[med-svn] [picard-tools] branch master updated (ddb817f -> 11db35e)
Olivier Sallou
osallou at debian.org
Fri Jun 6 21:35:21 UTC 2014
This is an automated email from the git hooks/post-receive script.
osallou pushed a change to branch master
in repository picard-tools.
from ddb817f picard-tools (1.110-1) unstable; urgency=medium
new db975ee Imported Upstream version 1.113
new 2263d6f Merge tag 'upstream/1.113'
new 11db35e new upstream release 1.113
The 3 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 | 11 +
build.xml | 5 +-
debian/README.source | 7 +
debian/changelog | 6 +
.../net/sf/picard/analysis/CollectWgsMetrics.java | 274 ++++
.../net/sf/picard/cmdline/CommandLineParser.java | 18 +-
.../sf/picard/filter/SecondaryAlignmentFilter.java | 20 +
.../sf/picard/illumina/CheckIlluminaDirectory.java | 78 +-
.../picard/illumina/ClusterDataToSamConverter.java | 22 +-
.../picard/illumina/ExtractIlluminaBarcodes.java | 5 +-
.../illumina/IlluminaBasecallsConverter.java | 83 +-
.../picard/illumina/IlluminaBasecallsToFastq.java | 1 +
.../sf/picard/illumina/IlluminaBasecallsToSam.java | 1 +
.../sf/picard/illumina/MarkIlluminaAdapters.java | 23 +-
.../net/sf/picard/illumina/parser/BclData.java | 30 +
.../net/sf/picard/illumina/parser/BclParser.java | 239 ++-
.../net/sf/picard/illumina/parser/CifParser.java | 79 -
.../net/sf/picard/illumina/parser/CnfParser.java | 67 -
.../illumina/parser/CycleIlluminaFileMap.java | 177 +--
.../illumina/parser/IlluminaDataProvider.java | 69 +-
.../parser/IlluminaDataProviderFactory.java | 167 +-
.../picard/illumina/parser/IlluminaDataType.java | 2 +-
.../sf/picard/illumina/parser/IlluminaFileMap.java | 27 +-
.../picard/illumina/parser/IlluminaFileUtil.java | 1345 +---------------
.../illumina/parser/IlluminaIntensityParser.java | 132 --
.../sf/picard/illumina/parser/IlluminaParser.java | 16 +-
.../parser/MultiTileBclCycleFilesIterator.java | 40 -
.../illumina/parser/MultiTileBclFileUtil.java | 115 ++
.../picard/illumina/parser/MultiTileBclParser.java | 112 +-
.../picard/illumina/parser/MultiTileFileUtil.java | 120 ++
.../illumina/parser/MultiTileFilterParser.java | 6 +
.../illumina/parser/MultiTileLocsParser.java | 5 +
.../illumina/parser/ParameterizedFileUtil.java | 174 +++
.../picard/illumina/parser/PerTileCycleParser.java | 203 +++
.../sf/picard/illumina/parser/PerTileFileUtil.java | 78 +
.../illumina/parser/PerTilePerCycleFileUtil.java | 268 ++++
.../illumina/parser/PerTilePerCycleParser.java | 197 ---
.../net/sf/picard/illumina/parser/QseqParser.java | 592 --------
.../net/sf/picard/illumina/parser/TileIndex.java | 12 +-
.../illumina/parser/fakers/BclFileFaker.java | 15 +-
.../illumina/parser/fakers/CifFileFaker.java | 31 -
.../illumina/parser/fakers/CnfFileFaker.java | 31 -
.../picard/illumina/parser/fakers/FileFaker.java | 26 +-
.../illumina/parser/fakers/QSeqFileFaker.java | 25 -
.../picard/illumina/parser/readers/BclReader.java | 467 +++---
src/java/net/sf/picard/io/IoUtil.java | 22 +-
src/java/net/sf/picard/metrics/MetricsFile.java | 22 +-
.../reference/AbstractFastaSequenceFile.java | 4 +-
.../sf/picard/reference/FastaSequenceIndex.java | 1 +
.../sf/picard/reference/ReferenceSequenceFile.java | 4 +
.../reference/ReferenceSequenceFileWalker.java | 5 +
.../net/sf/picard/sam/AbstractAlignmentMerger.java | 28 +-
src/java/net/sf/picard/sam/AddCommentsToBam.java | 57 +
src/java/net/sf/picard/sam/BuildBamIndex.java | 2 +-
src/java/net/sf/picard/sam/FilterSamReads.java | 7 +-
src/java/net/sf/picard/sam/FixMateInformation.java | 38 +-
src/java/net/sf/picard/sam/GatherBamFiles.java | 97 ++
src/java/net/sf/picard/sam/MarkDuplicates.java | 2 +-
src/java/net/sf/picard/sam/MergeBamAlignment.java | 7 +-
src/java/net/sf/picard/sam/ReplaceSamHeader.java | 60 +-
...RevertOriginalBaseQualitiesAndAddMateCigar.java | 22 +-
src/java/net/sf/picard/sam/SamAlignmentMerger.java | 7 +-
src/java/net/sf/picard/sam/SamFileValidator.java | 30 +-
src/java/net/sf/picard/util/AdapterMarker.java | 341 +++++
src/java/net/sf/picard/util/BasicInputParser.java | 4 +
src/java/net/sf/picard/util/IlluminaUtil.java | 45 +-
src/java/net/sf/picard/util/IntervalList.java | 402 ++++-
src/java/net/sf/picard/util/IntervalListTools.java | 142 +-
src/java/net/sf/picard/util/MathUtil.java | 11 +-
src/java/net/sf/picard/util/SamLocusIterator.java | 16 +-
src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java | 16 +-
src/java/net/sf/picard/vcf/MergeVcfs.java | 12 +-
src/java/net/sf/picard/vcf/SplitVcfs.java | 12 +-
src/java/net/sf/picard/vcf/VcfFormatConverter.java | 14 +-
.../net/sf/samtools/AbstractSAMHeaderRecord.java | 5 +
src/java/net/sf/samtools/BAMFileReader.java | 77 +-
src/java/net/sf/samtools/BAMFileWriter.java | 81 +-
src/java/net/sf/samtools/BamFileIoUtils.java | 155 ++
src/java/net/sf/samtools/Defaults.java | 15 +
src/java/net/sf/samtools/SAMFileWriterFactory.java | 2 +-
src/java/net/sf/samtools/SAMRecord.java | 264 +---
src/java/net/sf/samtools/SAMRecordSetBuilder.java | 19 +-
src/java/net/sf/samtools/SAMTag.java | 2 +-
src/java/net/sf/samtools/SAMUtils.java | 295 ++++
src/java/net/sf/samtools/SAMValidationError.java | 8 +-
src/java/net/sf/samtools/SamPairUtil.java | 62 +-
.../StreamInflatingIndexingOutputStream.java | 80 +
.../sf/samtools/TagValueAndUnsignedArrayFlag.java | 2 +-
src/java/net/sf/samtools/TextTagCodec.java | 10 +-
.../samtools/util/BlockCompressedInputStream.java | 7 +
.../net/sf/samtools/util/CloseableIterator.java | 6 +-
src/java/net/sf/samtools/util/IOUtil.java | 31 +
src/java/net/sf/samtools/util/LineReader.java | 4 +-
.../org/broad/tribble/AbstractFeatureReader.java | 31 +-
src/java/org/broad/tribble/index/IndexFactory.java | 5 +
.../java/org/broad/tribble/util/ftp/.gitignore | 0
.../writer/VariantContextWriterBuilder.java | 466 ++++++
.../writer/VariantContextWriterFactory.java | 14 +-
.../variant/vcf/AbstractVCFCodec.java | 31 +
.../variant/vcf/VCFCompoundHeaderLine.java | 7 +-
.../org/broadinstitute/variant/vcf/VCFEncoder.java | 4 +-
src/scripts/release_picard.sh | 5 +-
.../tests/java/net/sf/picard/fastq/.gitignore | 0
.../illumina/CheckIlluminaDirectoryTest.java | 84 +-
.../illumina/ExtractIlluminaBarcodesTest.java | 211 ++-
.../illumina/IlluminaBasecallsToFastqTest.java | 32 +-
.../IlluminaBasecallsToSamAdapterClippingTest.java | 32 +-
.../illumina/IlluminaBasecallsToSamTest.java | 29 +-
.../sf/picard/illumina/parser/BclParserTest.java | 443 +++---
.../net/sf/picard/illumina/parser/BinTdUtil.java | 473 ++----
.../parser/ClusterIntensityFileReaderTest.java | 102 --
.../illumina/parser/CycleIlluminaFileMapTest.java | 46 +-
.../picard/illumina/parser/FilterParserTest.java | 141 +-
.../illumina/parser/IlluminaDataProviderTest.java | 420 ++---
.../illumina/parser/IlluminaFileUtilTest.java | 684 +++------
.../parser/IlluminaIntensityParserTest.java | 147 --
.../illumina/parser/PerTilePerCycleParserTest.java | 185 +--
.../sf/picard/illumina/parser/PosParserTest.java | 2 +
.../net/sf/picard/illumina/parser/QSeqTdUtil.java | 707 ---------
.../sf/picard/illumina/parser/QseqParserTest.java | 356 -----
.../illumina/parser/fakers/BclFileFakerTest.java | 59 +
.../illumina/parser/readers/BclReaderTest.java | 45 +-
.../illumina/parser/readers/PosFileReaderTest.java | 50 +-
.../picard/reference/FastaSequenceIndexTest.java | 1 +
.../reference/IndexedFastaSequenceFileTest.java | 33 +
.../reference/ReferenceSequenceFileWalkerTest.java | 11 +-
.../net/sf/picard/sam/AddCommentsToBamTest.java | 63 +
src/tests/java/net/sf/picard/sam/CleanSamTest.java | 19 +-
.../net/sf/picard/sam/MergeBamAlignmentTest.java | 5 +-
.../java/net/sf/picard/sam/MergeSamFilesTest.java | 3 +-
.../net/sf/picard/sam/ValidateSamFileTest.java | 45 +
.../net/sf/picard/sam/testers/CleanSamTester.java | 18 +-
.../net/sf/picard/sam/testers/SamFileTester.java | 25 +-
.../net/sf/picard/util/ClippingUtilityTest.java | 386 ++++-
.../java/net/sf/picard/util/IntervalListTest.java | 387 +++++
.../net/sf/picard/util/IntervalListToolsTest.java | 21 +
.../java/net/sf/picard/vcf/SplitVcfsTest.java | 11 +-
.../net/sf/picard/vcf/VcfFormatConverterTest.java | 3 +-
.../java/net/sf/samtools/BAMFileIndexTest.java | 6 +-
.../java/net/sf/samtools/BAMFileWriterTest.java | 2 +-
.../java/net/sf/samtools/BamFileIoUtilsTest.java | 83 +
.../net/sf/samtools/SAMFileWriterFactoryTest.java | 6 +-
.../java/net/sf/samtools/SamPairUtilTest.java | 73 +-
.../tests/java/net/sf/samtools/apps/.gitignore | 0
src/tests/java/net/sf/samtools/util/IupacTest.java | 2 +-
.../tests/java/org/broad/tribble/source/.gitignore | 0
.../writer/TabixOnTheFlyIndexCreationTest.java | 10 +-
.../variantcontext/writer/VCFWriterUnitTest.java | 17 +-
.../VariantContextWriterBuilderUnitTest.java | 343 +++++
.../writer/VariantContextWritersUnitTest.java | 12 +-
.../variant/vcf/IndexFactoryUnitTest.java | 9 +-
.../variant/vcf/VCFCompoundHeaderLineUnitTest.java | 46 +
.../variant/vcf/VCFHeaderUnitTest.java | 40 +
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.../Intensities/BaseCalls/L001/C41.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C41.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C42.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C42.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C43.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C43.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C44.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C44.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C45.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C45.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C46.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C46.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C47.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C47.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C48.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C48.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C49.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C49.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C5.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C5.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C50.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C50.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C51.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C51.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C52.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C52.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C53.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C53.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C54.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C54.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C55.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C55.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C56.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C56.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C57.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C57.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C58.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C58.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C6.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C6.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C7.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C7.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C8.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C8.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C9.1/s_1_1201.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C9.1/s_1_2101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/s_1_1101.filter | Bin 0 -> 72 bytes
.../Intensities/BaseCalls/L001/s_1_1201.filter | Bin 0 -> 72 bytes
.../Intensities/BaseCalls/L001/s_1_2101.filter | Bin 0 -> 72 bytes
.../Intensities/BaseCalls/s_1_1101_barcode.txt.gz | Bin 0 -> 429 bytes
.../Intensities/BaseCalls/s_1_1201_barcode.txt.gz | Bin 0 -> 391 bytes
.../Intensities/BaseCalls/s_1_2101_barcode.txt.gz | Bin 0 -> 428 bytes
.../25T8B25T/Data/Intensities/L001/s_1_1101.clocs | Bin 0 -> 455 bytes
.../25T8B25T/Data/Intensities/L001/s_1_1201.clocs | Bin 0 -> 455 bytes
.../25T8B25T/Data/Intensities/L001/s_1_2101.clocs | Bin 0 -> 455 bytes
.../fastq/AAAAAAAA.1.fastq} | 0
.../fastq/AAAAAAAA.2.fastq} | 0
.../fastq/AAAAAAAA.barcode_1.fastq} | 0
.../fastq/AAAAGAAG.1.fastq} | 0
.../fastq/AAAAGAAG.2.fastq} | 0
.../fastq/AAAAGAAG.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/AACAATGG.1.fastq | 16 +
.../illumina/25T8B25T/fastq/AACAATGG.2.fastq | 16 +
.../25T8B25T/fastq/AACAATGG.barcode_1.fastq | 16 +
.../illumina/25T8B25T/fastq/AACGCATT.1.fastq | 28 +
.../illumina/25T8B25T/fastq/AACGCATT.2.fastq | 28 +
.../25T8B25T/fastq/AACGCATT.barcode_1.fastq | 28 +
.../fastq/ACAAAATT.1.fastq} | 0
.../fastq/ACAAAATT.2.fastq} | 0
.../fastq/ACAAAATT.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/ACAGGTAT.1.fastq | 16 +
.../illumina/25T8B25T/fastq/ACAGGTAT.2.fastq | 16 +
.../25T8B25T/fastq/ACAGGTAT.barcode_1.fastq | 16 +
.../illumina/25T8B25T/fastq/ACAGTTGA.1.fastq | 8 +
.../illumina/25T8B25T/fastq/ACAGTTGA.2.fastq | 8 +
.../25T8B25T/fastq/ACAGTTGA.barcode_1.fastq | 8 +
.../fastq/ACCAGTTG.1.fastq} | 0
.../fastq/ACCAGTTG.2.fastq} | 0
.../fastq/ACCAGTTG.barcode_1.fastq} | 0
.../fastq/ACGAAATC.1.fastq} | 0
.../fastq/ACGAAATC.2.fastq} | 0
.../fastq/ACGAAATC.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/ACTAAGAC.1.fastq | 16 +
.../illumina/25T8B25T/fastq/ACTAAGAC.2.fastq | 16 +
.../25T8B25T/fastq/ACTAAGAC.barcode_1.fastq | 16 +
.../fastq/ACTGTACC.1.fastq} | 0
.../fastq/ACTGTACC.2.fastq} | 0
.../fastq/ACTGTACC.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/ACTGTATC.1.fastq | 16 +
.../illumina/25T8B25T/fastq/ACTGTATC.2.fastq | 16 +
.../25T8B25T/fastq/ACTGTATC.barcode_1.fastq | 16 +
.../fastq/AGAAAAGA.1.fastq} | 0
.../fastq/AGAAAAGA.2.fastq} | 0
.../fastq/AGAAAAGA.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/AGCATGGA.1.fastq | 12 +
.../illumina/25T8B25T/fastq/AGCATGGA.2.fastq | 12 +
.../25T8B25T/fastq/AGCATGGA.barcode_1.fastq | 12 +
.../illumina/25T8B25T/fastq/AGGTAAGG.1.fastq | 16 +
.../illumina/25T8B25T/fastq/AGGTAAGG.2.fastq | 16 +
.../25T8B25T/fastq/AGGTAAGG.barcode_1.fastq | 16 +
.../illumina/25T8B25T/fastq/AGGTCGCA.1.fastq | 16 +
.../illumina/25T8B25T/fastq/AGGTCGCA.2.fastq | 16 +
.../25T8B25T/fastq/AGGTCGCA.barcode_1.fastq | 16 +
.../illumina/25T8B25T/fastq/ATTATCAA.1.fastq | 20 +
.../illumina/25T8B25T/fastq/ATTATCAA.2.fastq | 20 +
.../25T8B25T/fastq/ATTATCAA.barcode_1.fastq | 20 +
.../illumina/25T8B25T/fastq/ATTCCTCT.1.fastq | 16 +
.../illumina/25T8B25T/fastq/ATTCCTCT.2.fastq | 16 +
.../25T8B25T/fastq/ATTCCTCT.barcode_1.fastq | 16 +
.../illumina/25T8B25T/fastq/CAACTCTC.1.fastq | 20 +
.../illumina/25T8B25T/fastq/CAACTCTC.2.fastq | 20 +
.../25T8B25T/fastq/CAACTCTC.barcode_1.fastq | 20 +
.../fastq/CAATAGAC.1.fastq} | 0
.../fastq/CAATAGAC.2.fastq} | 0
.../fastq/CAATAGAC.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/CAATAGTC.1.fastq | 28 +
.../illumina/25T8B25T/fastq/CAATAGTC.2.fastq | 28 +
.../25T8B25T/fastq/CAATAGTC.barcode_1.fastq | 28 +
.../fastq/CAGCGGAT.1.fastq} | 0
.../fastq/CAGCGGAT.2.fastq} | 0
.../fastq/CAGCGGAT.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/CAGCGGTA.1.fastq | 20 +
.../illumina/25T8B25T/fastq/CAGCGGTA.2.fastq | 20 +
.../25T8B25T/fastq/CAGCGGTA.barcode_1.fastq | 20 +
.../illumina/25T8B25T/fastq/CCAACATT.1.fastq | 28 +
.../illumina/25T8B25T/fastq/CCAACATT.2.fastq | 28 +
.../25T8B25T/fastq/CCAACATT.barcode_1.fastq | 28 +
.../illumina/25T8B25T/fastq/CCAGCACC.1.fastq | 12 +
.../illumina/25T8B25T/fastq/CCAGCACC.2.fastq | 12 +
.../25T8B25T/fastq/CCAGCACC.barcode_1.fastq | 12 +
.../fastq/CCATGCGT.1.fastq} | 0
.../fastq/CCATGCGT.2.fastq} | 0
.../fastq/CCATGCGT.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/CGCCTTCC.1.fastq | 8 +
.../illumina/25T8B25T/fastq/CGCCTTCC.2.fastq | 8 +
.../25T8B25T/fastq/CGCCTTCC.barcode_1.fastq | 8 +
.../illumina/25T8B25T/fastq/CGCTATGT.1.fastq | 20 +
.../illumina/25T8B25T/fastq/CGCTATGT.2.fastq | 20 +
.../25T8B25T/fastq/CGCTATGT.barcode_1.fastq | 20 +
.../illumina/25T8B25T/fastq/CTAACTCG.1.fastq | 16 +
.../illumina/25T8B25T/fastq/CTAACTCG.2.fastq | 16 +
.../25T8B25T/fastq/CTAACTCG.barcode_1.fastq | 16 +
.../N-N-N.sam => 25T8B25T/fastq/CTATGCGC.1.fastq} | 0
.../N-N.sam => 25T8B25T/fastq/CTATGCGC.2.fastq} | 0
.../fastq/CTATGCGC.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/CTATGCGT.1.fastq | 28 +
.../illumina/25T8B25T/fastq/CTATGCGT.2.fastq | 28 +
.../25T8B25T/fastq/CTATGCGT.barcode_1.fastq | 28 +
.../illumina/25T8B25T/fastq/CTGCGGAT.1.fastq | 12 +
.../illumina/25T8B25T/fastq/CTGCGGAT.2.fastq | 12 +
.../25T8B25T/fastq/CTGCGGAT.barcode_1.fastq | 12 +
.../illumina/25T8B25T/fastq/CTGTAATC.1.fastq | 24 +
.../illumina/25T8B25T/fastq/CTGTAATC.2.fastq | 24 +
.../25T8B25T/fastq/CTGTAATC.barcode_1.fastq | 24 +
.../fastq/GAAAAAAA.1.fastq} | 0
.../s_1_1.bcl => 25T8B25T/fastq/GAAAAAAA.2.fastq} | 0
.../fastq/GAAAAAAA.barcode_1.fastq} | 0
.../fastq/GAACGAT..1.fastq} | 0
.../fastq/GAACGAT..2.fastq} | 0
.../fastq/GAACGAT..barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/GAAGGAAG.1.fastq | 12 +
.../illumina/25T8B25T/fastq/GAAGGAAG.2.fastq | 12 +
.../25T8B25T/fastq/GAAGGAAG.barcode_1.fastq | 12 +
.../illumina/25T8B25T/fastq/GACCAGGA.1.fastq | 28 +
.../illumina/25T8B25T/fastq/GACCAGGA.2.fastq | 28 +
.../25T8B25T/fastq/GACCAGGA.barcode_1.fastq | 28 +
.../fastq/GACCAGGC.1.fastq} | 0
.../fastq/GACCAGGC.2.fastq} | 0
.../fastq/GACCAGGC.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/GACCGTTG.1.fastq | 16 +
.../illumina/25T8B25T/fastq/GACCGTTG.2.fastq | 16 +
.../25T8B25T/fastq/GACCGTTG.barcode_1.fastq | 16 +
.../illumina/25T8B25T/fastq/GACCTAAC.1.fastq | 4 +
.../illumina/25T8B25T/fastq/GACCTAAC.2.fastq | 4 +
.../25T8B25T/fastq/GACCTAAC.barcode_1.fastq | 4 +
.../illumina/25T8B25T/fastq/GATATCCA.1.fastq | 12 +
.../illumina/25T8B25T/fastq/GATATCCA.2.fastq | 12 +
.../25T8B25T/fastq/GATATCCA.barcode_1.fastq | 12 +
.../illumina/25T8B25T/fastq/GCCGTCGA.1.fastq | 20 +
.../illumina/25T8B25T/fastq/GCCGTCGA.2.fastq | 20 +
.../25T8B25T/fastq/GCCGTCGA.barcode_1.fastq | 20 +
.../illumina/25T8B25T/fastq/GCCTAGCC.1.fastq | 20 +
.../illumina/25T8B25T/fastq/GCCTAGCC.2.fastq | 20 +
.../25T8B25T/fastq/GCCTAGCC.barcode_1.fastq | 20 +
.../illumina/25T8B25T/fastq/GTAACATC.1.fastq | 8 +
.../illumina/25T8B25T/fastq/GTAACATC.2.fastq | 8 +
.../25T8B25T/fastq/GTAACATC.barcode_1.fastq | 8 +
.../illumina/25T8B25T/fastq/GTCCACAG.1.fastq | 8 +
.../illumina/25T8B25T/fastq/GTCCACAG.2.fastq | 8 +
.../25T8B25T/fastq/GTCCACAG.barcode_1.fastq | 8 +
.../sf/picard/illumina/25T8B25T/fastq/N.1.fastq | 64 +
.../sf/picard/illumina/25T8B25T/fastq/N.2.fastq | 64 +
.../illumina/25T8B25T/fastq/N.barcode_1.fastq | 64 +
.../illumina/25T8B25T/fastq/TAAGCACA.1.fastq | 8 +
.../illumina/25T8B25T/fastq/TAAGCACA.2.fastq | 8 +
.../25T8B25T/fastq/TAAGCACA.barcode_1.fastq | 8 +
.../fastq/TACCGTCT.1.fastq} | 0
.../fastq/TACCGTCT.2.fastq} | 0
.../fastq/TACCGTCT.barcode_1.fastq} | 0
.../fastq/TAGCGGTA.1.fastq} | 0
.../fastq/TAGCGGTA.2.fastq} | 0
.../fastq/TAGCGGTA.barcode_1.fastq} | 0
.../fastq/TATCAGCC.1.fastq} | 0
.../fastq/TATCAGCC.2.fastq} | 0
.../fastq/TATCAGCC.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/TATCCAGG.1.fastq | 16 +
.../illumina/25T8B25T/fastq/TATCCAGG.2.fastq | 16 +
.../25T8B25T/fastq/TATCCAGG.barcode_1.fastq | 16 +
.../fastq/TATCCATG.1.fastq} | 0
.../fastq/TATCCATG.2.fastq} | 0
.../fastq/TATCCATG.barcode_1.fastq} | 0
.../fastq/TATCTCGG.1.fastq} | 0
.../fastq/TATCTCGG.2.fastq} | 0
.../fastq/TATCTCGG.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/TATCTGCC.1.fastq | 28 +
.../illumina/25T8B25T/fastq/TATCTGCC.2.fastq | 28 +
.../25T8B25T/fastq/TATCTGCC.barcode_1.fastq | 28 +
.../fastq/TCCGTCTA.1.fastq} | 0
.../fastq/TCCGTCTA.2.fastq} | 0
.../fastq/TCCGTCTA.barcode_1.fastq} | 0
.../illumina/25T8B25T/fastq/TCGCTAGA.1.fastq | 20 +
.../illumina/25T8B25T/fastq/TCGCTAGA.2.fastq | 20 +
.../25T8B25T/fastq/TCGCTAGA.barcode_1.fastq | 20 +
.../illumina/25T8B25T/fastq/TCTGCAAG.1.fastq | 4 +
.../illumina/25T8B25T/fastq/TCTGCAAG.2.fastq | 4 +
.../25T8B25T/fastq/TCTGCAAG.barcode_1.fastq | 4 +
.../illumina/25T8B25T/fastq/TGCAAGTA.1.fastq | 8 +
.../illumina/25T8B25T/fastq/TGCAAGTA.2.fastq | 8 +
.../25T8B25T/fastq/TGCAAGTA.barcode_1.fastq | 8 +
.../illumina/25T8B25T/fastq/TGCTGCTG.1.fastq | 16 +
.../illumina/25T8B25T/fastq/TGCTGCTG.2.fastq | 16 +
.../25T8B25T/fastq/TGCTGCTG.barcode_1.fastq | 16 +
.../illumina/25T8B25T/fastq/TGTAACTC.1.fastq | 4 +
.../illumina/25T8B25T/fastq/TGTAACTC.2.fastq | 4 +
.../25T8B25T/fastq/TGTAACTC.barcode_1.fastq | 4 +
.../illumina/25T8B25T/fastq/TGTAATCA.1.fastq | 12 +
.../illumina/25T8B25T/fastq/TGTAATCA.2.fastq | 12 +
.../25T8B25T/fastq/TGTAATCA.barcode_1.fastq | 12 +
.../illumina/25T8B25T/fastq/TTGTCTAT.1.fastq | 16 +
.../illumina/25T8B25T/fastq/TTGTCTAT.2.fastq | 16 +
.../25T8B25T/fastq/TTGTCTAT.barcode_1.fastq | 16 +
.../picard/illumina/25T8B25T/fastq/barcode.params | 63 +
.../illumina/25T8B25T/fastq/mp_barcode.params | 63 +
.../illumina/25T8B25T/fastq/nonBarcoded.1.fastq | 720 +++++++++
.../illumina/25T8B25T/fastq/nonBarcoded.2.fastq | 720 +++++++++
.../illumina/25T8B25T/fastq/testMultiplex.1.fastq | 720 +++++++++
.../25T8B25T/fastq/testMultiplex.barcode_1.fastq | 720 +++++++++
.../25T8B25T/fastq/testMultiplexRH.1.fastq | 720 +++++++++
.../25T8B25T/fastq/testMultiplexRH.2.fastq | 720 +++++++++
.../25T8B25T/fastq/testMultiplexRH.barcode_1.fastq | 720 +++++++++
.../sf/picard/illumina/25T8B25T/sams/AAAAAAAA.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/AAAAGAAG.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/AACAATGG.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/AACGCATT.sam | 16 +
.../sf/picard/illumina/25T8B25T/sams/ACAAAATT.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/ACAGGTAT.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/ACAGTTGA.sam | 6 +
.../sf/picard/illumina/25T8B25T/sams/ACCAGTTG.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/ACGAAATC.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/ACTAAGAC.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/ACTGTACC.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/ACTGTATC.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/AGAAAAGA.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/AGCATGGA.sam | 8 +
.../sf/picard/illumina/25T8B25T/sams/AGGTAAGG.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/AGGTCGCA.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/ATTATCAA.sam | 12 +
.../sf/picard/illumina/25T8B25T/sams/ATTCCTCT.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/CAACTCTC.sam | 12 +
.../sf/picard/illumina/25T8B25T/sams/CAATAGAC.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/CAATAGTC.sam | 16 +
.../sf/picard/illumina/25T8B25T/sams/CAGCGGAT.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/CAGCGGTA.sam | 12 +
.../sf/picard/illumina/25T8B25T/sams/CCAACATT.sam | 16 +
.../sf/picard/illumina/25T8B25T/sams/CCAGCACC.sam | 8 +
.../sf/picard/illumina/25T8B25T/sams/CCATGCGT.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/CGCCTTCC.sam | 6 +
.../sf/picard/illumina/25T8B25T/sams/CGCTATGT.sam | 12 +
.../sf/picard/illumina/25T8B25T/sams/CTAACTCG.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/CTATGCGC.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/CTATGCGT.sam | 16 +
.../sf/picard/illumina/25T8B25T/sams/CTGCGGAT.sam | 8 +
.../sf/picard/illumina/25T8B25T/sams/CTGTAATC.sam | 14 +
.../sf/picard/illumina/25T8B25T/sams/GAAAAAAA.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/GAACGAT..sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/GAAGGAAG.sam | 8 +
.../sf/picard/illumina/25T8B25T/sams/GACCAGGA.sam | 16 +
.../sf/picard/illumina/25T8B25T/sams/GACCAGGC.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/GACCGTTG.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/GACCTAAC.sam | 4 +
.../sf/picard/illumina/25T8B25T/sams/GATATCCA.sam | 8 +
.../sf/picard/illumina/25T8B25T/sams/GCCGTCGA.sam | 12 +
.../sf/picard/illumina/25T8B25T/sams/GCCTAGCC.sam | 12 +
.../sf/picard/illumina/25T8B25T/sams/GTAACATC.sam | 6 +
.../sf/picard/illumina/25T8B25T/sams/GTCCACAG.sam | 6 +
.../net/sf/picard/illumina/25T8B25T/sams/N.sam | 34 +
.../sf/picard/illumina/25T8B25T/sams/TAAGCACA.sam | 6 +
.../sf/picard/illumina/25T8B25T/sams/TACCGTCT.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/TAGCGGTA.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/TATCAGCC.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/TATCCAGG.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/TATCCATG.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/TATCTCGG.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/TATCTGCC.sam | 16 +
.../sf/picard/illumina/25T8B25T/sams/TCCGTCTA.sam | 2 +
.../sf/picard/illumina/25T8B25T/sams/TCGCTAGA.sam | 12 +
.../sf/picard/illumina/25T8B25T/sams/TCTGCAAG.sam | 4 +
.../sf/picard/illumina/25T8B25T/sams/TGCAAGTA.sam | 6 +
.../sf/picard/illumina/25T8B25T/sams/TGCTGCTG.sam | 10 +
.../sf/picard/illumina/25T8B25T/sams/TGTAACTC.sam | 4 +
.../sf/picard/illumina/25T8B25T/sams/TGTAATCA.sam | 8 +
.../sf/picard/illumina/25T8B25T/sams/TTGTCTAT.sam | 10 +
.../picard/illumina/25T8B25T/sams/barcode.params | 63 +
.../sams/multiplexed_positive_rgtags.params | 63 +
.../picard/illumina/25T8B25T/sams/nonBarcoded.sam | 182 +++
.../Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C63.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl | Bin 0 -> 64 bytes
.../Intensities/BaseCalls/L001/s_1_1101.filter | Bin 0 -> 72 bytes
.../Intensities/BaseCalls/s_1_1101_barcode.txt | 60 +
.../25T8B8B25T/Data/Intensities/L001/s_1_1101.locs | Bin 0 -> 492 bytes
.../25T8B8B25T/fastq/AACTTGACGCTCTCTT.1.fastq | 4 +
.../25T8B8B25T/fastq/AACTTGACGCTCTCTT.2.fastq | 4 +
.../fastq/AACTTGACGCTCTCTT.barcode_1.fastq | 4 +
.../fastq/AACTTGACGCTCTCTT.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/AAGACACTAGTCACCT.1.fastq | 4 +
.../25T8B8B25T/fastq/AAGACACTAGTCACCT.2.fastq | 4 +
.../fastq/AAGACACTAGTCACCT.barcode_1.fastq | 4 +
.../fastq/AAGACACTAGTCACCT.barcode_2.fastq | 4 +
.../fastq/AAGACACTAGTCTCCT.1.fastq} | 0
.../fastq/AAGACACTAGTCTCCT.2.fastq} | 0
.../fastq/AAGACACTAGTCTCCT.barcode_1.fastq} | 0
.../fastq/AAGACACTAGTCTCCT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/ACAGGTATCACTTCAT.1.fastq | 4 +
.../25T8B8B25T/fastq/ACAGGTATCACTTCAT.2.fastq | 4 +
.../fastq/ACAGGTATCACTTCAT.barcode_1.fastq | 4 +
.../fastq/ACAGGTATCACTTCAT.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/ACAGTTGAATCTTCTC.1.fastq | 8 +
.../25T8B8B25T/fastq/ACAGTTGAATCTTCTC.2.fastq | 8 +
.../fastq/ACAGTTGAATCTTCTC.barcode_1.fastq | 8 +
.../fastq/ACAGTTGAATCTTCTC.barcode_2.fastq | 8 +
.../25T8B8B25T/fastq/ACCAACTGCATCACTT.1.fastq | 4 +
.../25T8B8B25T/fastq/ACCAACTGCATCACTT.2.fastq | 4 +
.../fastq/ACCAACTGCATCACTT.barcode_1.fastq | 4 +
.../fastq/ACCAACTGCATCACTT.barcode_2.fastq | 4 +
.../fastq/ACCTACTGCTTCCCTT.1.fastq} | 0
.../fastq/ACCTACTGCTTCCCTT.2.fastq} | 0
.../fastq/ACCTACTGCTTCCCTT.barcode_1.fastq} | 0
.../fastq/ACCTACTGCTTCCCTT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/ACTAAGACGTCCTCAT.1.fastq | 4 +
.../25T8B8B25T/fastq/ACTAAGACGTCCTCAT.2.fastq | 4 +
.../fastq/ACTAAGACGTCCTCAT.barcode_1.fastq | 4 +
.../fastq/ACTAAGACGTCCTCAT.barcode_2.fastq | 4 +
.../fastq/AGGTCGCATTCCTTTC.1.fastq} | 0
.../fastq/AGGTCGCATTCCTTTC.2.fastq} | 0
.../fastq/AGGTCGCATTCCTTTC.barcode_1.fastq} | 0
.../fastq/AGGTCGCATTCCTTTC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/AGGTGCGAGACATTAA.1.fastq | 4 +
.../25T8B8B25T/fastq/AGGTGCGAGACATTAA.2.fastq | 4 +
.../fastq/AGGTGCGAGACATTAA.barcode_1.fastq | 4 +
.../fastq/AGGTGCGAGACATTAA.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/AGGTTATCTTAGCCAG.1.fastq | 4 +
.../25T8B8B25T/fastq/AGGTTATCTTAGCCAG.2.fastq | 4 +
.../fastq/AGGTTATCTTAGCCAG.barcode_1.fastq | 4 +
.../fastq/AGGTTATCTTAGCCAG.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/AGTTGCTTTGACTTGG.1.fastq | 4 +
.../25T8B8B25T/fastq/AGTTGCTTTGACTTGG.2.fastq | 4 +
.../fastq/AGTTGCTTTGACTTGG.barcode_1.fastq | 4 +
.../fastq/AGTTGCTTTGACTTGG.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.1.fastq | 4 +
.../25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.2.fastq | 4 +
.../fastq/ATAGCGTCTTGGTCTG.barcode_1.fastq | 4 +
.../fastq/ATAGCGTCTTGGTCTG.barcode_2.fastq | 4 +
.../fastq/ATTATCAACACCATAC.1.fastq} | 0
.../fastq/ATTATCAACACCATAC.2.fastq} | 0
.../fastq/ATTATCAACACCATAC.barcode_1.fastq} | 0
.../fastq/ATTATCAACACCATAC.barcode_2.fastq} | 0
.../fastq/ATTGTCTGGATTCACA.1.fastq} | 0
.../fastq/ATTGTCTGGATTCACA.2.fastq} | 0
.../fastq/ATTGTCTGGATTCACA.barcode_1.fastq} | 0
.../fastq/ATTGTCTGGATTCACA.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CAATAGTCCGACTCTC.1.fastq | 4 +
.../25T8B8B25T/fastq/CAATAGTCCGACTCTC.2.fastq | 4 +
.../fastq/CAATAGTCCGACTCTC.barcode_1.fastq | 4 +
.../fastq/CAATAGTCCGACTCTC.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/CAGCAAGGGCGATATT.1.fastq | 4 +
.../25T8B8B25T/fastq/CAGCAAGGGCGATATT.2.fastq | 4 +
.../fastq/CAGCAAGGGCGATATT.barcode_1.fastq | 4 +
.../fastq/CAGCAAGGGCGATATT.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/CAGCGGTAAGTACTGC.1.fastq | 4 +
.../25T8B8B25T/fastq/CAGCGGTAAGTACTGC.2.fastq | 4 +
.../fastq/CAGCGGTAAGTACTGC.barcode_1.fastq | 4 +
.../fastq/CAGCGGTAAGTACTGC.barcode_2.fastq | 4 +
.../fastq/CAGCGGTATGTACTGC.1.fastq} | 0
.../fastq/CAGCGGTATGTACTGC.2.fastq} | 0
.../fastq/CAGCGGTATGTACTGC.barcode_1.fastq} | 0
.../fastq/CAGCGGTATGTACTGC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CATGCTTATAGCATTG.1.fastq | 8 +
.../25T8B8B25T/fastq/CATGCTTATAGCATTG.2.fastq | 8 +
.../fastq/CATGCTTATAGCATTG.barcode_1.fastq | 8 +
.../fastq/CATGCTTATAGCATTG.barcode_2.fastq | 8 +
.../fastq/CATGCTTATAGCATTT.1.fastq} | 0
.../fastq/CATGCTTATAGCATTT.2.fastq} | 0
.../fastq/CATGCTTATAGCATTT.barcode_1.fastq} | 0
.../fastq/CATGCTTATAGCATTT.barcode_2.fastq} | 0
.../fastq/CATGCTTTTAGCATTG.1.fastq} | 0
.../fastq/CATGCTTTTAGCATTG.2.fastq} | 0
.../fastq/CATGCTTTTAGCATTG.barcode_1.fastq} | 0
.../fastq/CATGCTTTTAGCATTG.barcode_2.fastq} | 0
.../fastq/CATGTTCGCGCCTTTT.1.fastq} | 0
.../fastq/CATGTTCGCGCCTTTT.2.fastq} | 0
.../fastq/CATGTTCGCGCCTTTT.barcode_1.fastq} | 0
.../fastq/CATGTTCGCGCCTTTT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CCAGAGCTCAACTGAT.1.fastq | 8 +
.../25T8B8B25T/fastq/CCAGAGCTCAACTGAT.2.fastq | 8 +
.../fastq/CCAGAGCTCAACTGAT.barcode_1.fastq | 8 +
.../fastq/CCAGAGCTCAACTGAT.barcode_2.fastq | 8 +
.../fastq/CCCGATTTTCTCTCCC.1.fastq} | 0
.../fastq/CCCGATTTTCTCTCCC.2.fastq} | 0
.../fastq/CCCGATTTTCTCTCCC.barcode_1.fastq} | 0
.../fastq/CCCGATTTTCTCTCCC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CCTATGCCAATTGGCC.1.fastq | 4 +
.../25T8B8B25T/fastq/CCTATGCCAATTGGCC.2.fastq | 4 +
.../fastq/CCTATGCCAATTGGCC.barcode_1.fastq | 4 +
.../fastq/CCTATGCCAATTGGCC.barcode_2.fastq | 4 +
.../fastq/CCTATTCTTCGTTTTC.1.fastq} | 0
.../fastq/CCTATTCTTCGTTTTC.2.fastq} | 0
.../fastq/CCTATTCTTCGTTTTC.barcode_1.fastq} | 0
.../fastq/CCTATTCTTCGTTTTC.barcode_2.fastq} | 0
.../fastq/CCTCTTCTCTCGCTTT.1.fastq} | 0
.../fastq/CCTCTTCTCTCGCTTT.2.fastq} | 0
.../fastq/CCTCTTCTCTCGCTTT.barcode_1.fastq} | 0
.../fastq/CCTCTTCTCTCGCTTT.barcode_2.fastq} | 0
.../fastq/CCTCTTTCTTCTGCTC.1.fastq} | 0
.../fastq/CCTCTTTCTTCTGCTC.2.fastq} | 0
.../fastq/CCTCTTTCTTCTGCTC.barcode_1.fastq} | 0
.../fastq/CCTCTTTCTTCTGCTC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CCTTCGCAGAATCGAC.1.fastq | 4 +
.../25T8B8B25T/fastq/CCTTCGCAGAATCGAC.2.fastq | 4 +
.../fastq/CCTTCGCAGAATCGAC.barcode_1.fastq | 4 +
.../fastq/CCTTCGCAGAATCGAC.barcode_2.fastq | 4 +
.../fastq/CCTTCTTTTATCATTT.1.fastq} | 0
.../fastq/CCTTCTTTTATCATTT.2.fastq} | 0
.../fastq/CCTTCTTTTATCATTT.barcode_1.fastq} | 0
.../fastq/CCTTCTTTTATCATTT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CGCTATGTTTCACCTT.1.fastq | 4 +
.../25T8B8B25T/fastq/CGCTATGTTTCACCTT.2.fastq | 4 +
.../fastq/CGCTATGTTTCACCTT.barcode_1.fastq | 4 +
.../fastq/CGCTATGTTTCACCTT.barcode_2.fastq | 4 +
.../fastq/CGCTATGTTTCTCCTT.1.fastq} | 0
.../fastq/CGCTATGTTTCTCCTT.2.fastq} | 0
.../fastq/CGCTATGTTTCTCCTT.barcode_1.fastq} | 0
.../fastq/CGCTATGTTTCTCCTT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CTACCAGGTTCTTGGC.1.fastq | 4 +
.../25T8B8B25T/fastq/CTACCAGGTTCTTGGC.2.fastq | 4 +
.../fastq/CTACCAGGTTCTTGGC.barcode_1.fastq | 4 +
.../fastq/CTACCAGGTTCTTGGC.barcode_2.fastq | 4 +
.../fastq/CTCCCTCTTCCTTCTT.1.fastq} | 0
.../fastq/CTCCCTCTTCCTTCTT.2.fastq} | 0
.../fastq/CTCCCTCTTCCTTCTT.barcode_1.fastq} | 0
.../fastq/CTCCCTCTTCCTTCTT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/CTGTAATCCTATTAGC.1.fastq | 4 +
.../25T8B8B25T/fastq/CTGTAATCCTATTAGC.2.fastq | 4 +
.../fastq/CTGTAATCCTATTAGC.barcode_1.fastq | 4 +
.../fastq/CTGTAATCCTATTAGC.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/GACCAGGACCATCACA.1.fastq | 4 +
.../25T8B8B25T/fastq/GACCAGGACCATCACA.2.fastq | 4 +
.../fastq/GACCAGGACCATCACA.barcode_1.fastq | 4 +
.../fastq/GACCAGGACCATCACA.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/GCCGTCGAAGGTACCA.1.fastq | 8 +
.../25T8B8B25T/fastq/GCCGTCGAAGGTACCA.2.fastq | 8 +
.../fastq/GCCGTCGAAGGTACCA.barcode_1.fastq | 8 +
.../fastq/GCCGTCGAAGGTACCA.barcode_2.fastq | 8 +
.../fastq/GCCGTCGAAGGTACCC.1.fastq} | 0
.../fastq/GCCGTCGAAGGTACCC.2.fastq} | 0
.../fastq/GCCGTCGAAGGTACCC.barcode_1.fastq} | 0
.../fastq/GCCGTCGAAGGTACCC.barcode_2.fastq} | 0
.../fastq/GCCGTCGATGGTACCC.1.fastq} | 0
.../fastq/GCCGTCGATGGTACCC.2.fastq} | 0
.../fastq/GCCGTCGATGGTACCC.barcode_1.fastq} | 0
.../fastq/GCCGTCGATGGTACCC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/GCCTAGCCCTTGAATC.1.fastq | 4 +
.../25T8B8B25T/fastq/GCCTAGCCCTTGAATC.2.fastq | 4 +
.../fastq/GCCTAGCCCTTGAATC.barcode_1.fastq | 4 +
.../fastq/GCCTAGCCCTTGAATC.barcode_2.fastq | 4 +
.../fastq/GCTATCCACCTCCCCC.1.fastq} | 0
.../fastq/GCTATCCACCTCCCCC.2.fastq} | 0
.../fastq/GCTATCCACCTCCCCC.barcode_1.fastq} | 0
.../fastq/GCTATCCACCTCCCCC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/GTATAACAAATTCAAC.1.fastq | 4 +
.../25T8B8B25T/fastq/GTATAACAAATTCAAC.2.fastq | 4 +
.../fastq/GTATAACAAATTCAAC.barcode_1.fastq | 4 +
.../fastq/GTATAACAAATTCAAC.barcode_2.fastq | 4 +
.../fastq/GTATAACATATTCAAC.1.fastq} | 0
.../fastq/GTATAACATATTCAAC.2.fastq} | 0
.../fastq/GTATAACATATTCAAC.barcode_1.fastq} | 0
.../fastq/GTATAACATATTCAAC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/GTCTGATGGAACTTCG.1.fastq | 4 +
.../25T8B8B25T/fastq/GTCTGATGGAACTTCG.2.fastq | 4 +
.../fastq/GTCTGATGGAACTTCG.barcode_1.fastq | 4 +
.../fastq/GTCTGATGGAACTTCG.barcode_2.fastq | 4 +
.../fastq/GTCTGATGTCACTTCC.1.fastq} | 0
.../fastq/GTCTGATGTCACTTCC.2.fastq} | 0
.../fastq/GTCTGATGTCACTTCC.barcode_1.fastq} | 0
.../fastq/GTCTGATGTCACTTCC.barcode_2.fastq} | 0
.../sf/picard/illumina/25T8B8B25T/fastq/NN.1.fastq | 76 +
.../sf/picard/illumina/25T8B8B25T/fastq/NN.2.fastq | 76 +
.../illumina/25T8B8B25T/fastq/NN.barcode_1.fastq | 76 +
.../illumina/25T8B8B25T/fastq/NN.barcode_2.fastq | 76 +
.../25T8B8B25T/fastq/TACTTAGCGTCTGCAC.1.fastq | 8 +
.../25T8B8B25T/fastq/TACTTAGCGTCTGCAC.2.fastq | 8 +
.../fastq/TACTTAGCGTCTGCAC.barcode_1.fastq | 8 +
.../fastq/TACTTAGCGTCTGCAC.barcode_2.fastq | 8 +
.../fastq/TCCCCGTTCCAACTTC.1.fastq} | 0
.../fastq/TCCCCGTTCCAACTTC.2.fastq} | 0
.../fastq/TCCCCGTTCCAACTTC.barcode_1.fastq} | 0
.../fastq/TCCCCGTTCCAACTTC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/TCCTTGGTGCTGCACT.1.fastq | 4 +
.../25T8B8B25T/fastq/TCCTTGGTGCTGCACT.2.fastq | 4 +
.../fastq/TCCTTGGTGCTGCACT.barcode_1.fastq | 4 +
.../fastq/TCCTTGGTGCTGCACT.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/TCGCCTTGCCAACGCT.1.fastq | 4 +
.../25T8B8B25T/fastq/TCGCCTTGCCAACGCT.2.fastq | 4 +
.../fastq/TCGCCTTGCCAACGCT.barcode_1.fastq | 4 +
.../fastq/TCGCCTTGCCAACGCT.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/TGCAAGTACGAACTTC.1.fastq | 8 +
.../25T8B8B25T/fastq/TGCAAGTACGAACTTC.2.fastq | 8 +
.../fastq/TGCAAGTACGAACTTC.barcode_1.fastq | 8 +
.../fastq/TGCAAGTACGAACTTC.barcode_2.fastq | 8 +
.../25T8B8B25T/fastq/TGCTCGACTTCACAGA.1.fastq | 4 +
.../25T8B8B25T/fastq/TGCTCGACTTCACAGA.2.fastq | 4 +
.../fastq/TGCTCGACTTCACAGA.barcode_1.fastq | 4 +
.../fastq/TGCTCGACTTCACAGA.barcode_2.fastq | 4 +
.../fastq/TGCTCGACTTCACAGT.1.fastq} | 0
.../fastq/TGCTCGACTTCACAGT.2.fastq} | 0
.../fastq/TGCTCGACTTCACAGT.barcode_1.fastq} | 0
.../fastq/TGCTCGACTTCACAGT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/TGTAATCACCTCTAAC.1.fastq | 4 +
.../25T8B8B25T/fastq/TGTAATCACCTCTAAC.2.fastq | 4 +
.../fastq/TGTAATCACCTCTAAC.barcode_1.fastq | 4 +
.../fastq/TGTAATCACCTCTAAC.barcode_2.fastq | 4 +
.../fastq/TGTATCTCTTACTCTT.1.fastq} | 0
.../fastq/TGTATCTCTTACTCTT.2.fastq} | 0
.../fastq/TGTATCTCTTACTCTT.barcode_1.fastq} | 0
.../fastq/TGTATCTCTTACTCTT.barcode_2.fastq} | 0
.../fastq/TGTCGGTTTTTTGCTT.1.fastq} | 0
.../fastq/TGTCGGTTTTTTGCTT.2.fastq} | 0
.../fastq/TGTCGGTTTTTTGCTT.barcode_1.fastq} | 0
.../fastq/TGTCGGTTTTTTGCTT.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/TGTTCCGAAACCTCTT.1.fastq | 4 +
.../25T8B8B25T/fastq/TGTTCCGAAACCTCTT.2.fastq | 4 +
.../fastq/TGTTCCGAAACCTCTT.barcode_1.fastq | 4 +
.../fastq/TGTTCCGAAACCTCTT.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/TTAATCAGCTGGTATT.1.fastq | 4 +
.../25T8B8B25T/fastq/TTAATCAGCTGGTATT.2.fastq | 4 +
.../fastq/TTAATCAGCTGGTATT.barcode_1.fastq | 4 +
.../fastq/TTAATCAGCTGGTATT.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/TTATATCTTCATGTCT.1.fastq | 4 +
.../25T8B8B25T/fastq/TTATATCTTCATGTCT.2.fastq | 4 +
.../fastq/TTATATCTTCATGTCT.barcode_1.fastq | 4 +
.../fastq/TTATATCTTCATGTCT.barcode_2.fastq | 4 +
.../fastq/TTCCCCAGTGCTTTTA.1.fastq} | 0
.../fastq/TTCCCCAGTGCTTTTA.2.fastq} | 0
.../fastq/TTCCCCAGTGCTTTTA.barcode_1.fastq} | 0
.../fastq/TTCCCCAGTGCTTTTA.barcode_2.fastq} | 0
.../fastq/TTCCTCCTCACCATCC.1.fastq} | 0
.../fastq/TTCCTCCTCACCATCC.2.fastq} | 0
.../fastq/TTCCTCCTCACCATCC.barcode_1.fastq} | 0
.../fastq/TTCCTCCTCACCATCC.barcode_2.fastq} | 0
.../fastq/TTCTCATCTTCCTTCC.1.fastq} | 0
.../fastq/TTCTCATCTTCCTTCC.2.fastq} | 0
.../fastq/TTCTCATCTTCCTTCC.barcode_1.fastq} | 0
.../fastq/TTCTCATCTTCCTTCC.barcode_2.fastq} | 0
.../25T8B8B25T/fastq/TTGAATAGATATCCGA.1.fastq | 4 +
.../25T8B8B25T/fastq/TTGAATAGATATCCGA.2.fastq | 4 +
.../fastq/TTGAATAGATATCCGA.barcode_1.fastq | 4 +
.../fastq/TTGAATAGATATCCGA.barcode_2.fastq | 4 +
.../25T8B8B25T/fastq/barcode_double.params | 65 +
.../sf/picard/illumina/25T8B8B25T/library.params | 65 +
.../picard/illumina/25T8B8B25T/sams/AACTTGAC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/AAGACACT.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/ACAGGTAT.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/ACAGTTGA.sam | 6 +
.../picard/illumina/25T8B8B25T/sams/ACCAACTG.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/ACCTACTG.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/ACTAAGAC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/AGGTCGCA.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/AGGTGCGA.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/AGGTTATC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/AGTTGCTT.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/ATAGCGTC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/ATTATCAA.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/ATTGTCTG.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CAATAGTC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/CAGCAAGG.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/CAGCGGTA.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/CATGCTTA.sam | 6 +
.../picard/illumina/25T8B8B25T/sams/CATGCTTT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CATGTTCG.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CCAGAGCT.sam | 6 +
.../picard/illumina/25T8B8B25T/sams/CCCGATTT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CCTATGCC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/CCTATTCT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CCTCTTCT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CCTCTTTC.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CCTTCGCA.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/CCTTCTTT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CGCTATGT.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/CTACCAGG.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/CTCCCTCT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/CTGTAATC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/GACCAGGA.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/GCCGTCGA.sam | 6 +
.../picard/illumina/25T8B8B25T/sams/GCCTAGCC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/GCTATCCA.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/GTATAACA.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/GTCTGATG.sam | 4 +
.../net/sf/picard/illumina/25T8B8B25T/sams/N.sam | 40 +
.../picard/illumina/25T8B8B25T/sams/TACTTAGC.sam | 6 +
.../picard/illumina/25T8B8B25T/sams/TCCCCGTT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/TCCTTGGT.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/TCGCCTTG.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/TGCAAGTA.sam | 6 +
.../picard/illumina/25T8B8B25T/sams/TGCTCGAC.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/TGTAATCA.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/TGTATCTC.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/TGTCGGTT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/TGTTCCGA.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/TTAATCAG.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/TTATATCT.sam | 4 +
.../picard/illumina/25T8B8B25T/sams/TTCCCCAG.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/TTCCTCCT.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/TTCTCATC.sam | 2 +
.../picard/illumina/25T8B8B25T/sams/TTGAATAG.sam | 4 +
.../illumina/25T8B8B25T/sams/barcode_double.params | 65 +
.../Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C1.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C1.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C10.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C10.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C11.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C11.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C12.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C12.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C13.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C13.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C14.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C14.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C15.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C15.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C16.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C16.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C17.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C17.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C18.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C18.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C19.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C19.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C2.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C2.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C20.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C20.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C21.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C21.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C22.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C22.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C23.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C23.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C24.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C24.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C25.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C25.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C26.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C26.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C27.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C27.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C28.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C28.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C29.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C29.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C3.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C3.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C30.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C30.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C31.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C31.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C32.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C32.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C33.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C33.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C34.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C34.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C35.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C35.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C36.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C36.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C37.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C37.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C38.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C38.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C39.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C39.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C4.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C4.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C40.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C40.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C41.1/s_1_1201.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C41.1/s_1_2101.bcl | Bin 24 -> 0 bytes
.../Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl | Bin 24 -> 0 bytes
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.../ExtractIlluminaBarcodes/s_2_1_0002_qseq.txt | 23 -
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.../IlluminaBasecallsToFastqTest/AACTTGAC.1.fastq | 52 -
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.../IlluminaBasecallsToFastqTest/AAGGATGT.1.fastq | 52 -
.../AAGGATGT.barcode_1.fastq | 52 -
.../AAGGATGTTTCGCTGA.1.fastq | 52 -
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.../AAGGATGTTTCGCTGA.barcode_2.fastq | 52 -
.../IlluminaBasecallsToFastqTest/ACCAACTG.1.fastq | 36 -
.../ACCAACTG.barcode_1.fastq | 36 -
.../ACCAACTGTGTCGGAT.1.fastq | 36 -
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.../IlluminaBasecallsToFastqTest/AGCAATTC.1.fastq | 32 -
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.../AGCAATTCTGCTCGAC.barcode_2.fastq | 32 -
.../IlluminaBasecallsToFastqTest/AGTTGCTT.1.fastq | 32 -
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.../AGTTGCTTTCTGGCGA.barcode_1.fastq | 32 -
.../AGTTGCTTTCTGGCGA.barcode_2.fastq | 32 -
.../IlluminaBasecallsToFastqTest/ATTATGTT.1.fastq | 12 -
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.../IlluminaBasecallsToFastqTest/CACATCCT.1.fastq | 36 -
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.../IlluminaBasecallsToFastqTest/CAGGAGCC.1.fastq | 36 -
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.../IlluminaBasecallsToFastqTest/CATAGCGA.1.fastq | 48 -
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.../CATAGCGAGGTCCAGA.barcode_2.fastq | 48 -
.../IlluminaBasecallsToFastqTest/CATGCTTA.1.fastq | 20 -
.../CATGCTTA.barcode_1.fastq | 20 -
.../CATGCTTAGCACATCT.1.fastq | 20 -
.../CATGCTTAGCACATCT.barcode_1.fastq | 20 -
.../CATGCTTAGCACATCT.barcode_2.fastq | 20 -
.../IlluminaBasecallsToFastqTest/CCAGTTAG.1.fastq | 44 -
.../CCAGTTAG.barcode_1.fastq | 44 -
.../CCAGTTAGGCACACGA.1.fastq | 44 -
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.../IlluminaBasecallsToFastqTest/CTACCAGG.1.fastq | 24 -
.../CTACCAGG.barcode_1.fastq | 24 -
.../CTACCAGGCCTACCAT.1.fastq | 24 -
.../CTACCAGGCCTACCAT.barcode_1.fastq | 24 -
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.../IlluminaBasecallsToFastqTest/GCACACGA.1.fastq | 36 -
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.../GCACACGACCAGTTAG.barcode_2.fastq | 36 -
.../IlluminaBasecallsToFastqTest/GCACATCT.1.fastq | 12 -
.../GCACATCT.barcode_1.fastq | 12 -
.../GCACATCTCATGCTTA.1.fastq | 12 -
.../GCACATCTCATGCTTA.barcode_1.fastq | 12 -
.../GCACATCTCATGCTTA.barcode_2.fastq | 12 -
.../IlluminaBasecallsToFastqTest/GGTCCAGA.1.fastq | 28 -
.../GGTCCAGA.barcode_1.fastq | 28 -
.../GGTCCAGACATAGCGA.1.fastq | 28 -
.../GGTCCAGACATAGCGA.barcode_1.fastq | 28 -
.../GGTCCAGACATAGCGA.barcode_2.fastq | 28 -
.../IlluminaBasecallsToFastqTest/GTATAACA.1.fastq | 40 -
.../GTATAACA.barcode_1.fastq | 40 -
.../GTATAACACAGGAGCC.1.fastq | 40 -
.../GTATAACACAGGAGCC.barcode_1.fastq | 40 -
.../GTATAACACAGGAGCC.barcode_2.fastq | 40 -
.../IlluminaBasecallsToFastqTest/N.1.fastq | 892 -----------
.../IlluminaBasecallsToFastqTest/N.barcode_1.fastq | 892 -----------
.../IlluminaBasecallsToFastqTest/NN.1.fastq | 892 -----------
.../NN.barcode_1.fastq | 892 -----------
.../NN.barcode_2.fastq | 892 -----------
.../IlluminaBasecallsToFastqTest/TACTTAGC.1.fastq | 32 -
.../TACTTAGC.barcode_1.fastq | 32 -
.../TACTTAGCCACATCCT.1.fastq | 32 -
.../TACTTAGCCACATCCT.barcode_1.fastq | 32 -
.../TACTTAGCCACATCCT.barcode_2.fastq | 32 -
.../IlluminaBasecallsToFastqTest/TCGGAATG.1.fastq | 28 -
.../TCGGAATG.barcode_1.fastq | 28 -
.../TCGGAATGATTATGTT.1.fastq | 28 -
.../TCGGAATGATTATGTT.barcode_1.fastq | 28 -
.../TCGGAATGATTATGTT.barcode_2.fastq | 28 -
.../IlluminaBasecallsToFastqTest/TCTGGCGA.1.fastq | 20 -
.../TCTGGCGA.barcode_1.fastq | 20 -
.../TCTGGCGAAGTTGCTT.1.fastq | 20 -
.../TCTGGCGAAGTTGCTT.barcode_1.fastq | 20 -
.../TCTGGCGAAGTTGCTT.barcode_2.fastq | 20 -
.../IlluminaBasecallsToFastqTest/TGCTCGAC.1.fastq | 20 -
.../TGCTCGAC.barcode_1.fastq | 20 -
.../TGCTCGACAGCAATTC.1.fastq | 20 -
.../TGCTCGACAGCAATTC.barcode_1.fastq | 20 -
.../TGCTCGACAGCAATTC.barcode_2.fastq | 20 -
.../IlluminaBasecallsToFastqTest/TGTCGGAT.1.fastq | 16 -
.../TGTCGGAT.barcode_1.fastq | 16 -
.../TGTCGGATACCAACTG.1.fastq | 16 -
.../TGTCGGATACCAACTG.barcode_1.fastq | 16 -
.../TGTCGGATACCAACTG.barcode_2.fastq | 16 -
.../IlluminaBasecallsToFastqTest/TTCGCTGA.1.fastq | 20 -
.../TTCGCTGA.barcode_1.fastq | 20 -
.../TTCGCTGAAAGGATGT.1.fastq | 20 -
.../TTCGCTGAAAGGATGT.barcode_1.fastq | 20 -
.../TTCGCTGAAAGGATGT.barcode_2.fastq | 20 -
.../IlluminaBasecallsToFastqTest/TTGAGCCT.1.fastq | 24 -
.../TTGAGCCT.barcode_1.fastq | 24 -
.../TTGAGCCTAACTTGAC.1.fastq | 24 -
.../TTGAGCCTAACTTGAC.barcode_1.fastq | 24 -
.../TTGAGCCTAACTTGAC.barcode_2.fastq | 24 -
.../IlluminaBasecallsToFastqTest/barcode.params | 26 -
.../barcode_double.params | 26 -
.../nonBarcoded.1.fastq | 240 ---
.../nonBarcoded.2.fastq | 240 ---
.../testMultiplex.1.fastq | 1600 --------------------
.../testMultiplex.barcode_1.fastq | 1600 --------------------
.../IlluminaBasecallsToSamTest/AACTTGAC.sam | 15 -
.../AACTTGACTTGAGCCT.sam | 15 -
.../IlluminaBasecallsToSamTest/AAGGATGT.sam | 15 -
.../AAGGATGTTTCGCTGA.sam | 15 -
.../IlluminaBasecallsToSamTest/ACCAACTG.sam | 11 -
.../ACCAACTGTGTCGGAT.sam | 11 -
.../IlluminaBasecallsToSamTest/AGCAATTC.sam | 10 -
.../AGCAATTCTGCTCGAC.sam | 10 -
.../IlluminaBasecallsToSamTest/AGTTGCTT.sam | 10 -
.../AGTTGCTTTCTGGCGA.sam | 10 -
.../IlluminaBasecallsToSamTest/ATTATGTT.sam | 5 -
.../ATTATGTTTCGGAATG.sam | 5 -
.../IlluminaBasecallsToSamTest/CACATCCT.sam | 11 -
.../CACATCCTTACTTAGC.sam | 11 -
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.../illumina/IlluminaBasecallsToSamTest/N.sam | 225 ---
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.../IlluminaBasecallsToSamTest/TACTTAGC.sam | 10 -
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.../IlluminaBasecallsToSamTest/TCGGAATG.sam | 9 -
.../TCGGAATGATTATGTT.sam | 9 -
.../IlluminaBasecallsToSamTest/TCTGGCGA.sam | 7 -
.../TCTGGCGAAGTTGCTT.sam | 7 -
.../IlluminaBasecallsToSamTest/TGCTCGAC.sam | 7 -
.../TGCTCGACAGCAATTC.sam | 7 -
.../IlluminaBasecallsToSamTest/TGTCGGAT.sam | 6 -
.../TGTCGGATACCAACTG.sam | 6 -
.../IlluminaBasecallsToSamTest/TTCGCTGA.sam | 7 -
.../TTCGCTGAAAGGATGT.sam | 7 -
.../IlluminaBasecallsToSamTest/TTGAGCCT.sam | 8 -
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.../IlluminaBasecallsToSamTest/barcode.params | 26 -
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.../multiplexed_positive_rgtags.params | 26 -
.../negative_test.params | 25 -
.../IlluminaBasecallsToSamTest/nonBarcoded.sam | 122 --
.../nonMatchingBarcoded.sam | 225 ---
.../IlluminaBasecallsToSamTest/singleBarcoded.sam | 8 -
.../IlluminaTests/BasecallsDir/s_1_1_0001_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_1_1_0002_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_1_1_0003_qseq.txt | 20 -
.../IlluminaTests/BasecallsDir/s_1_2_0001_qseq.txt | 20 -
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.../IlluminaTests/BasecallsDir/s_6_3_0001_qseq.txt | 10 -
.../BasecallsDir/s_7_0001_barcode.txt | 200 ---
.../BasecallsDir/s_7_0002_barcode.txt | 200 ---
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.../IlluminaTests/BasecallsDir/s_7_1_0002_qseq.txt | 200 ---
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.../BasecallsDir/s_9_0001_barcode.txt | 200 ---
.../BasecallsDir/s_9_0002_barcode.txt | 200 ---
.../IlluminaTests/BasecallsDir/s_9_1_0001_qseq.txt | 200 ---
.../IlluminaTests/BasecallsDir/s_9_1_0002_qseq.txt | 200 ---
.../IlluminaTests/BasecallsDir/s_9_2_0001_qseq.txt | 200 ---
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.../IlluminaTests/BasecallsDir/s_9_3_0001_qseq.txt | 200 ---
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.../illumina/IlluminaTests/L001/C1.1/s_1_1.cif | Bin 1224093 -> 0 bytes
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.../rta/BasecallsDir/s_1_1_0001_qseq.txt | 20 -
.../rta/BasecallsDir/s_2_1_0001_qseq.txt | 20 -
.../Homerus_Simpsonus_assembly18.fasta.0.2bpb | 1 -
.../Homerus_Simpsonus_assembly18.fasta.1.2bpb | 1 -
.../MakeSquashedMap/Map_to_genomic_coordinates.txt | 3 -
.../sf/picard/illumina/MakeSquashedMap/test.dict | 3 -
.../picard/illumina/Map_to_genomic_coordinates.txt | 45 -
.../sf/picard/illumina/s_1_1_eland_extended.txt | 9 -
.../net/sf/picard/illumina/s_1_1_eland_query.txt | 1 -
testdata/net/sf/picard/illumina/s_1_1_export.txt | 9 -
.../sf/picard/illumina/s_1_2_eland_extended.txt | 9 -
.../net/sf/picard/illumina/s_1_2_eland_query.txt | 1 -
testdata/net/sf/picard/illumina/s_1_2_export.txt | 9 -
.../net/sf/picard/illumina/s_2_eland_extended.txt | 3 -
testdata/net/sf/picard/illumina/s_2_export.txt | 3 -
.../sf/picard/illumina/s_4_1_eland_extended.txt | 9 -
.../net/sf/picard/illumina/s_4_1_eland_query.txt | 1 -
testdata/net/sf/picard/illumina/s_4_1_export.txt | 9 -
.../sf/picard/illumina/s_4_2_eland_extended.txt | 9 -
.../net/sf/picard/illumina/s_4_2_eland_query.txt | 1 -
testdata/net/sf/picard/illumina/s_4_2_export.txt | 9 -
.../net/sf/picard/illumina/s_5_eland_extended.txt | 3 -
testdata/net/sf/picard/illumina/s_5_export.txt | 3 -
.../IntervalListchr123_empty.interval_list | 4 +
.../sf/picard/sam/CompareSAMs/bigger_seq_dict.sam | 4 +-
testdata/net/sf/picard/sam/CompareSAMs/chr21.sam | 4 +-
.../net/sf/picard/sam/CompareSAMs/diff_coords.sam | 4 +-
.../net/sf/picard/sam/CompareSAMs/example2.sam | 4 +-
.../sf/picard/sam/CompareSAMs/genomic_sorted.sam | 4 +-
.../sf/picard/sam/CompareSAMs/genomic_sorted_5.sam | 4 +-
.../sam/CompareSAMs/genomic_sorted_5_plus.sam | 4 +-
.../sf/picard/sam/CompareSAMs/group_same_coord.sam | 4 +-
.../CompareSAMs/group_same_coord_diff_order.sam | 4 +-
.../sf/picard/sam/CompareSAMs/has_non_primary.sam | 4 +-
.../sf/picard/sam/CompareSAMs/unmapped_first.sam | 4 +-
.../sf/picard/sam/CompareSAMs/unmapped_second.sam | 4 +-
.../net/sf/picard/sam/CompareSAMs/unsorted.sam | 4 +-
.../net/sf/picard/sam/MarkDuplicates/merge1.sam | 2 +-
.../net/sf/picard/sam/MarkDuplicates/merge2.sam | 2 +-
.../net/sf/picard/sam/MarkDuplicates/merge3.sam | 2 +-
.../sam/MergeBamAlignment/aligned.badorder.sam | 2 +-
.../sam/MergeBamAlignment/aligned.supplement.sam | 2 +-
.../MergeBamAlignment/allread1.trimmed.aligned.sam | 2 +-
.../MergeBamAlignment/allread2.trimmed.aligned.sam | 2 +-
.../sam/MergeBamAlignment/cliptest.unmapped.sam | 2 +-
.../firsthalf.read1.trimmed.aligned.sam | 2 +-
.../firsthalf.read2.trimmed.aligned.sam | 2 +-
.../sam/MergeBamAlignment/multihit.aligned.sam | 2 +-
.../multihit.filter.fragment.unmapped.sam | 2 +-
.../MergeBamAlignment/multihit.filter.unmapped.sam | 2 +-
.../sam/MergeBamAlignment/multihit.unmapped.sam | 2 +-
.../secondhalf.read1.trimmed.aligned.sam | 2 +-
.../secondhalf.read2.trimmed.aligned.sam | 2 +-
.../sam/MergeBamAlignment/unmapped.badorder.sam | 2 +-
.../sf/picard/sam/MergeBamAlignment/unmapped.sam | 2 +-
.../sam/MergeSamFiles/case1/chr11sub_file1.sam | 2 +-
.../sam/MergeSamFiles/case1/chr11sub_file2.sam | 2 +-
.../sam/MergeSamFiles/case1/expected_output.sam | 2 +-
.../sam/MergeSamFiles/case2/chr11sub_file1.sam | 2 +-
.../sam/MergeSamFiles/case2/chr11sub_file2.sam | 2 +-
.../sam/MergeSamFiles/case2/chr11sub_file3.sam | 2 +-
.../sam/MergeSamFiles/case2/chr11sub_file4.sam | 2 +-
.../sam/MergeSamFiles/case2/expected_output.sam | 6 +-
.../picard/sam/MergeSamFiles/unsorted_input/1.sam | 2 +-
.../picard/sam/MergeSamFiles/unsorted_input/2.sam | 2 +-
.../sam/ValidateSamFileTest/duplicate_rg.sam | 11 +
.../ValidateSamFileTest/missing_platform_unit.sam | 10 +
.../sf/picard/sam/ValidateSamFileTest/valid.sam | 21 +
testdata/net/sf/picard/sam/aligned.sam | 2 +-
.../net/sf/picard/sam/aligned_queryname_sorted.bam | Bin 0 -> 725 bytes
.../net/sf/picard/sam/aligned_queryname_sorted.sam | 2 +-
.../bam2fastq/nonpaired/.gitignore} | 0
.../bam2fastq/paired/bad/grouped-unpaired-mate.sam | 4 +-
.../sam/bam2fastq/paired/bad/unpaired-mate.sam | 2 +-
.../sam/bam2fastq/paired/ok/clipping_test.sam | 2 +-
.../paired/ok/first-mate-bof-last-mate-eof.sam | 2 +-
.../paired/ok/grouped-last-pair-mates-flipped.sam | 4 +-
.../paired/ok/last-pair-mates-flipped.sam | 2 +-
.../picard/sam/bam2fastq/paired/ok/sorted-pair.sam | 2 +-
testdata/net/sf/picard/sam/onehalfaligned.sam | 2 +-
testdata/net/sf/picard/sam/otherhalfaligned.sam | 2 +-
testdata/net/sf/picard/sam/readWithBadRname.sam | 4 +-
testdata/net/sf/picard/sam/revert_sam_basic.sam | 6 +-
testdata/net/sf/picard/sam/revert_sam_negative.sam | 6 +-
testdata/net/sf/picard/sam/samHeaderProvider.sam | 15 +
testdata/net/sf/picard/sam/sequenceWithSpace.sam | 4 +-
.../sam/summary_alignment_bisulfite_test.sam | 2 +-
.../sf/picard/sam/summary_alignment_stats_test.sam | 2 +-
.../sam/summary_alignment_stats_test_multiple.sam | 8 +-
testdata/net/sf/picard/sam/unmapped.sam | 2 +-
.../tmp/.gitignore} | 0
2820 files changed, 17293 insertions(+), 24585 deletions(-)
create mode 100644 .gitignore
create mode 100644 src/java/net/sf/picard/analysis/CollectWgsMetrics.java
create mode 100644 src/java/net/sf/picard/filter/SecondaryAlignmentFilter.java
create mode 100644 src/java/net/sf/picard/illumina/parser/BclData.java
delete mode 100644 src/java/net/sf/picard/illumina/parser/CifParser.java
delete mode 100644 src/java/net/sf/picard/illumina/parser/CnfParser.java
delete mode 100644 src/java/net/sf/picard/illumina/parser/IlluminaIntensityParser.java
delete mode 100644 src/java/net/sf/picard/illumina/parser/MultiTileBclCycleFilesIterator.java
create mode 100644 src/java/net/sf/picard/illumina/parser/MultiTileBclFileUtil.java
create mode 100644 src/java/net/sf/picard/illumina/parser/MultiTileFileUtil.java
create mode 100644 src/java/net/sf/picard/illumina/parser/ParameterizedFileUtil.java
create mode 100644 src/java/net/sf/picard/illumina/parser/PerTileCycleParser.java
create mode 100644 src/java/net/sf/picard/illumina/parser/PerTileFileUtil.java
create mode 100644 src/java/net/sf/picard/illumina/parser/PerTilePerCycleFileUtil.java
delete mode 100644 src/java/net/sf/picard/illumina/parser/PerTilePerCycleParser.java
delete mode 100644 src/java/net/sf/picard/illumina/parser/QseqParser.java
delete mode 100644 src/java/net/sf/picard/illumina/parser/fakers/CifFileFaker.java
delete mode 100644 src/java/net/sf/picard/illumina/parser/fakers/CnfFileFaker.java
delete mode 100644 src/java/net/sf/picard/illumina/parser/fakers/QSeqFileFaker.java
create mode 100644 src/java/net/sf/picard/sam/AddCommentsToBam.java
create mode 100644 src/java/net/sf/picard/sam/GatherBamFiles.java
create mode 100644 src/java/net/sf/picard/util/AdapterMarker.java
create mode 100644 src/java/net/sf/samtools/BamFileIoUtils.java
create mode 100644 src/java/net/sf/samtools/StreamInflatingIndexingOutputStream.java
copy testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => src/java/org/broad/tribble/util/ftp/.gitignore (100%)
create mode 100644 src/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterBuilder.java
rename testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC.sam => src/tests/java/net/sf/picard/fastq/.gitignore (100%)
delete mode 100644 src/tests/java/net/sf/picard/illumina/parser/ClusterIntensityFileReaderTest.java
delete mode 100644 src/tests/java/net/sf/picard/illumina/parser/IlluminaIntensityParserTest.java
delete mode 100644 src/tests/java/net/sf/picard/illumina/parser/QSeqTdUtil.java
delete mode 100644 src/tests/java/net/sf/picard/illumina/parser/QseqParserTest.java
create mode 100644 src/tests/java/net/sf/picard/illumina/parser/fakers/BclFileFakerTest.java
create mode 100644 src/tests/java/net/sf/picard/sam/AddCommentsToBamTest.java
create mode 100644 src/tests/java/net/sf/picard/util/IntervalListTest.java
create mode 100644 src/tests/java/net/sf/samtools/BamFileIoUtilsTest.java
rename testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AAGGATGT-AAGGATGT-AAGGATGT.sam => src/tests/java/net/sf/samtools/apps/.gitignore (100%)
rename testdata/net/sf/picard/illumina/IlluminaBasecallsToSamTest/AAGGATGT-AAGGATGT.sam => src/tests/java/org/broad/tribble/source/.gitignore (100%)
create mode 100644 src/tests/java/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterBuilderUnitTest.java
create mode 100644 src/tests/java/org/broadinstitute/variant/vcf/VCFCompoundHeaderLineUnitTest.java
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C100.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C101.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C102.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C103.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C104.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C105.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C106.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C107.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C108.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C109.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C110.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C111.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C112.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C113.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C114.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C115.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C116.1/s_1_1101.bcl
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create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C118.1/s_1_1101.bcl
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create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C120.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C121.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C122.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C123.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C124.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C125.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C126.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C127.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C128.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C129.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C130.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C131.1/s_1_1101.bcl
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create mode 100755 testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1201.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_2101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1201.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_2101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter
create mode 100755 testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1201.filter
create mode 100755 testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_2101.filter
create mode 100755 testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_1101_barcode.txt.gz
create mode 100755 testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_1201_barcode.txt.gz
create mode 100755 testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_2101_barcode.txt.gz
create mode 100755 testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_1101.clocs
create mode 100755 testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_1201.clocs
create mode 100755 testdata/net/sf/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_2101.clocs
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/ACCAACTG-ACCAACTG-ACCAACTG.sam => 25T8B25T/fastq/AAAAAAAA.1.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/ACCAACTG-ACCAACTG.sam => 25T8B25T/fastq/AAAAAAAA.2.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AGCAATTC-AGCAATTC-AGCAATTC.sam => 25T8B25T/fastq/AAAAAAAA.barcode_1.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AGCAATTC-AGCAATTC.sam => 25T8B25T/fastq/AAAAGAAG.1.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AGTTGCTT-AGTTGCTT-AGTTGCTT.sam => 25T8B25T/fastq/AAAAGAAG.2.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AGTTGCTT-AGTTGCTT.sam => 25T8B25T/fastq/AAAAGAAG.barcode_1.fastq} (100%)
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create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/AACGCATT.barcode_1.fastq
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/ATTATGTT-ATTATGTT-ATTATGTT.sam => 25T8B25T/fastq/ACAAAATT.1.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/ATTATGTT-ATTATGTT.sam => 25T8B25T/fastq/ACAAAATT.2.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/CACATCCT-CACATCCT-CACATCCT.sam => 25T8B25T/fastq/ACAAAATT.barcode_1.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGGTAT.1.fastq
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create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGGTAT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGTTGA.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGTTGA.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/ACAGTTGA.barcode_1.fastq
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/CACATCCT-CACATCCT.sam => 25T8B25T/fastq/ACCAGTTG.1.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/CAGGAGCC-CAGGAGCC-CAGGAGCC.sam => 25T8B25T/fastq/ACCAGTTG.2.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/CAGGAGCC-CAGGAGCC.sam => 25T8B25T/fastq/ACCAGTTG.barcode_1.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/CATAGCGA-CATAGCGA-CATAGCGA.sam => 25T8B25T/fastq/ACGAAATC.1.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/CATAGCGA-CATAGCGA.sam => 25T8B25T/fastq/ACGAAATC.2.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/CATGCTTA-CATGCTTA-CATGCTTA.sam => 25T8B25T/fastq/ACGAAATC.barcode_1.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTAAGAC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTAAGAC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTAAGAC.barcode_1.fastq
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/CATGCTTA-CATGCTTA.sam => 25T8B25T/fastq/ACTGTACC.1.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/CCAGTTAG-CCAGTTAG-CCAGTTAG.sam => 25T8B25T/fastq/ACTGTACC.2.fastq} (100%)
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create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/ACTGTATC.barcode_1.fastq
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/CCTACCAT-CCTACCAT-CCTACCAT.sam => 25T8B25T/fastq/AGAAAAGA.1.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/CCTACCAT-CCTACCAT.sam => 25T8B25T/fastq/AGAAAAGA.2.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/CTACCAGG-CTACCAGG-CTACCAGG.sam => 25T8B25T/fastq/AGAAAAGA.barcode_1.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/AGCATGGA.1.fastq
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create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/AGCATGGA.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTAAGG.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTAAGG.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTAAGG.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTCGCA.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTCGCA.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTCGCA.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTATCAA.1.fastq
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create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTATCAA.barcode_1.fastq
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create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGTC.1.fastq
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create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CAATAGTC.barcode_1.fastq
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rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/GCACATCT-GCACATCT.sam => 25T8B25T/fastq/CAGCGGAT.2.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/GGTCCAGA-GGTCCAGA-GGTCCAGA.sam => 25T8B25T/fastq/CAGCGGAT.barcode_1.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGTA.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGTA.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CAGCGGTA.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAACATT.1.fastq
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create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAACATT.barcode_1.fastq
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create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAGCACC.barcode_1.fastq
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/GGTCCAGA-GGTCCAGA.sam => 25T8B25T/fastq/CCATGCGT.1.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/GTATAACA-GTATAACA-GTATAACA.sam => 25T8B25T/fastq/CCATGCGT.2.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/GTATAACA-GTATAACA.sam => 25T8B25T/fastq/CCATGCGT.barcode_1.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCCTTCC.1.fastq
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create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCCTTCC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCTATGT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCTATGT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CGCTATGT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CTAACTCG.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CTAACTCG.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CTAACTCG.barcode_1.fastq
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/N-N-N.sam => 25T8B25T/fastq/CTATGCGC.1.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/N-N.sam => 25T8B25T/fastq/CTATGCGC.2.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaTests/L001/C1.1/s_1_1.bcl => 25T8B25T/fastq/CTATGCGC.barcode_1.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CTATGCGT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGCGGAT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGCGGAT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGCGGAT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGTAATC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGTAATC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CTGTAATC.barcode_1.fastq
rename testdata/net/sf/picard/illumina/{IlluminaTests/L001/C2.1/s_1_1.bcl.gz => 25T8B25T/fastq/GAAAAAAA.1.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaTests/L001/C3.1/s_1_1.bcl => 25T8B25T/fastq/GAAAAAAA.2.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaTests/L001/C4.1/s_1_1.bcl => 25T8B25T/fastq/GAAAAAAA.barcode_1.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaTests/Matrix/s_3_152_matrix.txt => 25T8B25T/fastq/GAACGAT..1.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaTests/Matrix/s_3_76_matrix.txt => 25T8B25T/fastq/GAACGAT..2.fastq} (100%)
rename testdata/net/sf/picard/illumina/{IlluminaTests/Matrix/s_6_152_matrix.txt => 25T8B25T/fastq/GAACGAT..barcode_1.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAGGAAG.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAGGAAG.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GAAGGAAG.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGA.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGA.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCAGGA.barcode_1.fastq
rename testdata/net/sf/picard/illumina/{s_2_eland_query.txt => 25T8B25T/fastq/GACCAGGC.1.fastq} (100%)
rename testdata/net/sf/picard/illumina/{s_5_eland_query.txt => 25T8B25T/fastq/GACCAGGC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/GACCAGGC.barcode_1.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCGTTG.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCGTTG.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCGTTG.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCTAAC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCTAAC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GACCTAAC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GATATCCA.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GATATCCA.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GATATCCA.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCGTCGA.1.fastq
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create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCGTCGA.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCTAGCC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCTAGCC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCTAGCC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GTAACATC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GTAACATC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GTAACATC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GTCCACAG.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GTCCACAG.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GTCCACAG.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/N.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/N.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/N.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TAAGCACA.1.fastq
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create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TAAGCACA.barcode_1.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TACCGTCT.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TACCGTCT.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TACCGTCT.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TAGCGGTA.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TAGCGGTA.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TAGCGGTA.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TATCAGCC.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TATCAGCC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TATCAGCC.barcode_1.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCAGG.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCAGG.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCCAGG.barcode_1.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TATCCATG.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TATCCATG.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TATCCATG.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TATCTCGG.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TATCTCGG.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TATCTCGG.barcode_1.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTGCC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTGCC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TATCTGCC.barcode_1.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TCCGTCTA.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TCCGTCTA.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B25T/fastq/TCCGTCTA.barcode_1.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TCGCTAGA.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TCGCTAGA.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TCGCTAGA.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TCTGCAAG.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TCTGCAAG.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TCTGCAAG.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCAAGTA.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCAAGTA.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCAAGTA.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCTGCTG.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCTGCTG.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TGCTGCTG.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAACTC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAACTC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAACTC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAATCA.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAATCA.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAATCA.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TTGTCTAT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TTGTCTAT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TTGTCTAT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/barcode.params
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/mp_barcode.params
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/nonBarcoded.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/nonBarcoded.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplex.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplex.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplexRH.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplexRH.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/testMultiplexRH.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/AAAAAAAA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/AAAAGAAG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/AACAATGG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/AACGCATT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/ACAAAATT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/ACAGGTAT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/ACAGTTGA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/ACCAGTTG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/ACGAAATC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/ACTAAGAC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/ACTGTACC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/ACTGTATC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/AGAAAAGA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/AGCATGGA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/AGGTAAGG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/AGGTCGCA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/ATTATCAA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/ATTCCTCT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/CAACTCTC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/CAATAGAC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/CAATAGTC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/CAGCGGAT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/CAGCGGTA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/CCAACATT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/CCAGCACC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/CCATGCGT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/CGCCTTCC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/CGCTATGT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/CTAACTCG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/CTATGCGC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/CTATGCGT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/CTGCGGAT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/CTGTAATC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/GAAAAAAA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/GAACGAT..sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/GAAGGAAG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/GACCAGGA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/GACCAGGC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/GACCGTTG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/GACCTAAC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/GATATCCA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/GCCGTCGA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/GCCTAGCC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/GTAACATC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/GTCCACAG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/N.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TAAGCACA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TACCGTCT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TAGCGGTA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TATCAGCC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TATCCAGG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TATCCATG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TATCTCGG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TATCTGCC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TCCGTCTA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TCGCTAGA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TCTGCAAG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TGCAAGTA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TGCTGCTG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TGTAACTC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TGTAATCA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/TTGTCTAT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/barcode.params
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/multiplexed_positive_rgtags.params
create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/sams/nonBarcoded.sam
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C63.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/s_1_1101_barcode.txt
create mode 100755 testdata/net/sf/picard/illumina/25T8B8B25T/Data/Intensities/L001/s_1_1101.locs
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/AAGACACTAGTCTCCT.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/AAGACACTAGTCTCCT.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/AAGACACTAGTCTCCT.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/AAGACACTAGTCTCCT.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/ACCTACTGCTTCCCTT.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/ACCTACTGCTTCCCTT.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/ACCTACTGCTTCCCTT.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/ACCTACTGCTTCCCTT.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/AGGTCGCATTCCTTTC.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/AGGTCGCATTCCTTTC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/AGGTCGCATTCCTTTC.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/AGGTCGCATTCCTTTC.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/ATTATCAACACCATAC.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/ATTATCAACACCATAC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/ATTATCAACACCATAC.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/ATTATCAACACCATAC.barcode_2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/ATTGTCTGGATTCACA.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/ATTGTCTGGATTCACA.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/ATTGTCTGGATTCACA.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/ATTGTCTGGATTCACA.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CAGCGGTATGTACTGC.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CAGCGGTATGTACTGC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CAGCGGTATGTACTGC.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CAGCGGTATGTACTGC.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CATGCTTATAGCATTT.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CATGCTTATAGCATTT.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CATGCTTATAGCATTT.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CATGCTTATAGCATTT.barcode_2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CATGCTTTTAGCATTG.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CATGCTTTTAGCATTG.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CATGCTTTTAGCATTG.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CATGCTTTTAGCATTG.barcode_2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CATGTTCGCGCCTTTT.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CATGTTCGCGCCTTTT.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CATGTTCGCGCCTTTT.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CATGTTCGCGCCTTTT.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCCGATTTTCTCTCCC.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCCGATTTTCTCTCCC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCCGATTTTCTCTCCC.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCCGATTTTCTCTCCC.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTATTCTTCGTTTTC.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTATTCTTCGTTTTC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTATTCTTCGTTTTC.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTATTCTTCGTTTTC.barcode_2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.barcode_2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTTCTTTTATCATTT.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTTCTTTTATCATTT.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTTCTTTTATCATTT.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CCTTCTTTTATCATTT.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CGCTATGTTTCTCCTT.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CGCTATGTTTCTCCTT.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CGCTATGTTTCTCCTT.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CGCTATGTTTCTCCTT.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GCCGTCGAAGGTACCC.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GCCGTCGAAGGTACCC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GCCGTCGAAGGTACCC.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GCCGTCGAAGGTACCC.barcode_2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GCCGTCGATGGTACCC.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GCCGTCGATGGTACCC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GCCGTCGATGGTACCC.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GCCGTCGATGGTACCC.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GCTATCCACCTCCCCC.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GCTATCCACCTCCCCC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GCTATCCACCTCCCCC.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GCTATCCACCTCCCCC.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GTATAACATATTCAAC.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GTATAACATATTCAAC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GTATAACATATTCAAC.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GTATAACATATTCAAC.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GTCTGATGTCACTTCC.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GTCTGATGTCACTTCC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GTCTGATGTCACTTCC.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/GTCTGATGTCACTTCC.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/NN.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TCCCCGTTCCAACTTC.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TCCCCGTTCCAACTTC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TCCCCGTTCCAACTTC.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TCCCCGTTCCAACTTC.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TGCTCGACTTCACAGT.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TGCTCGACTTCACAGT.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TGCTCGACTTCACAGT.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TGCTCGACTTCACAGT.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TGTATCTCTTACTCTT.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TGTATCTCTTACTCTT.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TGTATCTCTTACTCTT.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TGTATCTCTTACTCTT.barcode_2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.barcode_2.fastq
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.barcode_2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TTCCTCCTCACCATCC.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TTCCTCCTCACCATCC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TTCCTCCTCACCATCC.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TTCCTCCTCACCATCC.barcode_2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TTCTCATCTTCCTTCC.1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TTCTCATCTTCCTTCC.2.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TTCTCATCTTCCTTCC.barcode_1.fastq} (100%)
copy testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/AACTTGAC-AACTTGAC-AACTTGAC.sam => 25T8B8B25T/fastq/TTCTCATCTTCCTTCC.barcode_2.fastq} (100%)
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.barcode_1.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.barcode_2.fastq
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/fastq/barcode_double.params
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/library.params
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/AACTTGAC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/AAGACACT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACAGGTAT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACAGTTGA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACCAACTG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACCTACTG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/ACTAAGAC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGGTCGCA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGGTGCGA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGGTTATC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/AGTTGCTT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/ATAGCGTC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/ATTATCAA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/ATTGTCTG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CAATAGTC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CAGCAAGG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CAGCGGTA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CATGCTTA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CATGCTTT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CATGTTCG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCAGAGCT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCCGATTT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTATGCC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTATTCT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTCTTCT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTCTTTC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTTCGCA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CCTTCTTT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CGCTATGT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CTACCAGG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CTCCCTCT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/CTGTAATC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/GACCAGGA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/GCCGTCGA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/GCCTAGCC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/GCTATCCA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/GTATAACA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/GTCTGATG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/N.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TACTTAGC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TCCCCGTT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TCCTTGGT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TCGCCTTG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGCAAGTA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGCTCGAC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTAATCA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTATCTC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTCGGTT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TGTTCCGA.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTAATCAG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTATATCT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTCCCCAG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTCCTCCT.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTCTCATC.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/TTGAATAG.sam
create mode 100644 testdata/net/sf/picard/illumina/25T8B8B25T/sams/barcode_double.params
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