[med-svn] [picard-tools] 02/03: Merge tag 'upstream/1.113'

Olivier Sallou osallou at debian.org
Fri Jun 6 21:35:23 UTC 2014


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osallou pushed a commit to branch master
in repository picard-tools.

commit 2263d6f7dd5fb88ab42c78a57e1dfc9d25c56337
Merge: ddb817f db975ee
Author: Olivier Sallou <olivier.sallou at debian.org>
Date:   Fri Jun 6 23:34:00 2014 +0200

    Merge tag 'upstream/1.113'
    
    Upstream version 1.113

 .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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 .../sf/picard/illumina/s_1_1_eland_extended.txt    |    9 -
 .../net/sf/picard/illumina/s_1_1_eland_query.txt   |    1 -
 testdata/net/sf/picard/illumina/s_1_1_export.txt   |    9 -
 .../sf/picard/illumina/s_1_2_eland_extended.txt    |    9 -
 .../net/sf/picard/illumina/s_1_2_eland_query.txt   |    1 -
 testdata/net/sf/picard/illumina/s_1_2_export.txt   |    9 -
 .../net/sf/picard/illumina/s_2_eland_extended.txt  |    3 -
 testdata/net/sf/picard/illumina/s_2_export.txt     |    3 -
 .../sf/picard/illumina/s_4_1_eland_extended.txt    |    9 -
 .../net/sf/picard/illumina/s_4_1_eland_query.txt   |    1 -
 testdata/net/sf/picard/illumina/s_4_1_export.txt   |    9 -
 .../sf/picard/illumina/s_4_2_eland_extended.txt    |    9 -
 .../net/sf/picard/illumina/s_4_2_eland_query.txt   |    1 -
 testdata/net/sf/picard/illumina/s_4_2_export.txt   |    9 -
 .../net/sf/picard/illumina/s_5_eland_extended.txt  |    3 -
 testdata/net/sf/picard/illumina/s_5_export.txt     |    3 -
 .../IntervalListchr123_empty.interval_list         |    4 +
 .../sf/picard/sam/CompareSAMs/bigger_seq_dict.sam  |    4 +-
 testdata/net/sf/picard/sam/CompareSAMs/chr21.sam   |    4 +-
 .../net/sf/picard/sam/CompareSAMs/diff_coords.sam  |    4 +-
 .../net/sf/picard/sam/CompareSAMs/example2.sam     |    4 +-
 .../sf/picard/sam/CompareSAMs/genomic_sorted.sam   |    4 +-
 .../sf/picard/sam/CompareSAMs/genomic_sorted_5.sam |    4 +-
 .../sam/CompareSAMs/genomic_sorted_5_plus.sam      |    4 +-
 .../sf/picard/sam/CompareSAMs/group_same_coord.sam |    4 +-
 .../CompareSAMs/group_same_coord_diff_order.sam    |    4 +-
 .../sf/picard/sam/CompareSAMs/has_non_primary.sam  |    4 +-
 .../sf/picard/sam/CompareSAMs/unmapped_first.sam   |    4 +-
 .../sf/picard/sam/CompareSAMs/unmapped_second.sam  |    4 +-
 .../net/sf/picard/sam/CompareSAMs/unsorted.sam     |    4 +-
 .../net/sf/picard/sam/MarkDuplicates/merge1.sam    |    2 +-
 .../net/sf/picard/sam/MarkDuplicates/merge2.sam    |    2 +-
 .../net/sf/picard/sam/MarkDuplicates/merge3.sam    |    2 +-
 .../sam/MergeBamAlignment/aligned.badorder.sam     |    2 +-
 .../sam/MergeBamAlignment/aligned.supplement.sam   |    2 +-
 .../MergeBamAlignment/allread1.trimmed.aligned.sam |    2 +-
 .../MergeBamAlignment/allread2.trimmed.aligned.sam |    2 +-
 .../sam/MergeBamAlignment/cliptest.unmapped.sam    |    2 +-
 .../firsthalf.read1.trimmed.aligned.sam            |    2 +-
 .../firsthalf.read2.trimmed.aligned.sam            |    2 +-
 .../sam/MergeBamAlignment/multihit.aligned.sam     |    2 +-
 .../multihit.filter.fragment.unmapped.sam          |    2 +-
 .../MergeBamAlignment/multihit.filter.unmapped.sam |    2 +-
 .../sam/MergeBamAlignment/multihit.unmapped.sam    |    2 +-
 .../secondhalf.read1.trimmed.aligned.sam           |    2 +-
 .../secondhalf.read2.trimmed.aligned.sam           |    2 +-
 .../sam/MergeBamAlignment/unmapped.badorder.sam    |    2 +-
 .../sf/picard/sam/MergeBamAlignment/unmapped.sam   |    2 +-
 .../sam/MergeSamFiles/case1/chr11sub_file1.sam     |    2 +-
 .../sam/MergeSamFiles/case1/chr11sub_file2.sam     |    2 +-
 .../sam/MergeSamFiles/case1/expected_output.sam    |    2 +-
 .../sam/MergeSamFiles/case2/chr11sub_file1.sam     |    2 +-
 .../sam/MergeSamFiles/case2/chr11sub_file2.sam     |    2 +-
 .../sam/MergeSamFiles/case2/chr11sub_file3.sam     |    2 +-
 .../sam/MergeSamFiles/case2/chr11sub_file4.sam     |    2 +-
 .../sam/MergeSamFiles/case2/expected_output.sam    |    6 +-
 .../picard/sam/MergeSamFiles/unsorted_input/1.sam  |    2 +-
 .../picard/sam/MergeSamFiles/unsorted_input/2.sam  |    2 +-
 .../sam/ValidateSamFileTest/duplicate_rg.sam       |   11 +
 .../ValidateSamFileTest/missing_platform_unit.sam  |   10 +
 .../sf/picard/sam/ValidateSamFileTest/valid.sam    |   21 +
 testdata/net/sf/picard/sam/aligned.sam             |    2 +-
 .../net/sf/picard/sam/aligned_queryname_sorted.bam |  Bin 0 -> 725 bytes
 .../net/sf/picard/sam/aligned_queryname_sorted.sam |    2 +-
 .../bam2fastq/nonpaired/.gitignore}                |    0
 .../bam2fastq/paired/bad/grouped-unpaired-mate.sam |    4 +-
 .../sam/bam2fastq/paired/bad/unpaired-mate.sam     |    2 +-
 .../sam/bam2fastq/paired/ok/clipping_test.sam      |    2 +-
 .../paired/ok/first-mate-bof-last-mate-eof.sam     |    2 +-
 .../paired/ok/grouped-last-pair-mates-flipped.sam  |    4 +-
 .../paired/ok/last-pair-mates-flipped.sam          |    2 +-
 .../picard/sam/bam2fastq/paired/ok/sorted-pair.sam |    2 +-
 testdata/net/sf/picard/sam/onehalfaligned.sam      |    2 +-
 testdata/net/sf/picard/sam/otherhalfaligned.sam    |    2 +-
 testdata/net/sf/picard/sam/readWithBadRname.sam    |    4 +-
 testdata/net/sf/picard/sam/revert_sam_basic.sam    |    6 +-
 testdata/net/sf/picard/sam/revert_sam_negative.sam |    6 +-
 testdata/net/sf/picard/sam/samHeaderProvider.sam   |   15 +
 testdata/net/sf/picard/sam/sequenceWithSpace.sam   |    4 +-
 .../sam/summary_alignment_bisulfite_test.sam       |    2 +-
 .../sf/picard/sam/summary_alignment_stats_test.sam |    2 +-
 .../sam/summary_alignment_stats_test_multiple.sam  |    8 +-
 testdata/net/sf/picard/sam/unmapped.sam            |    2 +-
 .../tmp/.gitignore}                                |    0
 2818 files changed, 17280 insertions(+), 24585 deletions(-)

-- 
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