[med-svn] [picard-tools] branch upstream updated (c2bd278 -> 0c4debd)
Andreas Tille
tille at debian.org
Sun Feb 21 18:19:34 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository picard-tools.
from c2bd278 Imported Upstream version 1.141+dfsg.1
new 8fb7b72 Imported Upstream version 2.1.0+dfsg
new 0c4debd Imported Upstream version 2.1.0+dfsg
The 2 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 +-
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
.../{fastq => fastq_with_4M}/AAAAGAAG.1.fastq | 0
.../{fastq => fastq_with_4M}/AAAAGAAG.2.fastq | 0
.../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 +
.../{fastq => fastq_with_4M}/AACGCATT.1.fastq | 0
.../25T8B25T/fastq_with_4M/AACGCATT.2.fastq | 28 +
.../AACGCATT.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/AACGCATT.index_1.fastq | 28 +
.../{fastq => fastq_with_4M}/ACAAAATT.1.fastq | 0
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.../25T8B25T/fastq_with_4M/ACTAAGAC.2.fastq | 16 +
.../ACTAAGAC.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/ACTAAGAC.index_1.fastq | 16 +
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.../25T8B25T/fastq_with_4M/ACTGTATC.2.fastq | 16 +
.../ACTGTATC.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/ACTGTATC.index_1.fastq | 16 +
.../{fastq => fastq_with_4M}/AGAAAAGA.1.fastq | 0
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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
.../{fastq => fastq_with_4M}/CAATAGAC.2.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
.../{fastq => fastq_with_4M}/CCATGCGT.2.fastq | 0
.../CCATGCGT.barcode_1.fastq | 0
.../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 +
.../{fastq => fastq_with_4M}/CTATGCGC.1.fastq | 0
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.../CTATGCGC.barcode_1.fastq | 0
.../CTATGCGC.index_1.fastq} | 0
.../{fastq => fastq_with_4M}/CTATGCGT.1.fastq | 0
.../25T8B25T/fastq_with_4M/CTATGCGT.2.fastq | 28 +
.../CTATGCGT.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/CTATGCGT.index_1.fastq | 28 +
.../{fastq => fastq_with_4M}/CTGCGGAT.1.fastq | 0
.../25T8B25T/fastq_with_4M/CTGCGGAT.2.fastq | 12 +
.../CTGCGGAT.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/CTGCGGAT.index_1.fastq | 12 +
.../{fastq => fastq_with_4M}/CTGTAATC.1.fastq | 0
.../25T8B25T/fastq_with_4M/CTGTAATC.2.fastq | 24 +
.../CTGTAATC.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/CTGTAATC.index_1.fastq | 24 +
.../{fastq => fastq_with_4M}/GAAAAAAA.1.fastq | 0
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.../GAAAAAAA.index_1.fastq} | 0
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.../25T8B25T/fastq_with_4M/GAAGGAAG.2.fastq | 12 +
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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 +
.../{fastq => fastq_with_4M}/GACCAGGC.1.fastq | 0
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.../GACCAGGC.barcode_1.fastq | 0
.../GACCAGGC.index_1.fastq} | 0
.../{fastq => fastq_with_4M}/GACCGTTG.1.fastq | 0
.../25T8B25T/fastq_with_4M/GACCGTTG.2.fastq | 16 +
.../GACCGTTG.barcode_1.fastq | 0
.../25T8B25T/fastq_with_4M/GACCGTTG.index_1.fastq | 16 +
.../{fastq => fastq_with_4M}/GACCTAAC.1.fastq | 0
.../25T8B25T/fastq_with_4M/GACCTAAC.2.fastq | 4 +
.../GACCTAAC.barcode_1.fastq | 0
.../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 +
1083 files changed, 20401 insertions(+), 2418 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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