[med-svn] [picard-tools] branch upstream updated (ad4ec03 -> db975ee)

Olivier Sallou osallou at debian.org
Fri Jun 6 21:35:24 UTC 2014


This is an automated email from the git hooks/post-receive script.

osallou pushed a change to branch upstream
in repository picard-tools.

      from  ad4ec03   Imported Upstream version 1.110
       new  db975ee   Imported Upstream version 1.113

The 1 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 +-
 .../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/C31.1/s_1_2101.bcl  |  Bin 0 -> 64 bytes
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 .../Intensities/BaseCalls/L001/C32.1/s_1_1201.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C32.1/s_1_2101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C33.1/s_1_1201.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C33.1/s_1_2101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C34.1/s_1_1201.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C34.1/s_1_2101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C35.1/s_1_1201.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C35.1/s_1_2101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C36.1/s_1_1201.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C36.1/s_1_2101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C37.1/s_1_1201.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C37.1/s_1_2101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C38.1/s_1_1201.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C38.1/s_1_2101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C39.1/s_1_1201.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C39.1/s_1_2101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl   |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C4.1/s_1_1201.bcl   |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C4.1/s_1_2101.bcl   |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C40.1/s_1_1201.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C40.1/s_1_2101.bcl  |  Bin 0 -> 64 bytes
 .../Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl  |  Bin 0 -> 64 bytes
 .../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
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 .../fastq/AAAAAAAA.barcode_1.fastq}                |    0
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 .../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 +
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 .../25T8B25T/fastq/AACGCATT.barcode_1.fastq        |   28 +
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 .../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
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 .../fastq/ACGAAATC.1.fastq}                        |    0
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 .../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
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 .../illumina/25T8B25T/fastq/ACTGTATC.1.fastq       |   16 +
 .../illumina/25T8B25T/fastq/ACTGTATC.2.fastq       |   16 +
 .../25T8B25T/fastq/ACTGTATC.barcode_1.fastq        |   16 +
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 .../illumina/25T8B25T/fastq/AGCATGGA.1.fastq       |   12 +
 .../illumina/25T8B25T/fastq/AGCATGGA.2.fastq       |   12 +
 .../25T8B25T/fastq/AGCATGGA.barcode_1.fastq        |   12 +
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 .../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
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 .../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
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 .../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 +
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 .../illumina/25T8B25T/fastq/CGCCTTCC.1.fastq       |    8 +
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 .../25T8B25T/fastq/CGCCTTCC.barcode_1.fastq        |    8 +
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 .../fastq/CTATGCGC.barcode_1.fastq}                |    0
 .../illumina/25T8B25T/fastq/CTATGCGT.1.fastq       |   28 +
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 .../25T8B25T/fastq/CTGTAATC.barcode_1.fastq        |   24 +
 .../fastq/GAAAAAAA.1.fastq}                        |    0
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 .../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 +
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 .../illumina/25T8B25T/fastq/GACCGTTG.1.fastq       |   16 +
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 .../25T8B25T/fastq/GACCGTTG.barcode_1.fastq        |   16 +
 .../illumina/25T8B25T/fastq/GACCTAAC.1.fastq       |    4 +
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 .../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 +
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 .../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 +
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 .../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
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 .../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
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 .../net/sf/picard/sam/MarkDuplicates/merge3.sam    |    2 +-
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 .../MergeBamAlignment/allread2.trimmed.aligned.sam |    2 +-
 .../sam/MergeBamAlignment/cliptest.unmapped.sam    |    2 +-
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 .../sam/MergeBamAlignment/unmapped.badorder.sam    |    2 +-
 .../sf/picard/sam/MergeBamAlignment/unmapped.sam   |    2 +-
 .../sam/MergeSamFiles/case1/chr11sub_file1.sam     |    2 +-
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 .../sam/MergeSamFiles/case1/expected_output.sam    |    2 +-
 .../sam/MergeSamFiles/case2/chr11sub_file1.sam     |    2 +-
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 .../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 +
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 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 +-
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 2818 files changed, 17280 insertions(+), 24585 deletions(-)
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 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%)
 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/AACAATGG.1.fastq
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 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%)
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 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%)
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 rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/CCAGTTAG-CCAGTTAG-CCAGTTAG.sam => 25T8B25T/fastq/ACTGTACC.2.fastq} (100%)
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 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%)
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 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/AGCATGGA.2.fastq
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 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/AGGTAAGG.1.fastq
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 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
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 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
 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTCCTCT.1.fastq
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 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/ATTCCTCT.barcode_1.fastq
 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CAACTCTC.1.fastq
 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CAACTCTC.2.fastq
 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CAACTCTC.barcode_1.fastq
 rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/CTACCAGG-CTACCAGG.sam => 25T8B25T/fastq/CAATAGAC.1.fastq} (100%)
 rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/GCACACGA-GCACACGA-GCACACGA.sam => 25T8B25T/fastq/CAATAGAC.2.fastq} (100%)
 rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/GCACACGA-GCACACGA.sam => 25T8B25T/fastq/CAATAGAC.barcode_1.fastq} (100%)
 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
 rename testdata/net/sf/picard/illumina/{IlluminaBasecallsToSamTest/GCACATCT-GCACATCT-GCACATCT.sam => 25T8B25T/fastq/CAGCGGAT.1.fastq} (100%)
 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
 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAACATT.2.fastq
 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAACATT.barcode_1.fastq
 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAGCACC.1.fastq
 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/CCAGCACC.2.fastq
 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/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
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 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
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 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
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 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GATATCCA.1.fastq
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 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GCCTAGCC.1.fastq
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 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/GTAACATC.1.fastq
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 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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 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
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 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
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 create mode 100644 testdata/net/sf/picard/illumina/25T8B25T/fastq/TGTAATCA.1.fastq
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 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
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 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
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C1.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C1.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C10.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C10.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C11.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C11.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C12.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C12.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C13.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C13.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C14.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C14.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C15.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C15.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C16.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C16.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C17.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C17.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C18.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C18.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C19.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C19.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C2.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C2.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C20.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C20.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C21.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C21.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C22.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C22.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C23.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C23.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C24.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C24.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C25.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C25.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C26.1/s_1_1201.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C26.1/s_1_2101.bcl
 delete mode 100644 testdata/net/sf/picard/illumina/CompleteIlluminaDir/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl
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