8 +
.../illumina/25T8B25T/sams_with_4M/GCCGTCGA.sam | 12 +
.../illumina/25T8B25T/sams_with_4M/GCCTAGCC.sam | 12 +
.../illumina/25T8B25T/sams_with_4M/GTAACATC.sam | 6 +
.../illumina/25T8B25T/sams_with_4M/GTCCACAG.sam | 6 +
.../picard/illumina/25T8B25T/sams_with_4M/N.sam | 34 +
.../illumina/25T8B25T/sams_with_4M/TAAGCACA.sam | 6 +
.../25T8B25T/{sams => sams_with_4M}/TACCGTCT.sam | 0
.../25T8B25T/{sams => sams_with_4M}/TAGCGGTA.sam | 0
.../25T8B25T/{sams => sams_with_4M}/TATCAGCC.sam | 0
.../illumina/25T8B25T/sams_with_4M/TATCCAGG.sam | 10 +
.../25T8B25T/{sams => sams_with_4M}/TATCCATG.sam | 0
.../25T8B25T/{sams => sams_with_4M}/TATCTCGG.sam | 0
.../illumina/25T8B25T/sams_with_4M/TATCTGCC.sam | 16 +
.../25T8B25T/{sams => sams_with_4M}/TCCGTCTA.sam | 0
.../illumina/25T8B25T/sams_with_4M/TCGCTAGA.sam | 12 +
.../illumina/25T8B25T/sams_with_4M/TCTGCAAG.sam | 4 +
.../illumina/25T8B25T/sams_with_4M/TGCAAGTA.sam | 6 +
.../illumina/25T8B25T/sams_with_4M/TGCTGCTG.sam | 10 +
.../illumina/25T8B25T/sams_with_4M/TGTAACTC.sam | 4 +
.../illumina/25T8B25T/sams_with_4M/TGTAATCA.sam | 8 +
.../illumina/25T8B25T/sams_with_4M/TTGTCTAT.sam | 10 +
.../illumina/25T8B25T/sams_with_4M/barcode.params | 63 ++
.../final/nonBarcoded.sam} | 0
.../final/nonBarcodedWithMolecularIndex4M4M.sam} | 0
.../final/nonBarcodedWithMolecularIndex8M.sam} | 0
.../25T8B25T/sams_with_4M/indicies/AAAAAAAA.sam | 2 +
.../indicies/AAAAAAAA.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/AAAAGAAG.sam | 2 +
.../indicies/AAAAGAAG.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/AACAATGG.sam | 6 +
.../sams_with_4M/indicies/AACAATGG.sam.bak | 6 +
.../25T8B25T/sams_with_4M/indicies/AACGCATT.sam | 9 +
.../sams_with_4M/indicies/AACGCATT.sam.bak | 9 +
.../25T8B25T/sams_with_4M/indicies/ACAAAATT.sam | 2 +
.../indicies/ACAAAATT.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/ACAGGTAT.sam | 6 +
.../sams_with_4M/indicies/ACAGGTAT.sam.bak | 6 +
.../25T8B25T/sams_with_4M/indicies/ACAGTTGA.sam | 4 +
.../sams_with_4M/indicies/ACAGTTGA.sam.bak | 4 +
.../25T8B25T/sams_with_4M/indicies/ACCAGTTG.sam | 2 +
.../indicies/ACCAGTTG.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/ACGAAATC.sam | 2 +
.../indicies/ACGAAATC.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/ACTAAGAC.sam | 6 +
.../sams_with_4M/indicies/ACTAAGAC.sam.bak | 6 +
.../25T8B25T/sams_with_4M/indicies/ACTGTACC.sam | 2 +
.../indicies/ACTGTACC.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/ACTGTATC.sam | 6 +
.../sams_with_4M/indicies/ACTGTATC.sam.bak | 6 +
.../25T8B25T/sams_with_4M/indicies/AGAAAAGA.sam | 2 +
.../indicies/AGAAAAGA.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/AGCATGGA.sam | 5 +
.../sams_with_4M/indicies/AGCATGGA.sam.bak | 5 +
.../25T8B25T/sams_with_4M/indicies/AGGTAAGG.sam | 6 +
.../sams_with_4M/indicies/AGGTAAGG.sam.bak | 6 +
.../25T8B25T/sams_with_4M/indicies/AGGTCGCA.sam | 6 +
.../sams_with_4M/indicies/AGGTCGCA.sam.bak | 6 +
.../25T8B25T/sams_with_4M/indicies/ATTATCAA.sam | 7 +
.../sams_with_4M/indicies/ATTATCAA.sam.bak | 7 +
.../25T8B25T/sams_with_4M/indicies/ATTCCTCT.sam | 6 +
.../sams_with_4M/indicies/ATTCCTCT.sam.bak | 6 +
.../25T8B25T/sams_with_4M/indicies/CAACTCTC.sam | 7 +
.../sams_with_4M/indicies/CAACTCTC.sam.bak | 7 +
.../25T8B25T/sams_with_4M/indicies/CAATAGAC.sam | 2 +
.../indicies/CAATAGAC.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/CAATAGTC.sam | 9 +
.../sams_with_4M/indicies/CAATAGTC.sam.bak | 9 +
.../25T8B25T/sams_with_4M/indicies/CAGCGGAT.sam | 2 +
.../indicies/CAGCGGAT.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/CAGCGGTA.sam | 7 +
.../sams_with_4M/indicies/CAGCGGTA.sam.bak | 7 +
.../25T8B25T/sams_with_4M/indicies/CCAACATT.sam | 9 +
.../sams_with_4M/indicies/CCAACATT.sam.bak | 9 +
.../25T8B25T/sams_with_4M/indicies/CCAGCACC.sam | 5 +
.../sams_with_4M/indicies/CCAGCACC.sam.bak | 5 +
.../25T8B25T/sams_with_4M/indicies/CCATGCGT.sam | 2 +
.../indicies/CCATGCGT.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/CGCCTTCC.sam | 4 +
.../sams_with_4M/indicies/CGCCTTCC.sam.bak | 4 +
.../25T8B25T/sams_with_4M/indicies/CGCTATGT.sam | 7 +
.../sams_with_4M/indicies/CGCTATGT.sam.bak | 7 +
.../25T8B25T/sams_with_4M/indicies/CTAACTCG.sam | 6 +
.../sams_with_4M/indicies/CTAACTCG.sam.bak | 6 +
.../25T8B25T/sams_with_4M/indicies/CTATGCGC.sam | 2 +
.../indicies/CTATGCGC.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/CTATGCGT.sam | 9 +
.../sams_with_4M/indicies/CTATGCGT.sam.bak | 9 +
.../25T8B25T/sams_with_4M/indicies/CTGCGGAT.sam | 5 +
.../sams_with_4M/indicies/CTGCGGAT.sam.bak | 5 +
.../25T8B25T/sams_with_4M/indicies/CTGTAATC.sam | 8 +
.../sams_with_4M/indicies/CTGTAATC.sam.bak | 8 +
.../25T8B25T/sams_with_4M/indicies/GAAAAAAA.sam | 2 +
.../indicies/GAAAAAAA.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/GAACGAT..sam | 2 +
.../indicies/GAACGAT..sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/GAAGGAAG.sam | 5 +
.../sams_with_4M/indicies/GAAGGAAG.sam.bak | 5 +
.../25T8B25T/sams_with_4M/indicies/GACCAGGA.sam | 9 +
.../sams_with_4M/indicies/GACCAGGA.sam.bak | 9 +
.../25T8B25T/sams_with_4M/indicies/GACCAGGC.sam | 2 +
.../indicies/GACCAGGC.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/GACCGTTG.sam | 6 +
.../sams_with_4M/indicies/GACCGTTG.sam.bak | 6 +
.../25T8B25T/sams_with_4M/indicies/GACCTAAC.sam | 3 +
.../sams_with_4M/indicies/GACCTAAC.sam.bak | 3 +
.../25T8B25T/sams_with_4M/indicies/GATATCCA.sam | 5 +
.../sams_with_4M/indicies/GATATCCA.sam.bak | 5 +
.../25T8B25T/sams_with_4M/indicies/GCCGTCGA.sam | 7 +
.../sams_with_4M/indicies/GCCGTCGA.sam.bak | 7 +
.../25T8B25T/sams_with_4M/indicies/GCCTAGCC.sam | 7 +
.../sams_with_4M/indicies/GCCTAGCC.sam.bak | 7 +
.../25T8B25T/sams_with_4M/indicies/GTAACATC.sam | 4 +
.../sams_with_4M/indicies/GTAACATC.sam.bak | 4 +
.../25T8B25T/sams_with_4M/indicies/GTCCACAG.sam | 4 +
.../sams_with_4M/indicies/GTCCACAG.sam.bak | 4 +
.../illumina/25T8B25T/sams_with_4M/indicies/N.sam | 18 +
.../25T8B25T/sams_with_4M/indicies/N.sam.bak | 18 +
.../25T8B25T/sams_with_4M/indicies/TAAGCACA.sam | 4 +
.../sams_with_4M/indicies/TAAGCACA.sam.bak | 4 +
.../25T8B25T/sams_with_4M/indicies/TACCGTCT.sam | 2 +
.../indicies/TACCGTCT.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/TAGCGGTA.sam | 2 +
.../indicies/TAGCGGTA.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/TATCAGCC.sam | 2 +
.../indicies/TATCAGCC.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/TATCCAGG.sam | 6 +
.../sams_with_4M/indicies/TATCCAGG.sam.bak | 6 +
.../25T8B25T/sams_with_4M/indicies/TATCCATG.sam | 2 +
.../indicies/TATCCATG.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/TATCTCGG.sam | 2 +
.../indicies/TATCTCGG.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/TATCTGCC.sam | 9 +
.../sams_with_4M/indicies/TATCTGCC.sam.bak | 9 +
.../25T8B25T/sams_with_4M/indicies/TCCGTCTA.sam | 2 +
.../indicies/TCCGTCTA.sam.bak} | 0
.../25T8B25T/sams_with_4M/indicies/TCGCTAGA.sam | 7 +
.../sams_with_4M/indicies/TCGCTAGA.sam.bak | 7 +
.../25T8B25T/sams_with_4M/indicies/TCTGCAAG.sam | 3 +
.../sams_with_4M/indicies/TCTGCAAG.sam.bak | 3 +
.../25T8B25T/sams_with_4M/indicies/TGCAAGTA.sam | 4 +
.../sams_with_4M/indicies/TGCAAGTA.sam.bak | 4 +
.../25T8B25T/sams_with_4M/indicies/TGCTGCTG.sam | 6 +
.../sams_with_4M/indicies/TGCTGCTG.sam.bak | 6 +
.../25T8B25T/sams_with_4M/indicies/TGTAACTC.sam | 3 +
.../sams_with_4M/indicies/TGTAACTC.sam.bak | 3 +
.../25T8B25T/sams_with_4M/indicies/TGTAATCA.sam | 5 +
.../sams_with_4M/indicies/TGTAATCA.sam.bak | 5 +
.../25T8B25T/sams_with_4M/indicies/TTGTCTAT.sam | 6 +
.../sams_with_4M/indicies/TTGTCTAT.sam.bak | 6 +
.../25T8B25T/sams_with_4M/indicies/barcode.params | 63 ++
.../multiplexed_positive_rgtags.params} | 0
.../{sams => sams_with_4M/templates}/AAAAAAAA.sam | 0
.../{sams => sams_with_4M/templates}/AAAAGAAG.sam | 0
.../25T8B25T/sams_with_4M/templates/AACAATGG.sam | 10 +
.../25T8B25T/sams_with_4M/templates/AACGCATT.sam | 16 +
.../{sams => sams_with_4M/templates}/ACAAAATT.sam | 0
.../25T8B25T/sams_with_4M/templates/ACAGGTAT.sam | 10 +
.../25T8B25T/sams_with_4M/templates/ACAGTTGA.sam | 6 +
.../{sams => sams_with_4M/templates}/ACCAGTTG.sam | 0
.../{sams => sams_with_4M/templates}/ACGAAATC.sam | 0
.../25T8B25T/sams_with_4M/templates/ACTAAGAC.sam | 10 +
.../{sams => sams_with_4M/templates}/ACTGTACC.sam | 0
.../25T8B25T/sams_with_4M/templates/ACTGTATC.sam | 10 +
.../{sams => sams_with_4M/templates}/AGAAAAGA.sam | 0
.../25T8B25T/sams_with_4M/templates/AGCATGGA.sam | 8 +
.../25T8B25T/sams_with_4M/templates/AGGTAAGG.sam | 10 +
.../25T8B25T/sams_with_4M/templates/AGGTCGCA.sam | 10 +
.../25T8B25T/sams_with_4M/templates/ATTATCAA.sam | 12 +
.../25T8B25T/sams_with_4M/templates/ATTCCTCT.sam | 10 +
.../25T8B25T/sams_with_4M/templates/CAACTCTC.sam | 12 +
.../{sams => sams_with_4M/templates}/CAATAGAC.sam | 0
.../25T8B25T/sams_with_4M/templates/CAATAGTC.sam | 16 +
.../{sams => sams_with_4M/templates}/CAGCGGAT.sam | 0
.../25T8B25T/sams_with_4M/templates/CAGCGGTA.sam | 12 +
.../25T8B25T/sams_with_4M/templates/CCAACATT.sam | 16 +
.../25T8B25T/sams_with_4M/templates/CCAGCACC.sam | 8 +
.../{sams => sams_with_4M/templates}/CCATGCGT.sam | 0
.../25T8B25T/sams_with_4M/templates/CGCCTTCC.sam | 6 +
.../25T8B25T/sams_with_4M/templates/CGCTATGT.sam | 12 +
.../25T8B25T/sams_with_4M/templates/CTAACTCG.sam | 10 +
.../{sams => sams_with_4M/templates}/CTATGCGC.sam | 0
.../25T8B25T/sams_with_4M/templates/CTATGCGT.sam | 16 +
.../25T8B25T/sams_with_4M/templates/CTGCGGAT.sam | 8 +
.../25T8B25T/sams_with_4M/templates/CTGTAATC.sam | 14 +
.../{sams => sams_with_4M/templates}/GAAAAAAA.sam | 0
.../{sams => sams_with_4M/templates}/GAACGAT..sam | 0
.../25T8B25T/sams_with_4M/templates/GAAGGAAG.sam | 8 +
.../25T8B25T/sams_with_4M/templates/GACCAGGA.sam | 16 +
.../{sams => sams_with_4M/templates}/GACCAGGC.sam | 0
.../25T8B25T/sams_with_4M/templates/GACCGTTG.sam | 10 +
.../25T8B25T/sams_with_4M/templates/GACCTAAC.sam | 4 +
.../25T8B25T/sams_with_4M/templates/GATATCCA.sam | 8 +
.../25T8B25T/sams_with_4M/templates/GCCGTCGA.sam | 12 +
.../25T8B25T/sams_with_4M/templates/GCCTAGCC.sam | 12 +
.../25T8B25T/sams_with_4M/templates/GTAACATC.sam | 6 +
.../25T8B25T/sams_with_4M/templates/GTCCACAG.sam | 6 +
.../25T8B25T/sams_with_4M/templates/TAAGCACA.sam | 6 +
.../{sams => sams_with_4M/templates}/TACCGTCT.sam | 0
.../{sams => sams_with_4M/templates}/TAGCGGTA.sam | 0
.../{sams => sams_with_4M/templates}/TATCAGCC.sam | 0
.../25T8B25T/sams_with_4M/templates/TATCCAGG.sam | 10 +
.../{sams => sams_with_4M/templates}/TATCCATG.sam | 0
.../{sams => sams_with_4M/templates}/TATCTCGG.sam | 0
.../25T8B25T/sams_with_4M/templates/TATCTGCC.sam | 16 +
.../{sams => sams_with_4M/templates}/TCCGTCTA.sam | 0
.../25T8B25T/sams_with_4M/templates/TCGCTAGA.sam | 12 +
.../25T8B25T/sams_with_4M/templates/TCTGCAAG.sam | 4 +
.../25T8B25T/sams_with_4M/templates/TGCAAGTA.sam | 6 +
.../25T8B25T/sams_with_4M/templates/TGCTGCTG.sam | 10 +
.../25T8B25T/sams_with_4M/templates/TGTAACTC.sam | 4 +
.../25T8B25T/sams_with_4M/templates/TGTAATCA.sam | 8 +
.../25T8B25T/sams_with_4M/templates/TTGTCTAT.sam | 10 +
.../25T8B25T/{sams => sams_with_4M4M}/AAAAAAAA.sam | 0
.../25T8B25T/{sams => sams_with_4M4M}/AAAAGAAG.sam | 0
.../illumina/25T8B25T/sams_with_4M4M/AACAATGG.sam | 10 +
.../illumina/25T8B25T/sams_with_4M4M/AACGCATT.sam | 16 +
.../25T8B25T/{sams => sams_with_4M4M}/ACAAAATT.sam | 0
.../illumina/25T8B25T/sams_with_4M4M/ACAGGTAT.sam | 10 +
.../illumina/25T8B25T/sams_with_4M4M/ACAGTTGA.sam | 6 +
.../25T8B25T/{sams => sams_with_4M4M}/ACCAGTTG.sam | 0
.../25T8B25T/{sams => sams_with_4M4M}/ACGAAATC.sam | 0
.../illumina/25T8B25T/sams_with_4M4M/ACTAAGAC.sam | 10 +
.../25T8B25T/{sams => sams_with_4M4M}/ACTGTACC.sam | 0
.../illumina/25T8B25T/sams_with_4M4M/ACTGTATC.sam | 10 +
.../25T8B25T/{sams => sams_with_4M4M}/AGAAAAGA.sam | 0
.../illumina/25T8B25T/sams_with_4M4M/AGCATGGA.sam | 8 +
.../illumina/25T8B25T/sams_with_4M4M/AGGTAAGG.sam | 10 +
.../illumina/25T8B25T/sams_with_4M4M/AGGTCGCA.sam | 10 +
.../illumina/25T8B25T/sams_with_4M4M/ATTATCAA.sam | 12 +
.../illumina/25T8B25T/sams_with_4M4M/ATTCCTCT.sam | 10 +
.../illumina/25T8B25T/sams_with_4M4M/CAACTCTC.sam | 12 +
.../25T8B25T/{sams => sams_with_4M4M}/CAATAGAC.sam | 0
.../illumina/25T8B25T/sams_with_4M4M/CAATAGTC.sam | 16 +
.../25T8B25T/{sams => sams_with_4M4M}/CAGCGGAT.sam | 0
.../illumina/25T8B25T/sams_with_4M4M/CAGCGGTA.sam | 12 +
.../illumina/25T8B25T/sams_with_4M4M/CCAACATT.sam | 16 +
.../illumina/25T8B25T/sams_with_4M4M/CCAGCACC.sam | 8 +
.../25T8B25T/{sams => sams_with_4M4M}/CCATGCGT.sam | 0
.../illumina/25T8B25T/sams_with_4M4M/CGCCTTCC.sam | 6 +
.../illumina/25T8B25T/sams_with_4M4M/CGCTATGT.sam | 12 +
.../illumina/25T8B25T/sams_with_4M4M/CTAACTCG.sam | 10 +
.../25T8B25T/{sams => sams_with_4M4M}/CTATGCGC.sam | 0
.../illumina/25T8B25T/sams_with_4M4M/CTATGCGT.sam | 16 +
.../illumina/25T8B25T/sams_with_4M4M/CTGCGGAT.sam | 8 +
.../illumina/25T8B25T/sams_with_4M4M/CTGTAATC.sam | 14 +
.../25T8B25T/{sams => sams_with_4M4M}/GAAAAAAA.sam | 0
.../25T8B25T/{sams => sams_with_4M4M}/GAACGAT..sam | 0
.../illumina/25T8B25T/sams_with_4M4M/GAAGGAAG.sam | 8 +
.../illumina/25T8B25T/sams_with_4M4M/GACCAGGA.sam | 16 +
.../25T8B25T/{sams => sams_with_4M4M}/GACCAGGC.sam | 0
.../illumina/25T8B25T/sams_with_4M4M/GACCGTTG.sam | 10 +
.../illumina/25T8B25T/sams_with_4M4M/GACCTAAC.sam | 4 +
.../illumina/25T8B25T/sams_with_4M4M/GATATCCA.sam | 8 +
.../illumina/25T8B25T/sams_with_4M4M/GCCGTCGA.sam | 12 +
.../illumina/25T8B25T/sams_with_4M4M/GCCTAGCC.sam | 12 +
.../illumina/25T8B25T/sams_with_4M4M/GTAACATC.sam | 6 +
.../illumina/25T8B25T/sams_with_4M4M/GTCCACAG.sam | 6 +
.../picard/illumina/25T8B25T/sams_with_4M4M/N.sam | 34 +
.../illumina/25T8B25T/sams_with_4M4M/TAAGCACA.sam | 6 +
.../25T8B25T/{sams => sams_with_4M4M}/TACCGTCT.sam | 0
.../25T8B25T/{sams => sams_with_4M4M}/TAGCGGTA.sam | 0
.../25T8B25T/{sams => sams_with_4M4M}/TATCAGCC.sam | 0
.../illumina/25T8B25T/sams_with_4M4M/TATCCAGG.sam | 10 +
.../25T8B25T/{sams => sams_with_4M4M}/TATCCATG.sam | 0
.../25T8B25T/{sams => sams_with_4M4M}/TATCTCGG.sam | 0
.../illumina/25T8B25T/sams_with_4M4M/TATCTGCC.sam | 16 +
.../25T8B25T/{sams => sams_with_4M4M}/TCCGTCTA.sam | 0
.../illumina/25T8B25T/sams_with_4M4M/TCGCTAGA.sam | 12 +
.../illumina/25T8B25T/sams_with_4M4M/TCTGCAAG.sam | 4 +
.../illumina/25T8B25T/sams_with_4M4M/TGCAAGTA.sam | 6 +
.../illumina/25T8B25T/sams_with_4M4M/TGCTGCTG.sam | 10 +
.../illumina/25T8B25T/sams_with_4M4M/TGTAACTC.sam | 4 +
.../illumina/25T8B25T/sams_with_4M4M/TGTAATCA.sam | 8 +
.../illumina/25T8B25T/sams_with_4M4M/TTGTCTAT.sam | 10 +
.../25T8B25T/sams_with_4M4M/barcode.params | 63 ++
.../25T8B8B25T/sams/N_with_molecular_index.sam | 40 +
.../illumina/mark_illumina_adapters_test.sam | 4 +
testdata/picard/reference/test.dict | 9 +
.../test.fasta} | 0
testdata/picard/reference/test.fasta.fai | 8 +
testdata/picard/reference/test.intervals | 12 +
.../sam/CollectGcBiasMetrics/MSmallHeader.dict | 2 +
.../picard/sam/EstimateLibraryComplexity/dupes.sam | 16 +
.../picard/sam/FixMateInformation/missingMate.sam | 5 +
testdata/picard/sam/namesorted.test.sam | 12 +-
.../sam/summary_alignment_stats_test_chimeras.sam | 20 +
testdata/picard/util/interval_list_to_bed_test.bed | 13 +
.../util/interval_list_to_bed_test.interval_list | 19 +
testdata/picard/vcf/mini_gvcf.vcf | 290 ++++++
testdata/picard/vcf/mini_gvcf.vcf.idx | Bin 0 -> 165 bytes
testdata/picard/vcf/test.over.badContig.chain | 2 +
.../picard/vcf/testLiftoverUsingMissingContig.vcf | 4 +
1087 files changed, 20420 insertions(+), 2438 deletions(-)
create mode 100644 src/java/picard/analysis/AdapterUtility.java
create mode 100644 src/java/picard/analysis/ChimeraUtil.java
create mode 100644 src/java/picard/analysis/FingerprintingDetailMetrics.java
create mode 100644 src/java/picard/analysis/FingerprintingSummaryMetrics.java
create mode 100644 src/java/picard/analysis/TheoreticalSensitivity.java
copy src/java/picard/analysis/directed/{CalculateHsMetrics.java => CollectHsMetrics.java} (75%)
create mode 100644 src/java/picard/cmdline/programgroups/Alpha.java
copy src/java/picard/{illumina/parser/ReadType.java => filter/CountingDuplicateFilter.java} (63%)
create mode 100644 src/java/picard/filter/CountingFilter.java
copy src/java/picard/{illumina/parser/ReadType.java => filter/CountingMapQFilter.java} (63%)
copy src/java/picard/{illumina/parser/ReadType.java => filter/CountingPairedFilter.java} (63%)
create mode 100644 src/java/picard/fingerprint/CheckFingerprint.java
create mode 100644 src/java/picard/fingerprint/CrosscheckReadGroupFingerprints.java
create mode 100644 src/java/picard/fingerprint/DiploidGenotype.java
copy src/java/picard/{illumina/parser/ReadType.java => fingerprint/DiploidHaplotype.java} (63%)
create mode 100644 src/java/picard/fingerprint/Fingerprint.java
create mode 100644 src/java/picard/fingerprint/FingerprintChecker.java
copy src/java/picard/{illumina/parser/ReadType.java => fingerprint/FingerprintResults.java} (54%)
create mode 100644 src/java/picard/fingerprint/GenotypeReader.java
create mode 100644 src/java/picard/fingerprint/HaplotypeBlock.java
create mode 100644 src/java/picard/fingerprint/HaplotypeMap.java
create mode 100644 src/java/picard/fingerprint/HaplotypeProbabilities.java
create mode 100644 src/java/picard/fingerprint/HaplotypeProbabilitiesFromContaminatorSequence.java
create mode 100644 src/java/picard/fingerprint/HaplotypeProbabilitiesFromGenotype.java
create mode 100644 src/java/picard/fingerprint/HaplotypeProbabilitiesFromGenotypeLikelihoods.java
create mode 100644 src/java/picard/fingerprint/HaplotypeProbabilitiesFromSequence.java
create mode 100644 src/java/picard/fingerprint/HaplotypeProbabilitiesUsingLogLikelihoods.java
create mode 100644 src/java/picard/fingerprint/HaplotypeProbabilityOfNormalGivenTumor.java
create mode 100644 src/java/picard/fingerprint/LocusResult.java
create mode 100644 src/java/picard/fingerprint/MatchResults.java
create mode 100644 src/java/picard/fingerprint/Snp.java
create mode 100644 src/java/picard/reference/NonNFastaSize.java
create mode 100644 src/java/picard/sam/util/PhysicalLocationInt.java
copy src/java/picard/{illumina/parser/ReadType.java => sam/util/PhysicalLocationShort.java} (57%)
create mode 100644 src/java/picard/sam/util/ReadNameParser.java
delete mode 100644 src/java/picard/sam/util/ReadNameParsingUtils.java
create mode 100644 src/java/picard/util/IntervalListToBed.java
create mode 100644 src/java/picard/vcf/GvcfMetricAccumulator.java
create mode 100644 src/tests/java/picard/analysis/CollectQualityYieldMetricsTest.java
create mode 100644 src/tests/java/picard/analysis/CollectWgsMetricsTest.java
create mode 100644 src/tests/java/picard/analysis/TheoreticalSensitivityTest.java
create mode 100644 src/tests/java/picard/analysis/directed/CollectHsMetricsTest.java
create mode 100644 src/tests/java/picard/fingerprint/FingerprintCheckerTest.java
create mode 100755 src/tests/java/picard/fingerprint/HaplotypeMapTest.java
create mode 100644 src/tests/java/picard/fingerprint/HaplotypeProbabilitiesTest.java
create mode 100644 src/tests/java/picard/fingerprint/HaplotypeProbabilityOfNormalGivenTumorTest.java
create mode 100644 src/tests/java/picard/reference/NonNFastaSizeTest.java
create mode 100644 src/tests/java/picard/sam/FixMateInformationTest.java
create mode 100644 src/tests/java/picard/sam/markduplicates/EstimateLibraryComplexityTest.java
create mode 100644 src/tests/java/picard/sam/markduplicates/MarkDuplicateWithMissingBarcodeTest.java
create mode 100644 src/tests/java/picard/sam/markduplicates/MarkDuplicateWithMissingReadOneBarcodeTest.java
create mode 100644 src/tests/java/picard/sam/markduplicates/MarkDuplicateWithMissingReadTwoBarcodeTest.java
create mode 100644 src/tests/java/picard/sam/markduplicates/MarkDuplicateWithMissingSampleBarcodeTest.java
create mode 100644 src/tests/java/picard/sam/util/ReadNameParserTests.java
create mode 100644 src/tests/java/picard/util/IntervalListToBedTest.java
create mode 100644 src/tests/java/picard/vcf/CallingMetricAccumulatorTest.java
create mode 100644 testdata/picard/analysis/TheoreticalSensitivity/Solexa332667_BaseQ.histo
create mode 100644 testdata/picard/analysis/TheoreticalSensitivity/Solexa332667_DepthDist.histo
create mode 100644 testdata/picard/analysis/TheoreticalSensitivity/test_25103070136.targeted_pcr_metrics
create mode 100644 testdata/picard/analysis/TheoreticalSensitivity/test_NexPond-359781.hsMetrics
create mode 100644 testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-316269_sampled.wgs_metrics
create mode 100644 testdata/picard/analysis/TheoreticalSensitivity/test_Solexa-332667.wgs_metrics
create mode 100644 testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list
create mode 100644 testdata/picard/analysis/directed/CollectHsMetrics/lowbaseq.sam
create mode 100644 testdata/picard/analysis/directed/CollectHsMetrics/lowmapq.sam
create mode 100644 testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam
create mode 100644 testdata/picard/fingerprint/haplotypeMap.txt
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AAAAAAAA.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AAAAAAAA.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AAAAAAAA.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/AAAAAAAA.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AAAAGAAG.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AAAAGAAG.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AAAAGAAG.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/AAAAGAAG.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AACAATGG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/AACAATGG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AACAATGG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/AACAATGG.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AACGCATT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/AACGCATT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AACGCATT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/AACGCATT.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACAAAATT.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACAAAATT.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACAAAATT.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/ACAAAATT.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACAGGTAT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/ACAGGTAT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACAGGTAT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/ACAGGTAT.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACAGTTGA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/ACAGTTGA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACAGTTGA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/ACAGTTGA.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACCAGTTG.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACCAGTTG.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACCAGTTG.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/ACCAGTTG.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACGAAATC.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACGAAATC.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACGAAATC.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/ACGAAATC.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACTAAGAC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/ACTAAGAC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACTAAGAC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/ACTAAGAC.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACTGTACC.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACTGTACC.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACTGTACC.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/ACTGTACC.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACTGTATC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/ACTGTATC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ACTGTATC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/ACTGTATC.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AGAAAAGA.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AGAAAAGA.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AGAAAAGA.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/AGAAAAGA.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AGCATGGA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/AGCATGGA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AGCATGGA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/AGCATGGA.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AGGTAAGG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/AGGTAAGG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AGGTAAGG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/AGGTAAGG.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AGGTCGCA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/AGGTCGCA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/AGGTCGCA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/AGGTCGCA.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ATTATCAA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/ATTATCAA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ATTATCAA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/ATTATCAA.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ATTCCTCT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/ATTCCTCT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/ATTCCTCT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/ATTCCTCT.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CAACTCTC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CAACTCTC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CAACTCTC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CAACTCTC.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CAATAGAC.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CAATAGAC.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CAATAGAC.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/CAATAGAC.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CAATAGTC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CAATAGTC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CAATAGTC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CAATAGTC.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CAGCGGAT.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CAGCGGAT.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CAGCGGAT.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/CAGCGGAT.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CAGCGGTA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CAGCGGTA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CAGCGGTA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CAGCGGTA.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CCAACATT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CCAACATT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CCAACATT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CCAACATT.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CCAGCACC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CCAGCACC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CCAGCACC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CCAGCACC.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CCATGCGT.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CCATGCGT.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CCATGCGT.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/CCATGCGT.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CGCCTTCC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CGCCTTCC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CGCCTTCC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CGCCTTCC.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CGCTATGT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CGCTATGT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CGCTATGT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CGCTATGT.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CTAACTCG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CTAACTCG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CTAACTCG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CTAACTCG.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CTATGCGC.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CTATGCGC.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CTATGCGC.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/CTATGCGC.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CTATGCGT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CTATGCGT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CTATGCGT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CTATGCGT.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CTGCGGAT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CTGCGGAT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CTGCGGAT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CTGCGGAT.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CTGTAATC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CTGTAATC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/CTGTAATC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/CTGTAATC.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GAAAAAAA.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GAAAAAAA.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GAAAAAAA.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/GAAAAAAA.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GAACGAT..1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GAACGAT..2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GAACGAT..barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/GAACGAT..index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GAAGGAAG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GAAGGAAG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GAAGGAAG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GAAGGAAG.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GACCAGGA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GACCAGGA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GACCAGGA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GACCAGGA.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GACCAGGC.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GACCAGGC.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GACCAGGC.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/GACCAGGC.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GACCGTTG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GACCGTTG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GACCGTTG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GACCGTTG.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GACCTAAC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GACCTAAC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GACCTAAC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GACCTAAC.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GATATCCA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GATATCCA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GATATCCA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GATATCCA.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GCCGTCGA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GCCGTCGA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GCCGTCGA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GCCGTCGA.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GCCTAGCC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GCCTAGCC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GCCTAGCC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GCCTAGCC.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GTAACATC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GTAACATC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GTAACATC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GTAACATC.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GTCCACAG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GTCCACAG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/GTCCACAG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/GTCCACAG.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/N.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/N.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/N.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/N.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TAAGCACA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TAAGCACA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TAAGCACA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TAAGCACA.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TACCGTCT.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TACCGTCT.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TACCGTCT.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/TACCGTCT.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TAGCGGTA.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TAGCGGTA.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TAGCGGTA.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/TAGCGGTA.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TATCAGCC.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TATCAGCC.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TATCAGCC.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/TATCAGCC.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TATCCAGG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TATCCAGG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TATCCAGG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TATCCAGG.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TATCCATG.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TATCCATG.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TATCCATG.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/TATCCATG.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TATCTCGG.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TATCTCGG.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TATCTCGG.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/TATCTCGG.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TATCTGCC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TATCTGCC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TATCTGCC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TATCTGCC.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TCCGTCTA.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TCCGTCTA.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TCCGTCTA.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M/TCCGTCTA.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TCGCTAGA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TCGCTAGA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TCGCTAGA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TCGCTAGA.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TCTGCAAG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TCTGCAAG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TCTGCAAG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TCTGCAAG.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TGCAAGTA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TGCAAGTA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TGCAAGTA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TGCAAGTA.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TGCTGCTG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TGCTGCTG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TGCTGCTG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TGCTGCTG.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TGTAACTC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TGTAACTC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TGTAACTC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TGTAACTC.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TGTAATCA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TGTAATCA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TGTAATCA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TGTAATCA.index_1.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TTGTCTAT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TTGTCTAT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M}/TTGTCTAT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/TTGTCTAT.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M/mp_barcode.params
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AAAAGAAG.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AAAAGAAG.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AAAAGAAG.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/AAAAGAAG.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/AAAAGAAG.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AACAATGG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/AACAATGG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AACAATGG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/AACAATGG.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/AACAATGG.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AACGCATT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/AACGCATT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AACGCATT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/AACGCATT.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/AACGCATT.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACAAAATT.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACAAAATT.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACAAAATT.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/ACAAAATT.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/ACAAAATT.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACAGGTAT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ACAGGTAT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACAGGTAT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ACAGGTAT.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ACAGGTAT.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACAGTTGA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ACAGTTGA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACAGTTGA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ACAGTTGA.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ACAGTTGA.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACCAGTTG.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACCAGTTG.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACCAGTTG.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/ACCAGTTG.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/ACCAGTTG.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACGAAATC.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACGAAATC.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACGAAATC.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/ACGAAATC.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/ACGAAATC.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACTAAGAC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ACTAAGAC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACTAAGAC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ACTAAGAC.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ACTAAGAC.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACTGTACC.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACTGTACC.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACTGTACC.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/ACTGTACC.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/ACTGTACC.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACTGTATC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ACTGTATC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ACTGTATC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ACTGTATC.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ACTGTATC.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AGAAAAGA.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AGAAAAGA.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AGAAAAGA.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/AGAAAAGA.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/AGAAAAGA.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AGCATGGA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/AGCATGGA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AGCATGGA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/AGCATGGA.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/AGCATGGA.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AGGTAAGG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/AGGTAAGG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AGGTAAGG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/AGGTAAGG.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/AGGTAAGG.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AGGTCGCA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/AGGTCGCA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/AGGTCGCA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/AGGTCGCA.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/AGGTCGCA.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ATTATCAA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ATTATCAA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ATTATCAA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ATTATCAA.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ATTATCAA.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ATTCCTCT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ATTCCTCT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/ATTCCTCT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ATTCCTCT.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/ATTCCTCT.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CAACTCTC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CAACTCTC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CAACTCTC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CAACTCTC.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CAACTCTC.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CAATAGAC.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CAATAGAC.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CAATAGAC.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/CAATAGAC.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/CAATAGAC.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CAATAGTC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CAATAGTC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CAATAGTC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CAATAGTC.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CAATAGTC.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CAGCGGAT.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CAGCGGAT.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CAGCGGAT.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/CAGCGGAT.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/CAGCGGAT.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CAGCGGTA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CAGCGGTA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CAGCGGTA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CAGCGGTA.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CAGCGGTA.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CCAACATT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CCAACATT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CCAACATT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CCAACATT.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CCAACATT.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CCAGCACC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CCAGCACC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CCAGCACC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CCAGCACC.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CCAGCACC.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CCATGCGT.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CCATGCGT.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CCATGCGT.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/CCATGCGT.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/CCATGCGT.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CGCCTTCC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CGCCTTCC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CGCCTTCC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CGCCTTCC.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CGCCTTCC.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CGCTATGT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CGCTATGT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CGCTATGT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CGCTATGT.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CGCTATGT.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CTAACTCG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CTAACTCG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CTAACTCG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CTAACTCG.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CTAACTCG.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CTATGCGC.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CTATGCGC.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CTATGCGC.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/CTATGCGC.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/CTATGCGC.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CTATGCGT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CTATGCGT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CTATGCGT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CTATGCGT.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CTATGCGT.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CTGCGGAT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CTGCGGAT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CTGCGGAT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CTGCGGAT.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CTGCGGAT.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CTGTAATC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CTGTAATC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/CTGTAATC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CTGTAATC.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/CTGTAATC.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GAAAAAAA.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GAAAAAAA.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GAAAAAAA.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/GAAAAAAA.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/GAAAAAAA.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GAACGAT..1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GAACGAT..2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GAACGAT..barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/GAACGAT..index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/GAACGAT..index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GAAGGAAG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GAAGGAAG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GAAGGAAG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GAAGGAAG.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GAAGGAAG.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GACCAGGA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GACCAGGA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GACCAGGA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GACCAGGA.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GACCAGGA.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GACCAGGC.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GACCAGGC.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GACCAGGC.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/GACCAGGC.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/GACCAGGC.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GACCGTTG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GACCGTTG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GACCGTTG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GACCGTTG.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GACCGTTG.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GACCTAAC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GACCTAAC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GACCTAAC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GACCTAAC.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GACCTAAC.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GATATCCA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GATATCCA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GATATCCA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GATATCCA.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GATATCCA.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GCCGTCGA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GCCGTCGA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GCCGTCGA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GCCGTCGA.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GCCGTCGA.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GCCTAGCC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GCCTAGCC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GCCTAGCC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GCCTAGCC.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GCCTAGCC.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GTAACATC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GTAACATC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GTAACATC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GTAACATC.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GTAACATC.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GTCCACAG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GTCCACAG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/GTCCACAG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GTCCACAG.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/GTCCACAG.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/N.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/N.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/N.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/N.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/N.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TAAGCACA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TAAGCACA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TAAGCACA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TAAGCACA.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TAAGCACA.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TACCGTCT.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TACCGTCT.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TACCGTCT.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/TACCGTCT.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/TACCGTCT.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TAGCGGTA.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TAGCGGTA.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TAGCGGTA.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/TAGCGGTA.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/TAGCGGTA.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TATCAGCC.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TATCAGCC.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TATCAGCC.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/TATCAGCC.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/TATCAGCC.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TATCCAGG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TATCCAGG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TATCCAGG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TATCCAGG.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TATCCAGG.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TATCCATG.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TATCCATG.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TATCCATG.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/TATCCATG.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/TATCCATG.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TATCTCGG.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TATCTCGG.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TATCTCGG.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/TATCTCGG.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/TATCTCGG.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TATCTGCC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TATCTGCC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TATCTGCC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TATCTGCC.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TATCTGCC.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TCCGTCTA.1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TCCGTCTA.2.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TCCGTCTA.barcode_1.fastq (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/TCCGTCTA.index_1.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => fastq_with_4M4M/TCCGTCTA.index_2.fastq} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TCGCTAGA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TCGCTAGA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TCGCTAGA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TCGCTAGA.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TCGCTAGA.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TCTGCAAG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TCTGCAAG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TCTGCAAG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TCTGCAAG.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TCTGCAAG.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TGCAAGTA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TGCAAGTA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TGCAAGTA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TGCAAGTA.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TGCAAGTA.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TGCTGCTG.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TGCTGCTG.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TGCTGCTG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TGCTGCTG.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TGCTGCTG.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TGTAACTC.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TGTAACTC.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TGTAACTC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TGTAACTC.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TGTAACTC.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TGTAATCA.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TGTAATCA.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TGTAATCA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TGTAATCA.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TGTAATCA.index_2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TTGTCTAT.1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TTGTCTAT.2.fastq
copy testdata/picard/illumina/25T8B25T/{fastq => fastq_with_4M4M}/TTGTCTAT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TTGTCTAT.index_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/TTGTCTAT.index_2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq_with_4M4M/mp_barcode.params
create mode 100644 testdata/picard/illumina/25T8B25T/sams/nonBarcodedWithMolecularIndex4M4M.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams/nonBarcodedWithMolecularIndex8M.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/AAAAAAAA.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/AAAAGAAG.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/AACAATGG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/AACGCATT.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/ACAAAATT.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/ACAGGTAT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/ACAGTTGA.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/ACCAGTTG.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/ACGAAATC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/ACTAAGAC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/ACTGTACC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/ACTGTATC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/AGAAAAGA.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/AGCATGGA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/AGGTAAGG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/AGGTCGCA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/ATTATCAA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/ATTCCTCT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/CAACTCTC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/CAATAGAC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/CAATAGTC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/CAGCGGAT.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/CAGCGGTA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/CCAACATT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/CCAGCACC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/CCATGCGT.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/CGCCTTCC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/CGCTATGT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/CTAACTCG.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/CTATGCGC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/CTATGCGT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/CTGCGGAT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/CTGTAATC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/GAAAAAAA.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/GAACGAT..sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/GAAGGAAG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/GACCAGGA.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/GACCAGGC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/GACCGTTG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/GACCTAAC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/GATATCCA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/GCCGTCGA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/GCCTAGCC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/GTAACATC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/GTCCACAG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/N.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/TAAGCACA.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/TACCGTCT.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/TAGCGGTA.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/TATCAGCC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/TATCCAGG.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/TATCCATG.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/TATCTCGG.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/TATCTGCC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M}/TCCGTCTA.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/TCGCTAGA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/TCTGCAAG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/TGCAAGTA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/TGCTGCTG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/TGTAACTC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/TGTAATCA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/TTGTCTAT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/barcode.params
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => sams_with_4M/final/nonBarcoded.sam} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => sams_with_4M/final/nonBarcodedWithMolecularIndex4M4M.sam} (100%)
copy testdata/picard/illumina/25T8B25T/{fastq/AAAAAAAA.1.fastq => sams_with_4M/final/nonBarcodedWithMolecularIndex8M.sam} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AAAAAAAA.sam
copy testdata/picard/illumina/25T8B25T/{sams/AAAAAAAA.sam => sams_with_4M/indicies/AAAAAAAA.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AAAAGAAG.sam
copy testdata/picard/illumina/25T8B25T/{sams/AAAAGAAG.sam => sams_with_4M/indicies/AAAAGAAG.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AACAATGG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AACAATGG.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AACGCATT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AACGCATT.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAAAATT.sam
copy testdata/picard/illumina/25T8B25T/{sams/ACAAAATT.sam => sams_with_4M/indicies/ACAAAATT.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAGGTAT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAGGTAT.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAGTTGA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACAGTTGA.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACCAGTTG.sam
copy testdata/picard/illumina/25T8B25T/{sams/ACCAGTTG.sam => sams_with_4M/indicies/ACCAGTTG.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACGAAATC.sam
copy testdata/picard/illumina/25T8B25T/{sams/ACGAAATC.sam => sams_with_4M/indicies/ACGAAATC.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTAAGAC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTAAGAC.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTGTACC.sam
copy testdata/picard/illumina/25T8B25T/{sams/ACTGTACC.sam => sams_with_4M/indicies/ACTGTACC.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTGTATC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ACTGTATC.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGAAAAGA.sam
copy testdata/picard/illumina/25T8B25T/{sams/AGAAAAGA.sam => sams_with_4M/indicies/AGAAAAGA.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGCATGGA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGCATGGA.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGGTAAGG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGGTAAGG.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGGTCGCA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/AGGTCGCA.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ATTATCAA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ATTATCAA.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ATTCCTCT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/ATTCCTCT.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAACTCTC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAACTCTC.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAATAGAC.sam
copy testdata/picard/illumina/25T8B25T/{sams/CAATAGAC.sam => sams_with_4M/indicies/CAATAGAC.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAATAGTC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAATAGTC.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAGCGGAT.sam
copy testdata/picard/illumina/25T8B25T/{sams/CAGCGGAT.sam => sams_with_4M/indicies/CAGCGGAT.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAGCGGTA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CAGCGGTA.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCAACATT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCAACATT.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCAGCACC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCAGCACC.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CCATGCGT.sam
copy testdata/picard/illumina/25T8B25T/{sams/CCATGCGT.sam => sams_with_4M/indicies/CCATGCGT.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CGCCTTCC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CGCCTTCC.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CGCTATGT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CGCTATGT.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTAACTCG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTAACTCG.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTATGCGC.sam
copy testdata/picard/illumina/25T8B25T/{sams/CTATGCGC.sam => sams_with_4M/indicies/CTATGCGC.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTATGCGT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTATGCGT.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTGCGGAT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTGCGGAT.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTGTAATC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/CTGTAATC.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAAAAAAA.sam
copy testdata/picard/illumina/25T8B25T/{sams/GAAAAAAA.sam => sams_with_4M/indicies/GAAAAAAA.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAACGAT..sam
copy testdata/picard/illumina/25T8B25T/{sams/GAACGAT..sam => sams_with_4M/indicies/GAACGAT..sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAAGGAAG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GAAGGAAG.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCAGGA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCAGGA.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCAGGC.sam
copy testdata/picard/illumina/25T8B25T/{sams/GACCAGGC.sam => sams_with_4M/indicies/GACCAGGC.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCGTTG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCGTTG.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCTAAC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GACCTAAC.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GATATCCA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GATATCCA.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GCCGTCGA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GCCGTCGA.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GCCTAGCC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GCCTAGCC.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GTAACATC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GTAACATC.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GTCCACAG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/GTCCACAG.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/N.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/N.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TAAGCACA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TAAGCACA.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TACCGTCT.sam
copy testdata/picard/illumina/25T8B25T/{sams/TACCGTCT.sam => sams_with_4M/indicies/TACCGTCT.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TAGCGGTA.sam
copy testdata/picard/illumina/25T8B25T/{sams/TAGCGGTA.sam => sams_with_4M/indicies/TAGCGGTA.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCAGCC.sam
copy testdata/picard/illumina/25T8B25T/{sams/TATCAGCC.sam => sams_with_4M/indicies/TATCAGCC.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCCAGG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCCAGG.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCCATG.sam
copy testdata/picard/illumina/25T8B25T/{sams/TATCCATG.sam => sams_with_4M/indicies/TATCCATG.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCTCGG.sam
copy testdata/picard/illumina/25T8B25T/{sams/TATCTCGG.sam => sams_with_4M/indicies/TATCTCGG.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCTGCC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TATCTGCC.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCCGTCTA.sam
copy testdata/picard/illumina/25T8B25T/{sams/TCCGTCTA.sam => sams_with_4M/indicies/TCCGTCTA.sam.bak} (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCGCTAGA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCGCTAGA.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCTGCAAG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TCTGCAAG.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGCAAGTA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGCAAGTA.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGCTGCTG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGCTGCTG.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGTAACTC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGTAACTC.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGTAATCA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TGTAATCA.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TTGTCTAT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/TTGTCTAT.sam.bak
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/indicies/barcode.params
copy testdata/picard/illumina/25T8B25T/{fastq/barcode.params => sams_with_4M/multiplexed_positive_rgtags.params} (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/AAAAAAAA.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/AAAAGAAG.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/AACAATGG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/AACGCATT.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/ACAAAATT.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/ACAGGTAT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/ACAGTTGA.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/ACCAGTTG.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/ACGAAATC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/ACTAAGAC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/ACTGTACC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/ACTGTATC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/AGAAAAGA.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/AGCATGGA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/AGGTAAGG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/AGGTCGCA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/ATTATCAA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/ATTCCTCT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/CAACTCTC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/CAATAGAC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/CAATAGTC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/CAGCGGAT.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/CAGCGGTA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/CCAACATT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/CCAGCACC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/CCATGCGT.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/CGCCTTCC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/CGCTATGT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/CTAACTCG.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/CTATGCGC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/CTATGCGT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/CTGCGGAT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/CTGTAATC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/GAAAAAAA.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/GAACGAT..sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/GAAGGAAG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/GACCAGGA.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/GACCAGGC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/GACCGTTG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/GACCTAAC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/GATATCCA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/GCCGTCGA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/GCCTAGCC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/GTAACATC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/GTCCACAG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/TAAGCACA.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/TACCGTCT.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/TAGCGGTA.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/TATCAGCC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/TATCCAGG.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/TATCCATG.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/TATCTCGG.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/TATCTGCC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M/templates}/TCCGTCTA.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/TCGCTAGA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/TCTGCAAG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/TGCAAGTA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/TGCTGCTG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/TGTAACTC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/TGTAATCA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M/templates/TTGTCTAT.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/AAAAAAAA.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/AAAAGAAG.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/AACAATGG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/AACGCATT.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/ACAAAATT.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/ACAGGTAT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/ACAGTTGA.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/ACCAGTTG.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/ACGAAATC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/ACTAAGAC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/ACTGTACC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/ACTGTATC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/AGAAAAGA.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/AGCATGGA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/AGGTAAGG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/AGGTCGCA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/ATTATCAA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/ATTCCTCT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/CAACTCTC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/CAATAGAC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/CAATAGTC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/CAGCGGAT.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/CAGCGGTA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/CCAACATT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/CCAGCACC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/CCATGCGT.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/CGCCTTCC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/CGCTATGT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/CTAACTCG.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/CTATGCGC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/CTATGCGT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/CTGCGGAT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/CTGTAATC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/GAAAAAAA.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/GAACGAT..sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/GAAGGAAG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/GACCAGGA.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/GACCAGGC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/GACCGTTG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/GACCTAAC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/GATATCCA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/GCCGTCGA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/GCCTAGCC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/GTAACATC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/GTCCACAG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/N.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/TAAGCACA.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/TACCGTCT.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/TAGCGGTA.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/TATCAGCC.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/TATCCAGG.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/TATCCATG.sam (100%)
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/TATCTCGG.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/TATCTGCC.sam
copy testdata/picard/illumina/25T8B25T/{sams => sams_with_4M4M}/TCCGTCTA.sam (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/TCGCTAGA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/TCTGCAAG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/TGCAAGTA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/TGCTGCTG.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/TGTAACTC.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/TGTAATCA.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/TTGTCTAT.sam
create mode 100644 testdata/picard/illumina/25T8B25T/sams_with_4M4M/barcode.params
create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/N_with_molecular_index.sam
create mode 100755 testdata/picard/illumina/mark_illumina_adapters_test.sam
create mode 100644 testdata/picard/reference/test.dict
copy testdata/picard/{sam/summary_alignment_stats_test.fasta => reference/test.fasta} (100%)
create mode 100644 testdata/picard/reference/test.fasta.fai
create mode 100644 testdata/picard/reference/test.intervals
create mode 100644 testdata/picard/sam/CollectGcBiasMetrics/MSmallHeader.dict
create mode 100644 testdata/picard/sam/EstimateLibraryComplexity/dupes.sam
create mode 100644 testdata/picard/sam/FixMateInformation/missingMate.sam
create mode 100644 testdata/picard/sam/summary_alignment_stats_test_chimeras.sam
create mode 100644 testdata/picard/util/interval_list_to_bed_test.bed
create mode 100644 testdata/picard/util/interval_list_to_bed_test.interval_list
create mode 100755 testdata/picard/vcf/mini_gvcf.vcf
create mode 100644 testdata/picard/vcf/mini_gvcf.vcf.idx
create mode 100644 testdata/picard/vcf/test.over.badContig.chain
create mode 100644 testdata/picard/vcf/testLiftoverUsingMissingContig.vcf
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