[med-svn] [picard-tools] branch upstream updated (db975ee -> 4957015)

Vincent Danjean vdanjean at debian.org
Mon Sep 7 23:48:55 UTC 2015


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

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

      from  db975ee   Imported Upstream version 1.113
      adds  4957015   Imported Upstream version 1.138+dfsg.1

No new revisions were added by this update.

Summary of changes:
 .dockerignore                                      |    18 +
 .gitignore                                         |     6 +-
 .travis.yml                                        |    12 +
 Dockerfile                                         |    31 +
 Picard-public.iml                                  |    40 +-
 Picard-public.ipr                                  |     6 +-
 README.md                                          |    56 +
 build-tribble.xml                                  |   183 -
 build.sbt                                          |   142 +
 build.xml                                          |   528 +-
 project/plugins.sbt                                |     5 +
 src/c/inteldeflater/IntelDeflater.c                |   247 -
 src/java/net/sf/picard/PicardException.java        |    43 -
 src/java/net/sf/picard/Test.java                   |    57 -
 .../picard/analysis/AlignmentSummaryMetrics.java   |   162 -
 .../analysis/AlignmentSummaryMetricsCollector.java |   385 -
 .../analysis/CollectAlignmentSummaryMetrics.java   |   123 -
 .../sf/picard/analysis/CollectGcBiasMetrics.java   |   327 -
 .../picard/analysis/CollectInsertSizeMetrics.java  |   155 -
 .../sf/picard/analysis/CollectMultipleMetrics.java |   140 -
 .../sf/picard/analysis/CollectRnaSeqMetrics.java   |   148 -
 .../net/sf/picard/analysis/CollectWgsMetrics.java  |   274 -
 .../sf/picard/analysis/GcBiasDetailMetrics.java    |    63 -
 .../sf/picard/analysis/GcBiasSummaryMetrics.java   |    56 -
 .../net/sf/picard/analysis/InsertSizeMetrics.java  |    94 -
 .../net/sf/picard/analysis/MeanQualityByCycle.java |   204 -
 .../picard/analysis/MetricAccumulationLevel.java   |    32 -
 .../picard/analysis/QualityScoreDistribution.java  |   150 -
 src/java/net/sf/picard/analysis/RnaSeqMetrics.java |   111 -
 .../sf/picard/analysis/SinglePassSamProgram.java   |   158 -
 .../analysis/directed/CalculateHsMetrics.java      |    87 -
 .../analysis/directed/CollectTargetedMetrics.java  |   151 -
 .../directed/CollectTargetedPcrMetrics.java        |    62 -
 .../analysis/directed/HsMetricCollector.java       |   122 -
 .../net/sf/picard/analysis/directed/HsMetrics.java |   194 -
 .../directed/InsertSizeMetricsCollector.java       |   205 -
 .../analysis/directed/RnaSeqMetricsCollector.java  |   391 -
 .../analysis/directed/TargetMetricsCollector.java  |   748 -
 .../analysis/directed/TargetedPcrMetrics.java      |   119 -
 .../directed/TargetedPcrMetricsCollector.java      |    58 -
 .../sf/picard/annotation/AnnotationException.java  |    40 -
 src/java/net/sf/picard/annotation/Gene.java        |   222 -
 .../sf/picard/annotation/GeneAnnotationReader.java |    39 -
 .../net/sf/picard/annotation/LocusFunction.java    |    33 -
 .../net/sf/picard/annotation/RefFlatReader.java    |   191 -
 .../picard/cmdline/CommandLineParseException.java  |    36 -
 .../net/sf/picard/cmdline/CommandLineParser.java   |  1210 -
 .../CommandLineParserDefinitionException.java      |    36 -
 .../net/sf/picard/cmdline/CommandLineProgram.java  |   312 -
 .../sf/picard/cmdline/CreateHtmlDocForProgram.java |    44 -
 .../cmdline/CreateHtmlDocForStandardOptions.java   |    40 -
 src/java/net/sf/picard/cmdline/NestedOptions.java  |    39 -
 src/java/net/sf/picard/cmdline/Option.java         |    80 -
 .../net/sf/picard/cmdline/PositionalArguments.java |    52 -
 .../picard/cmdline/StandardOptionDefinitions.java  |    48 -
 src/java/net/sf/picard/cmdline/Usage.java          |    40 -
 src/java/net/sf/picard/fastq/AsyncFastqWriter.java |    20 -
 src/java/net/sf/picard/fastq/BamToBfq.java         |    93 -
 src/java/net/sf/picard/fastq/BamToBfqWriter.java   |   441 -
 src/java/net/sf/picard/fastq/BasicFastqWriter.java |    88 -
 .../sf/picard/fastq/Casava18ReadNameEncoder.java   |    46 -
 src/java/net/sf/picard/fastq/FastqConstants.java   |    32 -
 src/java/net/sf/picard/fastq/FastqReader.java      |   177 -
 src/java/net/sf/picard/fastq/FastqRecord.java      |    49 -
 src/java/net/sf/picard/fastq/FastqWriter.java      |    13 -
 .../net/sf/picard/fastq/FastqWriterFactory.java    |    31 -
 .../sf/picard/fastq/IlluminaReadNameEncoder.java   |    28 -
 src/java/net/sf/picard/fastq/ReadNameEncoder.java  |    17 -
 src/java/net/sf/picard/filter/AggregateFilter.java |    79 -
 src/java/net/sf/picard/filter/AlignedFilter.java   |    87 -
 .../net/sf/picard/filter/DuplicateReadFilter.java  |    52 -
 .../filter/FailsVendorReadQualityFilter.java       |    57 -
 .../net/sf/picard/filter/FilteringIterator.java    |   154 -
 src/java/net/sf/picard/filter/IntervalFilter.java  |    99 -
 .../picard/filter/NotPrimaryAlignmentFilter.java   |    54 -
 src/java/net/sf/picard/filter/ReadNameFilter.java  |   119 -
 src/java/net/sf/picard/filter/SamRecordFilter.java |    53 -
 .../sf/picard/filter/SecondaryAlignmentFilter.java |    20 -
 .../filter/SecondaryOrSupplementaryFilter.java     |    32 -
 .../net/sf/picard/filter/SolexaNoiseFilter.java    |    66 -
 src/java/net/sf/picard/filter/TagFilter.java       |    85 -
 .../sf/picard/filter/WholeReadClippedFilter.java   |    64 -
 .../sf/picard/illumina/CheckIlluminaDirectory.java |   256 -
 .../picard/illumina/ClusterDataToSamConverter.java |   174 -
 .../picard/illumina/ExtractIlluminaBarcodes.java   |   708 -
 .../illumina/IlluminaBasecallsConverter.java       |   858 -
 .../picard/illumina/IlluminaBasecallsToFastq.java  |   459 -
 .../sf/picard/illumina/IlluminaBasecallsToSam.java |   525 -
 .../sf/picard/illumina/MarkIlluminaAdapters.java   |   256 -
 .../sf/picard/illumina/parser/BarcodeParser.java   |    84 -
 .../net/sf/picard/illumina/parser/BclData.java     |    30 -
 .../net/sf/picard/illumina/parser/BclParser.java   |   295 -
 .../net/sf/picard/illumina/parser/ClusterData.java |   200 -
 .../parser/ClusterIntensityFileReader.java         |   213 -
 .../illumina/parser/CycleIlluminaFileMap.java      |    75 -
 .../sf/picard/illumina/parser/FilterParser.java    |    82 -
 .../illumina/parser/FourChannelIntensityData.java  |   103 -
 .../sf/picard/illumina/parser/IlluminaData.java    |    69 -
 .../illumina/parser/IlluminaDataProvider.java      |   230 -
 .../parser/IlluminaDataProviderFactory.java        |   367 -
 .../picard/illumina/parser/IlluminaDataType.java   |    35 -
 .../sf/picard/illumina/parser/IlluminaFileMap.java |    58 -
 .../parser/IlluminaFileNotFoundException.java      |    44 -
 .../picard/illumina/parser/IlluminaFileUtil.java   |   256 -
 .../illumina/parser/IlluminaMetricsCode.java       |    42 -
 .../sf/picard/illumina/parser/IlluminaParser.java  |    75 -
 .../illumina/parser/IlluminaTextIterator.java      |   122 -
 .../picard/illumina/parser/IntensityChannel.java   |    38 -
 .../illumina/parser/MultiTileBclFileUtil.java      |   115 -
 .../picard/illumina/parser/MultiTileBclParser.java |   171 -
 .../picard/illumina/parser/MultiTileFileUtil.java  |   120 -
 .../illumina/parser/MultiTileFilterParser.java     |    64 -
 .../illumina/parser/MultiTileLocsParser.java       |    82 -
 .../sf/picard/illumina/parser/MultiTileParser.java |   128 -
 .../sf/picard/illumina/parser/OutputMapping.java   |   183 -
 .../illumina/parser/ParameterizedFileUtil.java     |   174 -
 .../picard/illumina/parser/PerTileCycleParser.java |   203 -
 .../sf/picard/illumina/parser/PerTileFileUtil.java |    78 -
 .../sf/picard/illumina/parser/PerTileParser.java   |   142 -
 .../illumina/parser/PerTilePerCycleFileUtil.java   |   268 -
 .../net/sf/picard/illumina/parser/PosParser.java   |   133 -
 src/java/net/sf/picard/illumina/parser/Range.java  |    65 -
 .../net/sf/picard/illumina/parser/ReadData.java    |    96 -
 .../sf/picard/illumina/parser/ReadDescriptor.java  |    57 -
 .../sf/picard/illumina/parser/ReadStructure.java   |   358 -
 .../net/sf/picard/illumina/parser/ReadType.java    |    39 -
 src/java/net/sf/picard/illumina/parser/Tile.java   |   114 -
 .../net/sf/picard/illumina/parser/TileIndex.java   |   162 -
 .../sf/picard/illumina/parser/TileMetricsUtil.java |   154 -
 .../picard/illumina/parser/TilePhasingValue.java   |    30 -
 .../picard/illumina/parser/TileTemplateRead.java   |    32 -
 .../illumina/parser/fakers/BarcodeFileFaker.java   |    25 -
 .../illumina/parser/fakers/BciFileFaker.java       |    52 -
 .../illumina/parser/fakers/BclFileFaker.java       |    30 -
 .../illumina/parser/fakers/ClocsFileFaker.java     |    25 -
 .../picard/illumina/parser/fakers/FileFaker.java   |    79 -
 .../illumina/parser/fakers/FilterFileFaker.java    |    26 -
 .../illumina/parser/fakers/LocsFileFaker.java      |    28 -
 .../parser/fakers/MultiTileBclFileFaker.java       |    32 -
 .../parser/fakers/MultiTileLocsFileFaker.java      |    30 -
 .../illumina/parser/fakers/PosFileFaker.java       |    25 -
 .../AbstractIlluminaPositionFileReader.java        |   177 -
 .../illumina/parser/readers/BarcodeFileReader.java |    52 -
 .../illumina/parser/readers/BclIndexReader.java    |    75 -
 .../readers/BclQualityEvaluationStrategy.java      |    95 -
 .../picard/illumina/parser/readers/BclReader.java  |   343 -
 .../illumina/parser/readers/ClocsFileReader.java   |   157 -
 .../illumina/parser/readers/FilterFileReader.java  |   114 -
 .../illumina/parser/readers/LocsFileReader.java    |   119 -
 .../parser/readers/MMapBackedIteratorFactory.java  |   298 -
 .../illumina/parser/readers/PosFileReader.java     |    89 -
 .../parser/readers/TileMetricsOutReader.java       |   167 -
 src/java/net/sf/picard/io/FastLineReader.java      |   171 -
 src/java/net/sf/picard/io/IoUtil.java              |   686 -
 src/java/net/sf/picard/liftover/Chain.java         |   410 -
 src/java/net/sf/picard/liftover/LiftOver.java      |   292 -
 src/java/net/sf/picard/metrics/Header.java         |    41 -
 src/java/net/sf/picard/metrics/MetricBase.java     |   128 -
 src/java/net/sf/picard/metrics/MetricsFile.java    |   521 -
 .../net/sf/picard/metrics/MultiLevelCollector.java |   335 -
 .../net/sf/picard/metrics/MultilevelMetrics.java   |    16 -
 .../sf/picard/metrics/PerUnitMetricCollector.java  |    58 -
 .../sf/picard/metrics/SAMRecordAndReference.java   |    22 -
 .../SAMRecordAndReferenceMultiLevelCollector.java  |    14 -
 .../metrics/SAMRecordMultiLevelCollector.java      |    13 -
 src/java/net/sf/picard/metrics/StringHeader.java   |    72 -
 src/java/net/sf/picard/metrics/VersionHeader.java  |    81 -
 src/java/net/sf/picard/pedigree/PedFile.java       |   147 -
 src/java/net/sf/picard/pedigree/Sex.java           |    26 -
 .../reference/AbstractFastaSequenceFile.java       |   126 -
 .../net/sf/picard/reference/ExtractSequences.java  |   108 -
 .../net/sf/picard/reference/FastaSequenceFile.java |   156 -
 .../sf/picard/reference/FastaSequenceIndex.java    |   312 -
 .../picard/reference/IndexedFastaSequenceFile.java |   263 -
 .../net/sf/picard/reference/NormalizeFasta.java    |    93 -
 .../net/sf/picard/reference/ReferenceSequence.java |    72 -
 .../sf/picard/reference/ReferenceSequenceFile.java |    89 -
 .../reference/ReferenceSequenceFileFactory.java    |    90 -
 .../reference/ReferenceSequenceFileWalker.java     |   101 -
 .../net/sf/picard/sam/AbstractAlignmentMerger.java |   698 -
 .../sam/AbstractDuplicateFindingAlgorithm.java     |   175 -
 src/java/net/sf/picard/sam/AddCommentsToBam.java   |    57 -
 .../net/sf/picard/sam/AddOrReplaceReadGroups.java  |   112 -
 src/java/net/sf/picard/sam/BamIndexStats.java      |    77 -
 .../sam/BestEndMapqPrimaryAlignmentStrategy.java   |   101 -
 .../BestMapqPrimaryAlignmentSelectionStrategy.java |    95 -
 src/java/net/sf/picard/sam/BuildBamIndex.java      |   149 -
 src/java/net/sf/picard/sam/CleanSam.java           |   103 -
 .../sf/picard/sam/ComparableSamRecordIterator.java |    92 -
 src/java/net/sf/picard/sam/CompareSAMs.java        |   515 -
 .../sf/picard/sam/CoordinateSortedPairInfoMap.java |   289 -
 .../sf/picard/sam/CreateSequenceDictionary.java    |   180 -
 src/java/net/sf/picard/sam/DiskReadEndsMap.java    |   107 -
 src/java/net/sf/picard/sam/DownsampleSam.java      |    93 -
 src/java/net/sf/picard/sam/DuplicationMetrics.java |   203 -
 ...tFragmentPrimaryAlignmentSelectionStrategy.java |    93 -
 .../sf/picard/sam/EstimateLibraryComplexity.java   |   487 -
 src/java/net/sf/picard/sam/FastqToSam.java         |   362 -
 src/java/net/sf/picard/sam/FilterSamReads.java     |   233 -
 src/java/net/sf/picard/sam/FixMateInformation.java |   292 -
 src/java/net/sf/picard/sam/GatherBamFiles.java     |    97 -
 src/java/net/sf/picard/sam/HitsForInsert.java      |   283 -
 src/java/net/sf/picard/sam/MarkDuplicates.java     |   772 -
 src/java/net/sf/picard/sam/MergeBamAlignment.java  |   285 -
 src/java/net/sf/picard/sam/MergeSamFiles.java      |   166 -
 .../sf/picard/sam/MergingSamRecordIterator.java    |   245 -
 ...stDistantPrimaryAlignmentSelectionStrategy.java |   183 -
 .../sf/picard/sam/MultiHitAlignedReadIterator.java |   209 -
 .../sam/PrimaryAlignmentSelectionStrategy.java     |    37 -
 src/java/net/sf/picard/sam/RAMReadEndsMap.java     |    72 -
 src/java/net/sf/picard/sam/ReadEnds.java           |    63 -
 src/java/net/sf/picard/sam/ReadEndsCodec.java      |   106 -
 src/java/net/sf/picard/sam/ReadEndsMap.java        |    59 -
 src/java/net/sf/picard/sam/ReorderSam.java         |   233 -
 src/java/net/sf/picard/sam/ReplaceSamHeader.java   |   114 -
 .../net/sf/picard/sam/ReservedTagConstants.java    |    72 -
 ...RevertOriginalBaseQualitiesAndAddMateCigar.java |   244 -
 src/java/net/sf/picard/sam/RevertSam.java          |   343 -
 src/java/net/sf/picard/sam/SamAlignmentMerger.java |   353 -
 .../net/sf/picard/sam/SamFileHeaderMerger.java     |   775 -
 src/java/net/sf/picard/sam/SamFileValidator.java   |   800 -
 src/java/net/sf/picard/sam/SamFormatConverter.java |    80 -
 src/java/net/sf/picard/sam/SamToFastq.java         |   438 -
 src/java/net/sf/picard/sam/SortSam.java            |    81 -
 src/java/net/sf/picard/sam/ValidateSamFile.java    |   178 -
 src/java/net/sf/picard/sam/ViewSam.java            |   108 -
 .../net/sf/picard/util/AbstractInputParser.java    |   200 -
 src/java/net/sf/picard/util/AdapterMarker.java     |   341 -
 src/java/net/sf/picard/util/AdapterPair.java       |    16 -
 src/java/net/sf/picard/util/AsyncIterator.java     |   170 -
 src/java/net/sf/picard/util/BasicInputParser.java  |   176 -
 src/java/net/sf/picard/util/CigarUtil.java         |   289 -
 src/java/net/sf/picard/util/ClippingUtility.java   |   278 -
 src/java/net/sf/picard/util/CsvInputParser.java    |    36 -
 .../util/DelimitedTextFileWithHeaderIterator.java  |   111 -
 .../net/sf/picard/util/FastqQualityFormat.java     |    36 -
 .../sf/picard/util/FileAppendStreamLRUCache.java   |    76 -
 .../picard/util/FileChannelJDKBugWorkAround.java   |    64 -
 src/java/net/sf/picard/util/FormatUtil.java        |   181 -
 src/java/net/sf/picard/util/Histogram.java         |   466 -
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 src/java/net/sf/picard/util/Interval.java          |   193 -
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 src/java/net/sf/picard/util/IntervalListTools.java |   352 -
 src/java/net/sf/picard/util/IntervalTree.java      |  1227 -
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 src/java/net/sf/picard/util/ListMap.java           |    48 -
 src/java/net/sf/picard/util/Locus.java             |    36 -
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 src/java/net/sf/picard/util/LocusImpl.java         |    49 -
 src/java/net/sf/picard/util/Log.java               |   211 -
 src/java/net/sf/picard/util/MathUtil.java          |   277 -
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 src/java/net/sf/picard/util/MetricsDoclet.java     |   179 -
 src/java/net/sf/picard/util/OverlapDetector.java   |   119 -
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 src/java/net/sf/picard/util/ProcessExecutor.java   |   235 -
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 .../sf/picard/util/QualityEncodingDetector.java    |   359 -
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 src/java/net/sf/picard/util/RExecutor.java         |   111 -
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 .../net/sf/picard/util/ResourceLimitedMap.java     |   105 -
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 src/java/net/sf/picard/util/SamLocusIterator.java  |   498 -
 .../util/SamRecordIntervalIteratorFactory.java     |   159 -
 .../net/sf/picard/util/SolexaQualityConverter.java |   124 -
 src/java/net/sf/picard/util/TabbedInputParser.java |    64 -
 .../util/TabbedTextFileWithHeaderParser.java       |   173 -
 src/java/net/sf/picard/util/UnsignedTypeUtil.java  |    28 -
 .../util/WholeGenomeReferenceSequenceMask.java     |    80 -
 src/java/net/sf/picard/vcf/MakeSitesOnlyVcf.java   |   105 -
 src/java/net/sf/picard/vcf/MergeVcfs.java          |   159 -
 src/java/net/sf/picard/vcf/SplitVcfs.java          |   120 -
 src/java/net/sf/picard/vcf/VcfFormatConverter.java |   117 -
 src/java/net/sf/samtools/AbstractBAMFileIndex.java |   636 -
 .../net/sf/samtools/AbstractSAMHeaderRecord.java   |   109 -
 src/java/net/sf/samtools/AlignmentBlock.java       |    54 -
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 src/java/net/sf/samtools/BAMFileReader.java        |   987 -
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 src/java/net/sf/samtools/SAMFileWriterImpl.java    |   231 -
 src/java/net/sf/samtools/SAMFormatException.java   |    44 -
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 src/java/net/sf/samtools/SAMLineParser.java        |   457 -
 src/java/net/sf/samtools/SAMProgramRecord.java     |   128 -
 src/java/net/sf/samtools/SAMReadGroupRecord.java   |   145 -
 src/java/net/sf/samtools/SAMRecord.java            |  1732 --
 src/java/net/sf/samtools/SAMRecordComparator.java  |    40 -
 .../sf/samtools/SAMRecordCoordinateComparator.java |    95 -
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 src/java/net/sf/samtools/SAMTagUtil.java           |   122 -
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 .../MarkDuplicatesWithMateCigarTester.java         |    46 +
 .../SimpleMarkDuplicatesWithMateCigar.java         |   222 +
 .../SimpleMarkDuplicatesWithMateCigarTest.java     |    44 +
 .../SimpleMarkDuplicatesWithMateCigarTester.java   |    45 +
 .../util/OpticalDuplicateFinderTest.java           |    76 +
 .../java/picard/sam/testers/CleanSamTester.java    |    65 +
 .../java/picard/sam/testers/SamFileTester.java     |   307 +
 .../java/picard/sam/testers/ValidateSamTester.java |    22 +
 .../java/picard/util/BedToIntervalListTest.java    |   103 +
 .../java/picard/util/ClippingUtilityTest.java      |   380 +
 .../DelimitedTextFileWithHeaderIteratorTest.java   |    96 +
 src/tests/java/picard/util/FifoBufferTest.java     |    74 +
 .../util/FileChannelJDKBugWorkAroundTest.java      |    36 +
 src/tests/java/picard/util/IlluminaUtilTest.java   |    87 +
 .../picard/util/IntervalListScattererTest.java     |   203 +
 src/tests/java/picard/util/MathUtilTest.java       |    86 +
 .../java/picard/util/MergingIteratorTest.java      |   177 +
 src/tests/java/picard/util/RExecutorTest.java      |    50 +
 .../java/picard/util/ScatterIntervalsByNsTest.java |   165 +
 .../util/TabbedTextFileWithHeaderParserTest.java   |    94 +
 .../java/picard/util/TextFileParsersTest.java      |   314 +
 .../java/picard/util/UnsignedTypeUtilTest.java     |    75 +
 .../picard/vcf/AbstractVcfMergingClpTester.java    |   174 +
 .../vcf/CollectVariantCallingMetricsTest.java      |   119 +
 .../vcf/GenotypeConcordanceGA4GHSchemeTest.java    |   157 +
 ...otypeConcordanceGA4GHSchemeWithMissingTest.java |    79 +
 .../java/picard/vcf/GenotypeConcordanceTest.java   |   495 +
 src/tests/java/picard/vcf/MergeVcfsTest.java       |    14 +
 src/tests/java/picard/vcf/SortVcfsTest.java        |   120 +
 src/tests/java/picard/vcf/SplitVcfsTest.java       |    59 +
 src/tests/java/picard/vcf/TestFilterVcf.java       |   142 +
 .../vcf/UpdateVcfSequenceDictionaryTest.java       |    74 +
 .../picard/vcf/VariantContextComparatorTest.java   |   107 +
 .../java/picard/vcf/VcfFormatConverterTest.java    |   127 +
 .../vcf/processor/AccumulatorExecutorTest.java     |    86 +
 .../picard/vcf/processor/ByWholeContigTest.java    |    46 +
 .../java/picard/vcf/processor/ThreadsafeTest.java  |    96 +
 .../vcf/processor/VcfFileSegmentGeneratorTest.java |    55 +
 .../vcf/processor/WidthLimitingDecoratorTest.java  |   122 +
 src/tests/resources/testng.xml                     |    39 +
 .../illumina/25T8B25T/fastq/AACAATGG.1.fastq       |    16 -
 .../illumina/25T8B25T/fastq/AACAATGG.2.fastq       |    16 -
 .../25T8B25T/fastq/AACAATGG.barcode_1.fastq        |    16 -
 .../illumina/25T8B25T/fastq/AACGCATT.1.fastq       |    28 -
 .../illumina/25T8B25T/fastq/AACGCATT.2.fastq       |    28 -
 .../25T8B25T/fastq/AACGCATT.barcode_1.fastq        |    28 -
 .../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 -
 .../illumina/25T8B25T/fastq/ACTAAGAC.1.fastq       |    16 -
 .../illumina/25T8B25T/fastq/ACTAAGAC.2.fastq       |    16 -
 .../25T8B25T/fastq/ACTAAGAC.barcode_1.fastq        |    16 -
 .../illumina/25T8B25T/fastq/ACTGTATC.1.fastq       |    16 -
 .../illumina/25T8B25T/fastq/ACTGTATC.2.fastq       |    16 -
 .../25T8B25T/fastq/ACTGTATC.barcode_1.fastq        |    16 -
 .../illumina/25T8B25T/fastq/AGCATGGA.1.fastq       |    12 -
 .../illumina/25T8B25T/fastq/AGCATGGA.2.fastq       |    12 -
 .../25T8B25T/fastq/AGCATGGA.barcode_1.fastq        |    12 -
 .../illumina/25T8B25T/fastq/AGGTAAGG.1.fastq       |    16 -
 .../illumina/25T8B25T/fastq/AGGTAAGG.2.fastq       |    16 -
 .../25T8B25T/fastq/AGGTAAGG.barcode_1.fastq        |    16 -
 .../illumina/25T8B25T/fastq/AGGTCGCA.1.fastq       |    16 -
 .../illumina/25T8B25T/fastq/AGGTCGCA.2.fastq       |    16 -
 .../25T8B25T/fastq/AGGTCGCA.barcode_1.fastq        |    16 -
 .../illumina/25T8B25T/fastq/ATTATCAA.1.fastq       |    20 -
 .../illumina/25T8B25T/fastq/ATTATCAA.2.fastq       |    20 -
 .../25T8B25T/fastq/ATTATCAA.barcode_1.fastq        |    20 -
 .../illumina/25T8B25T/fastq/ATTCCTCT.1.fastq       |    16 -
 .../illumina/25T8B25T/fastq/ATTCCTCT.2.fastq       |    16 -
 .../25T8B25T/fastq/ATTCCTCT.barcode_1.fastq        |    16 -
 .../illumina/25T8B25T/fastq/CAACTCTC.1.fastq       |    20 -
 .../illumina/25T8B25T/fastq/CAACTCTC.2.fastq       |    20 -
 .../25T8B25T/fastq/CAACTCTC.barcode_1.fastq        |    20 -
 .../illumina/25T8B25T/fastq/CAATAGTC.1.fastq       |    28 -
 .../illumina/25T8B25T/fastq/CAATAGTC.2.fastq       |    28 -
 .../25T8B25T/fastq/CAATAGTC.barcode_1.fastq        |    28 -
 .../illumina/25T8B25T/fastq/CAGCGGTA.1.fastq       |    20 -
 .../illumina/25T8B25T/fastq/CAGCGGTA.2.fastq       |    20 -
 .../25T8B25T/fastq/CAGCGGTA.barcode_1.fastq        |    20 -
 .../illumina/25T8B25T/fastq/CCAACATT.1.fastq       |    28 -
 .../illumina/25T8B25T/fastq/CCAACATT.2.fastq       |    28 -
 .../25T8B25T/fastq/CCAACATT.barcode_1.fastq        |    28 -
 .../illumina/25T8B25T/fastq/CCAGCACC.1.fastq       |    12 -
 .../illumina/25T8B25T/fastq/CCAGCACC.2.fastq       |    12 -
 .../25T8B25T/fastq/CCAGCACC.barcode_1.fastq        |    12 -
 .../illumina/25T8B25T/fastq/CGCCTTCC.1.fastq       |     8 -
 .../illumina/25T8B25T/fastq/CGCCTTCC.2.fastq       |     8 -
 .../25T8B25T/fastq/CGCCTTCC.barcode_1.fastq        |     8 -
 .../illumina/25T8B25T/fastq/CGCTATGT.1.fastq       |    20 -
 .../illumina/25T8B25T/fastq/CGCTATGT.2.fastq       |    20 -
 .../25T8B25T/fastq/CGCTATGT.barcode_1.fastq        |    20 -
 .../illumina/25T8B25T/fastq/CTAACTCG.1.fastq       |    16 -
 .../illumina/25T8B25T/fastq/CTAACTCG.2.fastq       |    16 -
 .../25T8B25T/fastq/CTAACTCG.barcode_1.fastq        |    16 -
 .../illumina/25T8B25T/fastq/CTATGCGT.1.fastq       |    28 -
 .../illumina/25T8B25T/fastq/CTATGCGT.2.fastq       |    28 -
 .../25T8B25T/fastq/CTATGCGT.barcode_1.fastq        |    28 -
 .../illumina/25T8B25T/fastq/CTGCGGAT.1.fastq       |    12 -
 .../illumina/25T8B25T/fastq/CTGCGGAT.2.fastq       |    12 -
 .../25T8B25T/fastq/CTGCGGAT.barcode_1.fastq        |    12 -
 .../illumina/25T8B25T/fastq/CTGTAATC.1.fastq       |    24 -
 .../illumina/25T8B25T/fastq/CTGTAATC.2.fastq       |    24 -
 .../25T8B25T/fastq/CTGTAATC.barcode_1.fastq        |    24 -
 .../illumina/25T8B25T/fastq/GAAGGAAG.1.fastq       |    12 -
 .../illumina/25T8B25T/fastq/GAAGGAAG.2.fastq       |    12 -
 .../25T8B25T/fastq/GAAGGAAG.barcode_1.fastq        |    12 -
 .../illumina/25T8B25T/fastq/GACCAGGA.1.fastq       |    28 -
 .../illumina/25T8B25T/fastq/GACCAGGA.2.fastq       |    28 -
 .../25T8B25T/fastq/GACCAGGA.barcode_1.fastq        |    28 -
 .../illumina/25T8B25T/fastq/GACCGTTG.1.fastq       |    16 -
 .../illumina/25T8B25T/fastq/GACCGTTG.2.fastq       |    16 -
 .../25T8B25T/fastq/GACCGTTG.barcode_1.fastq        |    16 -
 .../illumina/25T8B25T/fastq/GACCTAAC.1.fastq       |     4 -
 .../illumina/25T8B25T/fastq/GACCTAAC.2.fastq       |     4 -
 .../25T8B25T/fastq/GACCTAAC.barcode_1.fastq        |     4 -
 .../illumina/25T8B25T/fastq/GATATCCA.1.fastq       |    12 -
 .../illumina/25T8B25T/fastq/GATATCCA.2.fastq       |    12 -
 .../25T8B25T/fastq/GATATCCA.barcode_1.fastq        |    12 -
 .../illumina/25T8B25T/fastq/GCCGTCGA.1.fastq       |    20 -
 .../illumina/25T8B25T/fastq/GCCGTCGA.2.fastq       |    20 -
 .../25T8B25T/fastq/GCCGTCGA.barcode_1.fastq        |    20 -
 .../illumina/25T8B25T/fastq/GCCTAGCC.1.fastq       |    20 -
 .../illumina/25T8B25T/fastq/GCCTAGCC.2.fastq       |    20 -
 .../25T8B25T/fastq/GCCTAGCC.barcode_1.fastq        |    20 -
 .../illumina/25T8B25T/fastq/GTAACATC.1.fastq       |     8 -
 .../illumina/25T8B25T/fastq/GTAACATC.2.fastq       |     8 -
 .../25T8B25T/fastq/GTAACATC.barcode_1.fastq        |     8 -
 .../illumina/25T8B25T/fastq/GTCCACAG.1.fastq       |     8 -
 .../illumina/25T8B25T/fastq/GTCCACAG.2.fastq       |     8 -
 .../25T8B25T/fastq/GTCCACAG.barcode_1.fastq        |     8 -
 .../sf/picard/illumina/25T8B25T/fastq/N.1.fastq    |    64 -
 .../sf/picard/illumina/25T8B25T/fastq/N.2.fastq    |    64 -
 .../illumina/25T8B25T/fastq/N.barcode_1.fastq      |    64 -
 .../illumina/25T8B25T/fastq/TAAGCACA.1.fastq       |     8 -
 .../illumina/25T8B25T/fastq/TAAGCACA.2.fastq       |     8 -
 .../25T8B25T/fastq/TAAGCACA.barcode_1.fastq        |     8 -
 .../illumina/25T8B25T/fastq/TATCCAGG.1.fastq       |    16 -
 .../illumina/25T8B25T/fastq/TATCCAGG.2.fastq       |    16 -
 .../25T8B25T/fastq/TATCCAGG.barcode_1.fastq        |    16 -
 .../illumina/25T8B25T/fastq/TATCTGCC.1.fastq       |    28 -
 .../illumina/25T8B25T/fastq/TATCTGCC.2.fastq       |    28 -
 .../25T8B25T/fastq/TATCTGCC.barcode_1.fastq        |    28 -
 .../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 -
 .../illumina/25T8B25T/fastq/nonBarcoded.1.fastq    |   720 -
 .../illumina/25T8B25T/fastq/nonBarcoded.2.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/nonBarcoded.sam  |   182 -
 .../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 -
 .../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 -
 .../25T8B8B25T/fastq/ACTAAGACGTCCTCAT.1.fastq      |     4 -
 .../25T8B8B25T/fastq/ACTAAGACGTCCTCAT.2.fastq      |     4 -
 .../fastq/ACTAAGACGTCCTCAT.barcode_1.fastq         |     4 -
 .../fastq/ACTAAGACGTCCTCAT.barcode_2.fastq         |     4 -
 .../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 -
 .../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 -
 .../25T8B8B25T/fastq/CATGCTTATAGCATTG.1.fastq      |     8 -
 .../25T8B8B25T/fastq/CATGCTTATAGCATTG.2.fastq      |     8 -
 .../fastq/CATGCTTATAGCATTG.barcode_1.fastq         |     8 -
 .../fastq/CATGCTTATAGCATTG.barcode_2.fastq         |     8 -
 .../25T8B8B25T/fastq/CCAGAGCTCAACTGAT.1.fastq      |     8 -
 .../25T8B8B25T/fastq/CCAGAGCTCAACTGAT.2.fastq      |     8 -
 .../fastq/CCAGAGCTCAACTGAT.barcode_1.fastq         |     8 -
 .../fastq/CCAGAGCTCAACTGAT.barcode_2.fastq         |     8 -
 .../25T8B8B25T/fastq/CCCGATTTTCTCTCCC.1.fastq      |     0
 .../25T8B8B25T/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 -
 .../25T8B8B25T/fastq/CCTATTCTTCGTTTTC.1.fastq      |     0
 .../25T8B8B25T/fastq/CCTATTCTTCGTTTTC.2.fastq      |     0
 .../fastq/CCTATTCTTCGTTTTC.barcode_1.fastq         |     0
 .../fastq/CCTATTCTTCGTTTTC.barcode_2.fastq         |     0
 .../25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.1.fastq      |     0
 .../25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.2.fastq      |     0
 .../fastq/CCTCTTCTCTCGCTTT.barcode_1.fastq         |     0
 .../fastq/CCTCTTCTCTCGCTTT.barcode_2.fastq         |     0
 .../25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.1.fastq      |     0
 .../25T8B8B25T/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 -
 .../25T8B8B25T/fastq/CCTTCTTTTATCATTT.1.fastq      |     0
 .../25T8B8B25T/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 -
 .../25T8B8B25T/fastq/CGCTATGTTTCTCCTT.1.fastq      |     0
 .../25T8B8B25T/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 -
 .../25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.1.fastq      |     0
 .../25T8B8B25T/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 -
 .../25T8B8B25T/fastq/GCCGTCGAAGGTACCC.1.fastq      |     0
 .../25T8B8B25T/fastq/GCCGTCGAAGGTACCC.2.fastq      |     0
 .../fastq/GCCGTCGAAGGTACCC.barcode_1.fastq         |     0
 .../fastq/GCCGTCGAAGGTACCC.barcode_2.fastq         |     0
 .../25T8B8B25T/fastq/GCCGTCGATGGTACCC.1.fastq      |     0
 .../25T8B8B25T/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 -
 .../25T8B8B25T/fastq/GCTATCCACCTCCCCC.1.fastq      |     0
 .../25T8B8B25T/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 -
 .../25T8B8B25T/fastq/GTATAACATATTCAAC.1.fastq      |     0
 .../25T8B8B25T/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 -
 .../25T8B8B25T/fastq/GTCTGATGTCACTTCC.1.fastq      |     0
 .../25T8B8B25T/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 -
 .../25T8B8B25T/fastq/TCCCCGTTCCAACTTC.1.fastq      |     0
 .../25T8B8B25T/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 -
 .../25T8B8B25T/fastq/TGCTCGACTTCACAGT.1.fastq      |     0
 .../25T8B8B25T/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 -
 .../25T8B8B25T/fastq/TGTATCTCTTACTCTT.1.fastq      |     0
 .../25T8B8B25T/fastq/TGTATCTCTTACTCTT.2.fastq      |     0
 .../fastq/TGTATCTCTTACTCTT.barcode_1.fastq         |     0
 .../fastq/TGTATCTCTTACTCTT.barcode_2.fastq         |     0
 .../25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.1.fastq      |     0
 .../25T8B8B25T/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 -
 .../25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.1.fastq      |     0
 .../25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.2.fastq      |     0
 .../fastq/TTCCCCAGTGCTTTTA.barcode_1.fastq         |     0
 .../fastq/TTCCCCAGTGCTTTTA.barcode_2.fastq         |     0
 .../25T8B8B25T/fastq/TTCCTCCTCACCATCC.1.fastq      |     0
 .../25T8B8B25T/fastq/TTCCTCCTCACCATCC.2.fastq      |     0
 .../fastq/TTCCTCCTCACCATCC.barcode_1.fastq         |     0
 .../fastq/TTCCTCCTCACCATCC.barcode_2.fastq         |     0
 .../25T8B8B25T/fastq/TTCTCATCTTCCTTCC.1.fastq      |     0
 .../25T8B8B25T/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 -
 .../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 -
 .../picard/illumina/readerTests/s_1_1104_pos.txt   |     0
 .../intervallist/IntervalListFromVCFTest.vcf       |    53 -
 .../IntervalListFromVCFTestComp.interval_list      |     7 -
 ...ntervalListFromVCFTestCompInverse.interval_list |    10 -
 ...lListFromVCFTestCompInverseManual.interval_list |    10 -
 .../intervallist/IntervalListFromVCFTestManual.vcf |    57 -
 ...IntervalListFromVCFTestManualComp.interval_list |    12 -
 .../IntervalListchr123_empty.interval_list         |     4 -
 testdata/net/sf/picard/io/5newline5.txt            |     2 -
 testdata/net/sf/picard/io/empty.txt                |     0
 testdata/net/sf/picard/io/slurptest.txt            |     3 -
 .../net/sf/picard/liftover/hg18ToHg19.over.chain   | 30850 -------------------
 .../reference/Homo_sapiens_assembly18.fasta.fai    |    45 -
 .../reference/Homo_sapiens_assembly18.trimmed.dict |     3 -
 .../Homo_sapiens_assembly18.trimmed.fasta          | 16946 ----------
 .../Homo_sapiens_assembly18.trimmed.fasta.fai      |     2 -
 .../Homo_sapiens_assembly18.trimmed.nodict.fasta   | 16946 ----------
 ...omo_sapiens_assembly18.trimmed.nodict.fasta.fai |     2 -
 testdata/net/sf/picard/reference/testing.fai       |     7 -
 testdata/net/sf/picard/sam/Chromosome1to10.bam     |   Bin 3708 -> 0 bytes
 testdata/net/sf/picard/sam/Chromosome5to9.bam      |   Bin 1991 -> 0 bytes
 .../sf/picard/sam/MergeBamAlignment/cliptest.dict  |     2 -
 .../sam/MergeSamFiles/case1/expected_output.sam    |    13 -
 .../sam/MergeSamFiles/case2/expected_output.sam    |    21 -
 .../picard/sam/ValidateSamFileTest/bad_index.bai   |   Bin 1621416 -> 0 bytes
 .../picard/sam/ValidateSamFileTest/bad_index.bam   |   Bin 594149 -> 0 bytes
 .../picard/sam/ValidateSamFileTest/buggyHeader.sam |    30 -
 .../sam/ValidateSamFileTest/duplicate_rg.sam       |    11 -
 .../picard/sam/ValidateSamFileTest/hanging_tab.sam |     3 -
 .../inappropriate_mate_cigar_string.sam            |    13 -
 .../invalid_mate_cigar_string.sam                  |    19 -
 .../invalid_queryname_sort_order.sam               |    27 -
 .../sam/ValidateSamFileTest/missing_fields.sam     |     3 -
 .../ValidateSamFileTest/missing_platform_unit.sam  |    10 -
 .../picard/sam/ValidateSamFileTest/truncated.bam   |   Bin 336031 -> 0 bytes
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 .../illumina/25T8B25T/fastq/ACTAAGAC.2.fastq       |    16 +
 .../25T8B25T/fastq/ACTAAGAC.barcode_1.fastq        |    16 +
 .../illumina/25T8B25T/fastq/ACTGTACC.1.fastq       |     0
 .../illumina/25T8B25T/fastq/ACTGTACC.2.fastq       |     0
 .../25T8B25T/fastq/ACTGTACC.barcode_1.fastq        |     0
 .../illumina/25T8B25T/fastq/ACTGTATC.1.fastq       |    16 +
 .../illumina/25T8B25T/fastq/ACTGTATC.2.fastq       |    16 +
 .../25T8B25T/fastq/ACTGTATC.barcode_1.fastq        |    16 +
 .../illumina/25T8B25T/fastq/AGAAAAGA.1.fastq       |     0
 .../illumina/25T8B25T/fastq/AGAAAAGA.2.fastq       |     0
 .../25T8B25T/fastq/AGAAAAGA.barcode_1.fastq        |     0
 .../illumina/25T8B25T/fastq/AGCATGGA.1.fastq       |    12 +
 .../illumina/25T8B25T/fastq/AGCATGGA.2.fastq       |    12 +
 .../25T8B25T/fastq/AGCATGGA.barcode_1.fastq        |    12 +
 .../illumina/25T8B25T/fastq/AGGTAAGG.1.fastq       |    16 +
 .../illumina/25T8B25T/fastq/AGGTAAGG.2.fastq       |    16 +
 .../25T8B25T/fastq/AGGTAAGG.barcode_1.fastq        |    16 +
 .../illumina/25T8B25T/fastq/AGGTCGCA.1.fastq       |    16 +
 .../illumina/25T8B25T/fastq/AGGTCGCA.2.fastq       |    16 +
 .../25T8B25T/fastq/AGGTCGCA.barcode_1.fastq        |    16 +
 .../illumina/25T8B25T/fastq/ATTATCAA.1.fastq       |    20 +
 .../illumina/25T8B25T/fastq/ATTATCAA.2.fastq       |    20 +
 .../25T8B25T/fastq/ATTATCAA.barcode_1.fastq        |    20 +
 .../illumina/25T8B25T/fastq/ATTCCTCT.1.fastq       |    16 +
 .../illumina/25T8B25T/fastq/ATTCCTCT.2.fastq       |    16 +
 .../25T8B25T/fastq/ATTCCTCT.barcode_1.fastq        |    16 +
 .../illumina/25T8B25T/fastq/CAACTCTC.1.fastq       |    20 +
 .../illumina/25T8B25T/fastq/CAACTCTC.2.fastq       |    20 +
 .../25T8B25T/fastq/CAACTCTC.barcode_1.fastq        |    20 +
 .../illumina/25T8B25T/fastq/CAATAGAC.1.fastq       |     0
 .../illumina/25T8B25T/fastq/CAATAGAC.2.fastq       |     0
 .../25T8B25T/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 +
 .../illumina/25T8B25T/fastq/CAGCGGAT.1.fastq       |     0
 .../illumina/25T8B25T/fastq/CAGCGGAT.2.fastq       |     0
 .../25T8B25T/fastq/CAGCGGAT.barcode_1.fastq        |     0
 .../illumina/25T8B25T/fastq/CAGCGGTA.1.fastq       |    20 +
 .../illumina/25T8B25T/fastq/CAGCGGTA.2.fastq       |    20 +
 .../25T8B25T/fastq/CAGCGGTA.barcode_1.fastq        |    20 +
 .../illumina/25T8B25T/fastq/CCAACATT.1.fastq       |    28 +
 .../illumina/25T8B25T/fastq/CCAACATT.2.fastq       |    28 +
 .../25T8B25T/fastq/CCAACATT.barcode_1.fastq        |    28 +
 .../illumina/25T8B25T/fastq/CCAGCACC.1.fastq       |    12 +
 .../illumina/25T8B25T/fastq/CCAGCACC.2.fastq       |    12 +
 .../25T8B25T/fastq/CCAGCACC.barcode_1.fastq        |    12 +
 .../illumina/25T8B25T/fastq/CCATGCGT.1.fastq       |     0
 .../illumina/25T8B25T/fastq/CCATGCGT.2.fastq       |     0
 .../25T8B25T/fastq/CCATGCGT.barcode_1.fastq        |     0
 .../illumina/25T8B25T/fastq/CGCCTTCC.1.fastq       |     8 +
 .../illumina/25T8B25T/fastq/CGCCTTCC.2.fastq       |     8 +
 .../25T8B25T/fastq/CGCCTTCC.barcode_1.fastq        |     8 +
 .../illumina/25T8B25T/fastq/CGCTATGT.1.fastq       |    20 +
 .../illumina/25T8B25T/fastq/CGCTATGT.2.fastq       |    20 +
 .../25T8B25T/fastq/CGCTATGT.barcode_1.fastq        |    20 +
 .../illumina/25T8B25T/fastq/CTAACTCG.1.fastq       |    16 +
 .../illumina/25T8B25T/fastq/CTAACTCG.2.fastq       |    16 +
 .../25T8B25T/fastq/CTAACTCG.barcode_1.fastq        |    16 +
 .../illumina/25T8B25T/fastq/CTATGCGC.1.fastq       |     0
 .../illumina/25T8B25T/fastq/CTATGCGC.2.fastq       |     0
 .../25T8B25T/fastq/CTATGCGC.barcode_1.fastq        |     0
 .../illumina/25T8B25T/fastq/CTATGCGT.1.fastq       |    28 +
 .../illumina/25T8B25T/fastq/CTATGCGT.2.fastq       |    28 +
 .../25T8B25T/fastq/CTATGCGT.barcode_1.fastq        |    28 +
 .../illumina/25T8B25T/fastq/CTGCGGAT.1.fastq       |    12 +
 .../illumina/25T8B25T/fastq/CTGCGGAT.2.fastq       |    12 +
 .../25T8B25T/fastq/CTGCGGAT.barcode_1.fastq        |    12 +
 .../illumina/25T8B25T/fastq/CTGTAATC.1.fastq       |    24 +
 .../illumina/25T8B25T/fastq/CTGTAATC.2.fastq       |    24 +
 .../25T8B25T/fastq/CTGTAATC.barcode_1.fastq        |    24 +
 .../illumina/25T8B25T/fastq/GAAAAAAA.1.fastq       |     0
 .../illumina/25T8B25T/fastq/GAAAAAAA.2.fastq       |     0
 .../25T8B25T/fastq/GAAAAAAA.barcode_1.fastq        |     0
 .../illumina/25T8B25T/fastq/GAACGAT..1.fastq       |     0
 .../illumina/25T8B25T/fastq/GAACGAT..2.fastq       |     0
 .../25T8B25T/fastq/GAACGAT..barcode_1.fastq        |     0
 .../illumina/25T8B25T/fastq/GAAGGAAG.1.fastq       |    12 +
 .../illumina/25T8B25T/fastq/GAAGGAAG.2.fastq       |    12 +
 .../25T8B25T/fastq/GAAGGAAG.barcode_1.fastq        |    12 +
 .../illumina/25T8B25T/fastq/GACCAGGA.1.fastq       |    28 +
 .../illumina/25T8B25T/fastq/GACCAGGA.2.fastq       |    28 +
 .../25T8B25T/fastq/GACCAGGA.barcode_1.fastq        |    28 +
 .../illumina/25T8B25T/fastq/GACCAGGC.1.fastq       |     0
 .../illumina/25T8B25T/fastq/GACCAGGC.2.fastq       |     0
 .../25T8B25T/fastq/GACCAGGC.barcode_1.fastq        |     0
 .../illumina/25T8B25T/fastq/GACCGTTG.1.fastq       |    16 +
 .../illumina/25T8B25T/fastq/GACCGTTG.2.fastq       |    16 +
 .../25T8B25T/fastq/GACCGTTG.barcode_1.fastq        |    16 +
 .../illumina/25T8B25T/fastq/GACCTAAC.1.fastq       |     4 +
 .../illumina/25T8B25T/fastq/GACCTAAC.2.fastq       |     4 +
 .../25T8B25T/fastq/GACCTAAC.barcode_1.fastq        |     4 +
 .../illumina/25T8B25T/fastq/GATATCCA.1.fastq       |    12 +
 .../illumina/25T8B25T/fastq/GATATCCA.2.fastq       |    12 +
 .../25T8B25T/fastq/GATATCCA.barcode_1.fastq        |    12 +
 .../illumina/25T8B25T/fastq/GCCGTCGA.1.fastq       |    20 +
 .../illumina/25T8B25T/fastq/GCCGTCGA.2.fastq       |    20 +
 .../25T8B25T/fastq/GCCGTCGA.barcode_1.fastq        |    20 +
 .../illumina/25T8B25T/fastq/GCCTAGCC.1.fastq       |    20 +
 .../illumina/25T8B25T/fastq/GCCTAGCC.2.fastq       |    20 +
 .../25T8B25T/fastq/GCCTAGCC.barcode_1.fastq        |    20 +
 .../illumina/25T8B25T/fastq/GTAACATC.1.fastq       |     8 +
 .../illumina/25T8B25T/fastq/GTAACATC.2.fastq       |     8 +
 .../25T8B25T/fastq/GTAACATC.barcode_1.fastq        |     8 +
 .../illumina/25T8B25T/fastq/GTCCACAG.1.fastq       |     8 +
 .../illumina/25T8B25T/fastq/GTCCACAG.2.fastq       |     8 +
 .../25T8B25T/fastq/GTCCACAG.barcode_1.fastq        |     8 +
 testdata/picard/illumina/25T8B25T/fastq/N.1.fastq  |    64 +
 testdata/picard/illumina/25T8B25T/fastq/N.2.fastq  |    64 +
 .../illumina/25T8B25T/fastq/N.barcode_1.fastq      |    64 +
 .../illumina/25T8B25T/fastq/TAAGCACA.1.fastq       |     8 +
 .../illumina/25T8B25T/fastq/TAAGCACA.2.fastq       |     8 +
 .../25T8B25T/fastq/TAAGCACA.barcode_1.fastq        |     8 +
 .../illumina/25T8B25T/fastq/TACCGTCT.1.fastq       |     0
 .../illumina/25T8B25T/fastq/TACCGTCT.2.fastq       |     0
 .../25T8B25T/fastq/TACCGTCT.barcode_1.fastq        |     0
 .../illumina/25T8B25T/fastq/TAGCGGTA.1.fastq       |     0
 .../illumina/25T8B25T/fastq/TAGCGGTA.2.fastq       |     0
 .../25T8B25T/fastq/TAGCGGTA.barcode_1.fastq        |     0
 .../illumina/25T8B25T/fastq/TATCAGCC.1.fastq       |     0
 .../illumina/25T8B25T/fastq/TATCAGCC.2.fastq       |     0
 .../25T8B25T/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 +
 .../illumina/25T8B25T/fastq/TATCCATG.1.fastq       |     0
 .../illumina/25T8B25T/fastq/TATCCATG.2.fastq       |     0
 .../25T8B25T/fastq/TATCCATG.barcode_1.fastq        |     0
 .../illumina/25T8B25T/fastq/TATCTCGG.1.fastq       |     0
 .../illumina/25T8B25T/fastq/TATCTCGG.2.fastq       |     0
 .../25T8B25T/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 +
 .../illumina/25T8B25T/fastq/TCCGTCTA.1.fastq       |     0
 .../illumina/25T8B25T/fastq/TCCGTCTA.2.fastq       |     0
 .../25T8B25T/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  |     0
 .../illumina/25T8B25T/fastq/mp_barcode.params      |     0
 .../illumina/25T8B25T/fastq/nonBarcoded.1.fastq    |   720 +
 .../illumina/25T8B25T/fastq/nonBarcoded.2.fastq    |   720 +
 .../illumina/25T8B25T/fastq/testMultiplex.1.fastq  |     0
 .../25T8B25T/fastq/testMultiplex.barcode_1.fastq   |     0
 .../25T8B25T/fastq/testMultiplexRH.1.fastq         |     0
 .../25T8B25T/fastq/testMultiplexRH.2.fastq         |     0
 .../25T8B25T/fastq/testMultiplexRH.barcode_1.fastq |     0
 .../picard/illumina/25T8B25T/sams/AAAAAAAA.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/AAAAGAAG.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/AACAATGG.sam     |    10 +
 .../picard/illumina/25T8B25T/sams/AACGCATT.sam     |    16 +
 .../picard/illumina/25T8B25T/sams/ACAAAATT.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/ACAGGTAT.sam     |    10 +
 .../picard/illumina/25T8B25T/sams/ACAGTTGA.sam     |     6 +
 .../picard/illumina/25T8B25T/sams/ACCAGTTG.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/ACGAAATC.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/ACTAAGAC.sam     |    10 +
 .../picard/illumina/25T8B25T/sams/ACTGTACC.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/ACTGTATC.sam     |    10 +
 .../picard/illumina/25T8B25T/sams/AGAAAAGA.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/AGCATGGA.sam     |     8 +
 .../picard/illumina/25T8B25T/sams/AGGTAAGG.sam     |    10 +
 .../picard/illumina/25T8B25T/sams/AGGTCGCA.sam     |    10 +
 .../picard/illumina/25T8B25T/sams/ATTATCAA.sam     |    12 +
 .../picard/illumina/25T8B25T/sams/ATTCCTCT.sam     |    10 +
 .../picard/illumina/25T8B25T/sams/CAACTCTC.sam     |    12 +
 .../picard/illumina/25T8B25T/sams/CAATAGAC.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/CAATAGTC.sam     |    16 +
 .../picard/illumina/25T8B25T/sams/CAGCGGAT.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/CAGCGGTA.sam     |    12 +
 .../picard/illumina/25T8B25T/sams/CCAACATT.sam     |    16 +
 .../picard/illumina/25T8B25T/sams/CCAGCACC.sam     |     8 +
 .../picard/illumina/25T8B25T/sams/CCATGCGT.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/CGCCTTCC.sam     |     6 +
 .../picard/illumina/25T8B25T/sams/CGCTATGT.sam     |    12 +
 .../picard/illumina/25T8B25T/sams/CTAACTCG.sam     |    10 +
 .../picard/illumina/25T8B25T/sams/CTATGCGC.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/CTATGCGT.sam     |    16 +
 .../picard/illumina/25T8B25T/sams/CTGCGGAT.sam     |     8 +
 .../picard/illumina/25T8B25T/sams/CTGTAATC.sam     |    14 +
 .../picard/illumina/25T8B25T/sams/GAAAAAAA.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/GAACGAT..sam     |     2 +
 .../picard/illumina/25T8B25T/sams/GAAGGAAG.sam     |     8 +
 .../picard/illumina/25T8B25T/sams/GACCAGGA.sam     |    16 +
 .../picard/illumina/25T8B25T/sams/GACCAGGC.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/GACCGTTG.sam     |    10 +
 .../picard/illumina/25T8B25T/sams/GACCTAAC.sam     |     4 +
 .../picard/illumina/25T8B25T/sams/GATATCCA.sam     |     8 +
 .../picard/illumina/25T8B25T/sams/GCCGTCGA.sam     |    12 +
 .../picard/illumina/25T8B25T/sams/GCCTAGCC.sam     |    12 +
 .../picard/illumina/25T8B25T/sams/GTAACATC.sam     |     6 +
 .../picard/illumina/25T8B25T/sams/GTCCACAG.sam     |     6 +
 testdata/picard/illumina/25T8B25T/sams/N.sam       |    34 +
 .../picard/illumina/25T8B25T/sams/TAAGCACA.sam     |     6 +
 .../picard/illumina/25T8B25T/sams/TACCGTCT.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/TAGCGGTA.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/TATCAGCC.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/TATCCAGG.sam     |    10 +
 .../picard/illumina/25T8B25T/sams/TATCCATG.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/TATCTCGG.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/TATCTGCC.sam     |    16 +
 .../picard/illumina/25T8B25T/sams/TCCGTCTA.sam     |     2 +
 .../picard/illumina/25T8B25T/sams/TCGCTAGA.sam     |    12 +
 .../picard/illumina/25T8B25T/sams/TCTGCAAG.sam     |     4 +
 .../picard/illumina/25T8B25T/sams/TGCAAGTA.sam     |     6 +
 .../picard/illumina/25T8B25T/sams/TGCTGCTG.sam     |    10 +
 .../picard/illumina/25T8B25T/sams/TGTAACTC.sam     |     4 +
 .../picard/illumina/25T8B25T/sams/TGTAATCA.sam     |     8 +
 .../picard/illumina/25T8B25T/sams/TTGTCTAT.sam     |    10 +
 .../picard/illumina/25T8B25T/sams/barcode.params   |     0
 .../sams/multiplexed_positive_rgtags.params        |     0
 .../picard/illumina/25T8B25T/sams/nonBarcoded.sam  |   182 +
 .../Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl   |   Bin
 .../Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl   |   Bin
 .../Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl   |   Bin
 .../Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl   |   Bin
 .../Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl   |   Bin
 .../Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl   |   Bin
 .../Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C63.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl   |   Bin
 .../Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl   |   Bin
 .../Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl   |   Bin
 .../Intensities/BaseCalls/L001/s_1_1101.filter     |   Bin
 .../Intensities/BaseCalls/s_1_1101_barcode.txt     |     0
 .../25T8B8B25T/Data/Intensities/L001/s_1_1101.locs |   Bin
 .../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 +
 .../25T8B8B25T/fastq/AAGACACTAGTCTCCT.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/ACCTACTGCTTCCCTT.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/AGGTCGCATTCCTTTC.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/ATTATCAACACCATAC.1.fastq      |     0
 .../25T8B8B25T/fastq/ATTATCAACACCATAC.2.fastq      |     0
 .../fastq/ATTATCAACACCATAC.barcode_1.fastq         |     0
 .../fastq/ATTATCAACACCATAC.barcode_2.fastq         |     0
 .../25T8B8B25T/fastq/ATTGTCTGGATTCACA.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/CAGCGGTATGTACTGC.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/CATGCTTATAGCATTT.1.fastq      |     0
 .../25T8B8B25T/fastq/CATGCTTATAGCATTT.2.fastq      |     0
 .../fastq/CATGCTTATAGCATTT.barcode_1.fastq         |     0
 .../fastq/CATGCTTATAGCATTT.barcode_2.fastq         |     0
 .../25T8B8B25T/fastq/CATGCTTTTAGCATTG.1.fastq      |     0
 .../25T8B8B25T/fastq/CATGCTTTTAGCATTG.2.fastq      |     0
 .../fastq/CATGCTTTTAGCATTG.barcode_1.fastq         |     0
 .../fastq/CATGCTTTTAGCATTG.barcode_2.fastq         |     0
 .../25T8B8B25T/fastq/CATGTTCGCGCCTTTT.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/CCCGATTTTCTCTCCC.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/CCTATTCTTCGTTTTC.1.fastq      |     0
 .../25T8B8B25T/fastq/CCTATTCTTCGTTTTC.2.fastq      |     0
 .../fastq/CCTATTCTTCGTTTTC.barcode_1.fastq         |     0
 .../fastq/CCTATTCTTCGTTTTC.barcode_2.fastq         |     0
 .../25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.1.fastq      |     0
 .../25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.2.fastq      |     0
 .../fastq/CCTCTTCTCTCGCTTT.barcode_1.fastq         |     0
 .../fastq/CCTCTTCTCTCGCTTT.barcode_2.fastq         |     0
 .../25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/CCTTCTTTTATCATTT.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/CGCTATGTTTCTCCTT.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/GCCGTCGAAGGTACCC.1.fastq      |     0
 .../25T8B8B25T/fastq/GCCGTCGAAGGTACCC.2.fastq      |     0
 .../fastq/GCCGTCGAAGGTACCC.barcode_1.fastq         |     0
 .../fastq/GCCGTCGAAGGTACCC.barcode_2.fastq         |     0
 .../25T8B8B25T/fastq/GCCGTCGATGGTACCC.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/GCTATCCACCTCCCCC.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/GTATAACATATTCAAC.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/GTCTGATGTCACTTCC.1.fastq      |     0
 .../25T8B8B25T/fastq/GTCTGATGTCACTTCC.2.fastq      |     0
 .../fastq/GTCTGATGTCACTTCC.barcode_1.fastq         |     0
 .../fastq/GTCTGATGTCACTTCC.barcode_2.fastq         |     0
 .../picard/illumina/25T8B8B25T/fastq/NN.1.fastq    |    76 +
 .../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 +
 .../25T8B8B25T/fastq/TCCCCGTTCCAACTTC.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/TGCTCGACTTCACAGT.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/TGTATCTCTTACTCTT.1.fastq      |     0
 .../25T8B8B25T/fastq/TGTATCTCTTACTCTT.2.fastq      |     0
 .../fastq/TGTATCTCTTACTCTT.barcode_1.fastq         |     0
 .../fastq/TGTATCTCTTACTCTT.barcode_2.fastq         |     0
 .../25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.1.fastq      |     0
 .../25T8B8B25T/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 +
 .../25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.1.fastq      |     0
 .../25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.2.fastq      |     0
 .../fastq/TTCCCCAGTGCTTTTA.barcode_1.fastq         |     0
 .../fastq/TTCCCCAGTGCTTTTA.barcode_2.fastq         |     0
 .../25T8B8B25T/fastq/TTCCTCCTCACCATCC.1.fastq      |     0
 .../25T8B8B25T/fastq/TTCCTCCTCACCATCC.2.fastq      |     0
 .../fastq/TTCCTCCTCACCATCC.barcode_1.fastq         |     0
 .../fastq/TTCCTCCTCACCATCC.barcode_2.fastq         |     0
 .../25T8B8B25T/fastq/TTCTCATCTTCCTTCC.1.fastq      |     0
 .../25T8B8B25T/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         |     0
 .../picard/illumina/25T8B8B25T/library.params      |     0
 .../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 +
 testdata/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 |     0
 .../Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl   |   Bin
 .../Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C100.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C101.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C102.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C103.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C104.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C105.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C106.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C107.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C108.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C109.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C110.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C111.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C112.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C113.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C114.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C115.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C116.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C117.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C118.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C119.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C120.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C121.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C122.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C123.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C124.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C125.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C126.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C127.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C128.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C129.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C130.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C131.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C132.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C133.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C134.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C135.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C136.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C137.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C138.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C139.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C140.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C141.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C142.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C143.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C144.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C145.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C146.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C147.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C148.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C149.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C150.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C151.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C152.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C153.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C154.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C155.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C156.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C157.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C158.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C159.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C160.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C161.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C162.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C163.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C164.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C165.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C166.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C167.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C168.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C169.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C170.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C171.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C172.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C173.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C174.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C175.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C176.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C177.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C178.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C179.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C180.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C181.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C182.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C183.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C184.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C185.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C186.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C187.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C188.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C189.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C190.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C191.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C192.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C193.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C194.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C195.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C196.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C197.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C198.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C199.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl   |   Bin
 .../Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C200.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C201.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C202.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C203.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C204.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C205.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C206.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C207.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C208.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C209.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C210.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C211.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C212.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C213.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C214.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C215.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C216.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C217.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C218.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C219.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C220.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C221.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C222.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C223.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C224.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C225.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C226.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C227.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C228.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C229.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C230.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C231.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C232.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C233.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C234.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C235.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C236.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C237.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C238.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C239.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C240.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C241.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C242.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C243.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C244.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C245.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C246.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C247.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C248.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C249.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C250.1/s_1_1101.bcl |   Bin
 .../Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl   |   Bin
 .../Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl  |   Bin
 .../Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl  |   Bin
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 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C100.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C101.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C102.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C103.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C104.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C105.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C106.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C107.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C108.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C109.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C115.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C123.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C239.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C240.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C241.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C242.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C243.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C244.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C245.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C246.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C247.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C248.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C249.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C250.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C67.1/s_1_1101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C68.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C70.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C80.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C86.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C89.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C90.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C95.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/C98.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L001/s_1_1101.filter (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C1.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C10.1/s_2_1101.bcl (100%)
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 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C69.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C7.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C70.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C71.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C72.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C73.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C74.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C75.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C76.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C77.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C78.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C79.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C8.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C80.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C81.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C82.1/s_2_1101.bcl (100%)
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 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C89.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C9.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C90.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C91.1/s_2_1101.bcl (100%)
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 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C95.1/s_2_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C96.1/s_2_1101.bcl (100%)
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 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C98.1/s_2_1101.bcl (100%)
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 rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/s_2_1101.filter (100%)
 copy testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/L001/s_1_1101.clocs (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C1.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C26.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C27.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C28.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C29.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C3.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1201.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C31.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C32.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C33.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C34.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C35.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C36.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C37.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C38.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C39.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C4.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C40.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C41.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C42.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C43.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C44.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1201.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1201.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C46.1/s_1_2101.bcl (100%)
 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1201.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_1101_barcode.txt.gz (100%)
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 copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_1101.clocs (100%)
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 create mode 100644 testdata/picard/illumina/25T8B25T/fastq/CAACTCTC.1.fastq
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 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C63.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/s_1_1101_barcode.txt (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/L001/s_1_1101.locs (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AACTTGACGCTCTCTT.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCACCT.barcode_2.fastq
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCTCCT.1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCTCCT.2.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCTCCT.barcode_1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/AAGACACTAGTCTCCT.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACAGGTATCACTTCAT.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACAGTTGAATCTTCTC.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACCAACTGCATCACTT.barcode_2.fastq
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/ACCTACTGCTTCCCTT.1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/ACCTACTGCTTCCCTT.2.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/ACCTACTGCTTCCCTT.barcode_1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/ACCTACTGCTTCCCTT.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ACTAAGACGTCCTCAT.barcode_2.fastq
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/AGGTCGCATTCCTTTC.1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/AGGTCGCATTCCTTTC.2.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/AGGTCGCATTCCTTTC.barcode_1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/AGGTCGCATTCCTTTC.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AGGTGCGAGACATTAA.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AGGTTATCTTAGCCAG.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/AGTTGCTTTGACTTGG.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.barcode_2.fastq
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/ATTATCAACACCATAC.1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/ATTATCAACACCATAC.2.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/ATTATCAACACCATAC.barcode_1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/ATTATCAACACCATAC.barcode_2.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/ATTGTCTGGATTCACA.1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/ATTGTCTGGATTCACA.2.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/ATTGTCTGGATTCACA.barcode_1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/ATTGTCTGGATTCACA.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CAATAGTCCGACTCTC.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CAGCAAGGGCGATATT.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CAGCGGTAAGTACTGC.barcode_2.fastq
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CAGCGGTATGTACTGC.1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CAGCGGTATGTACTGC.2.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CAGCGGTATGTACTGC.barcode_1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CAGCGGTATGTACTGC.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTG.barcode_2.fastq
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTT.1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTT.2.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTT.barcode_1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CATGCTTATAGCATTT.barcode_2.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CATGCTTTTAGCATTG.1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CATGCTTTTAGCATTG.2.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CATGCTTTTAGCATTG.barcode_1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CATGCTTTTAGCATTG.barcode_2.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CATGTTCGCGCCTTTT.1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CATGTTCGCGCCTTTT.2.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CATGTTCGCGCCTTTT.barcode_1.fastq (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/CATGTTCGCGCCTTTT.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CCAGAGCTCAACTGAT.barcode_2.fastq
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCCGATTTTCTCTCCC.1.fastq (100%)
 rename src/tests/java/net/sf/picard/fastq/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCCGATTTTCTCTCCC.2.fastq (100%)
 rename src/tests/java/net/sf/samtools/apps/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCCGATTTTCTCTCCC.barcode_1.fastq (100%)
 rename src/tests/java/org/broad/tribble/source/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCCGATTTTCTCTCCC.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CCTATGCCAATTGGCC.barcode_2.fastq
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTATTCTTCGTTTTC.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTATTCTTCGTTTTC.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTATTCTTCGTTTTC.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTATTCTTCGTTTTC.barcode_2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.barcode_2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CCTTCGCAGAATCGAC.barcode_2.fastq
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTTCTTTTATCATTT.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTTCTTTTATCATTT.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTTCTTTTATCATTT.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CCTTCTTTTATCATTT.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCACCTT.barcode_2.fastq
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCTCCTT.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCTCCTT.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCTCCTT.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CGCTATGTTTCTCCTT.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CTACCAGGTTCTTGGC.barcode_2.fastq
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/CTGTAATCCTATTAGC.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GACCAGGACCATCACA.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCA.barcode_2.fastq
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCC.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCC.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCC.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GCCGTCGAAGGTACCC.barcode_2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GCCGTCGATGGTACCC.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GCCGTCGATGGTACCC.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GCCGTCGATGGTACCC.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GCCGTCGATGGTACCC.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GCCTAGCCCTTGAATC.barcode_2.fastq
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GCTATCCACCTCCCCC.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GCTATCCACCTCCCCC.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GCTATCCACCTCCCCC.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GCTATCCACCTCCCCC.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GTATAACAAATTCAAC.barcode_2.fastq
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GTATAACATATTCAAC.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GTATAACATATTCAAC.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GTATAACATATTCAAC.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GTATAACATATTCAAC.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/GTCTGATGGAACTTCG.barcode_2.fastq
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GTCTGATGTCACTTCC.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GTCTGATGTCACTTCC.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GTCTGATGTCACTTCC.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/GTCTGATGTCACTTCC.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/NN.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/NN.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/NN.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/NN.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TACTTAGCGTCTGCAC.barcode_2.fastq
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TCCCCGTTCCAACTTC.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TCCCCGTTCCAACTTC.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TCCCCGTTCCAACTTC.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TCCCCGTTCCAACTTC.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TCCTTGGTGCTGCACT.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TCGCCTTGCCAACGCT.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGCAAGTACGAACTTC.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGA.barcode_2.fastq
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGT.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGT.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGT.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TGCTCGACTTCACAGT.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGTAATCACCTCTAAC.barcode_2.fastq
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TGTATCTCTTACTCTT.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TGTATCTCTTACTCTT.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TGTATCTCTTACTCTT.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TGTATCTCTTACTCTT.barcode_2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TGTTCCGAAACCTCTT.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TTAATCAGCTGGTATT.barcode_2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TTATATCTTCATGTCT.barcode_2.fastq
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.barcode_2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TTCCTCCTCACCATCC.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TTCCTCCTCACCATCC.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TTCCTCCTCACCATCC.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TTCCTCCTCACCATCC.barcode_2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TTCTCATCTTCCTTCC.1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TTCTCATCTTCCTTCC.2.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TTCTCATCTTCCTTCC.barcode_1.fastq (100%)
 copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/25T8B8B25T/fastq/TTCTCATCTTCCTTCC.barcode_2.fastq (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.2.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.barcode_1.fastq
 create mode 100644 testdata/picard/illumina/25T8B8B25T/fastq/TTGAATAGATATCCGA.barcode_2.fastq
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/fastq/barcode_double.params (100%)
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/library.params (100%)
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/AACTTGAC.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/AAGACACT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/ACAGGTAT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/ACAGTTGA.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/ACCAACTG.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/ACCTACTG.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/ACTAAGAC.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/AGGTCGCA.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/AGGTGCGA.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/AGGTTATC.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/AGTTGCTT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/ATAGCGTC.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/ATTATCAA.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/ATTGTCTG.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CAATAGTC.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CAGCAAGG.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CAGCGGTA.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CATGCTTA.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CATGCTTT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CATGTTCG.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CCAGAGCT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CCCGATTT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CCTATGCC.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CCTATTCT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CCTCTTCT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CCTCTTTC.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CCTTCGCA.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CCTTCTTT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CGCTATGT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CTACCAGG.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CTCCCTCT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/CTGTAATC.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/GACCAGGA.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/GCCGTCGA.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/GCCTAGCC.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/GCTATCCA.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/GTATAACA.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/GTCTGATG.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/N.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TACTTAGC.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TCCCCGTT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TCCTTGGT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TCGCCTTG.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TGCAAGTA.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TGCTCGAC.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TGTAATCA.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TGTATCTC.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TGTCGGTT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TGTTCCGA.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TTAATCAG.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TTATATCT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TTCCCCAG.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TTCCTCCT.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TTCTCATC.sam
 create mode 100644 testdata/picard/illumina/25T8B8B25T/sams/TTGAATAG.sam
 rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/sams/barcode_double.params (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C100.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C101.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C102.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C103.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C104.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C105.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C106.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C107.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C108.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C109.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C110.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C111.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C112.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C113.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C114.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C115.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C116.1/s_1_1101.bcl (100%)
 rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C117.1/s_1_1101.bcl (100%)
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 copy testdata/{net/sf/picard/sam/fastq2bam/ok-paired/illumina-sanger_full_range_as_sanger-62.fastq => picard/sam/fastq2bam/sequential-files/single_end_R1_001.fastq} (100%)
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