[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 -
src/java/net/sf/picard/util/IlluminaUtil.java | 223 -
src/java/net/sf/picard/util/Interval.java | 193 -
src/java/net/sf/picard/util/IntervalList.java | 654 -
.../util/IntervalListReferenceSequenceMask.java | 123 -
src/java/net/sf/picard/util/IntervalListTools.java | 352 -
src/java/net/sf/picard/util/IntervalTree.java | 1227 -
src/java/net/sf/picard/util/IntervalTreeMap.java | 293 -
src/java/net/sf/picard/util/IntervalUtil.java | 76 -
src/java/net/sf/picard/util/IterableAdapter.java | 29 -
.../net/sf/picard/util/IterableOnceIterator.java | 42 -
src/java/net/sf/picard/util/ListMap.java | 48 -
src/java/net/sf/picard/util/Locus.java | 36 -
src/java/net/sf/picard/util/LocusComparator.java | 39 -
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 -
src/java/net/sf/picard/util/MergingIterator.java | 147 -
src/java/net/sf/picard/util/MetricsDoclet.java | 179 -
src/java/net/sf/picard/util/OverlapDetector.java | 119 -
src/java/net/sf/picard/util/PeekableIterator.java | 82 -
src/java/net/sf/picard/util/ProcessExecutor.java | 235 -
src/java/net/sf/picard/util/ProgressLogger.java | 136 -
.../sf/picard/util/QualityEncodingDetector.java | 359 -
src/java/net/sf/picard/util/QualityUtil.java | 78 -
src/java/net/sf/picard/util/RExecutor.java | 111 -
.../net/sf/picard/util/ReferenceSequenceMask.java | 55 -
.../net/sf/picard/util/ResourceLimitedMap.java | 105 -
.../sf/picard/util/ResourceLimitedMapFunctor.java | 47 -
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 -
src/java/net/sf/samtools/AsyncSAMFileWriter.java | 59 -
src/java/net/sf/samtools/BAMFileConstants.java | 45 -
src/java/net/sf/samtools/BAMFileReader.java | 987 -
src/java/net/sf/samtools/BAMFileWriter.java | 199 -
src/java/net/sf/samtools/BAMIndex.java | 65 -
src/java/net/sf/samtools/BAMIndexContent.java | 69 -
src/java/net/sf/samtools/BAMIndexMetaData.java | 243 -
src/java/net/sf/samtools/BAMIndexWriter.java | 52 -
src/java/net/sf/samtools/BAMIndexer.java | 259 -
src/java/net/sf/samtools/BAMRecord.java | 360 -
src/java/net/sf/samtools/BAMRecordCodec.java | 207 -
src/java/net/sf/samtools/BamFileIoUtils.java | 155 -
src/java/net/sf/samtools/BamIndexValidator.java | 89 -
src/java/net/sf/samtools/Bin.java | 162 -
src/java/net/sf/samtools/BinList.java | 119 -
src/java/net/sf/samtools/BinaryBAMIndexWriter.java | 205 -
src/java/net/sf/samtools/BinaryCigarCodec.java | 99 -
src/java/net/sf/samtools/BinaryTagCodec.java | 422 -
src/java/net/sf/samtools/BinningIndexBuilder.java | 187 -
src/java/net/sf/samtools/BinningIndexContent.java | 262 -
src/java/net/sf/samtools/BrowseableBAMIndex.java | 54 -
src/java/net/sf/samtools/CachingBAMFileIndex.java | 166 -
src/java/net/sf/samtools/Chunk.java | 167 -
src/java/net/sf/samtools/Cigar.java | 268 -
src/java/net/sf/samtools/CigarElement.java | 66 -
src/java/net/sf/samtools/CigarOperator.java | 186 -
.../net/sf/samtools/DefaultSAMRecordFactory.java | 44 -
src/java/net/sf/samtools/Defaults.java | 84 -
.../net/sf/samtools/DiskBasedBAMFileIndex.java | 78 -
.../net/sf/samtools/FileTruncatedException.java | 46 -
src/java/net/sf/samtools/FixBAMFile.java | 45 -
src/java/net/sf/samtools/GenomicIndexUtil.java | 100 -
src/java/net/sf/samtools/LinearIndex.java | 126 -
.../sf/samtools/NotPrimarySkippingIterator.java | 62 -
.../SAMBinaryTagAndUnsignedArrayValue.java | 48 -
src/java/net/sf/samtools/SAMBinaryTagAndValue.java | 125 -
src/java/net/sf/samtools/SAMException.java | 44 -
src/java/net/sf/samtools/SAMFileHeader.java | 348 -
src/java/net/sf/samtools/SAMFileReader.java | 915 -
src/java/net/sf/samtools/SAMFileSource.java | 68 -
src/java/net/sf/samtools/SAMFileSpan.java | 291 -
.../net/sf/samtools/SAMFileTruncatedReader.java | 68 -
src/java/net/sf/samtools/SAMFileWriter.java | 48 -
src/java/net/sf/samtools/SAMFileWriterFactory.java | 259 -
src/java/net/sf/samtools/SAMFileWriterImpl.java | 231 -
src/java/net/sf/samtools/SAMFormatException.java | 44 -
.../net/sf/samtools/SAMHeaderRecordComparator.java | 66 -
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 -
src/java/net/sf/samtools/SAMRecordFactory.java | 28 -
src/java/net/sf/samtools/SAMRecordIterator.java | 52 -
.../sf/samtools/SAMRecordQueryNameComparator.java | 86 -
src/java/net/sf/samtools/SAMRecordSetBuilder.java | 466 -
src/java/net/sf/samtools/SAMRecordUtil.java | 81 -
.../net/sf/samtools/SAMSequenceDictionary.java | 162 -
src/java/net/sf/samtools/SAMSequenceRecord.java | 225 -
src/java/net/sf/samtools/SAMSortOrderChecker.java | 86 -
src/java/net/sf/samtools/SAMTag.java | 32 -
src/java/net/sf/samtools/SAMTagUtil.java | 122 -
src/java/net/sf/samtools/SAMTestUtil.java | 90 -
src/java/net/sf/samtools/SAMTextHeaderCodec.java | 465 -
src/java/net/sf/samtools/SAMTextReader.java | 247 -
src/java/net/sf/samtools/SAMTextWriter.java | 183 -
src/java/net/sf/samtools/SAMTools.java | 119 -
src/java/net/sf/samtools/SAMUtils.java | 925 -
src/java/net/sf/samtools/SAMValidationError.java | 288 -
src/java/net/sf/samtools/SQTagUtil.java | 154 -
src/java/net/sf/samtools/SamPairUtil.java | 319 -
.../SecondaryOrSupplementarySkippingIterator.java | 41 -
.../StreamInflatingIndexingOutputStream.java | 80 -
.../sf/samtools/TagValueAndUnsignedArrayFlag.java | 42 -
src/java/net/sf/samtools/TextCigarCodec.java | 104 -
src/java/net/sf/samtools/TextTagCodec.java | 321 -
.../net/sf/samtools/TextualBAMIndexWriter.java | 185 -
src/java/net/sf/samtools/apps/TimeChannel.java | 60 -
.../net/sf/samtools/apps/TimeRandomAccessFile.java | 55 -
.../net/sf/samtools/example/ExampleSamUsage.java | 63 -
.../seekablestream/ISeekableStreamFactory.java | 33 -
.../seekablestream/SeekableBufferedStream.java | 124 -
.../samtools/seekablestream/SeekableFTPStream.java | 120 -
.../seekablestream/SeekableFTPStreamHelper.java | 166 -
.../seekablestream/SeekableFileStream.java | 125 -
.../seekablestream/SeekableHTTPStream.java | 186 -
.../sf/samtools/seekablestream/SeekableStream.java | 69 -
.../seekablestream/SeekableStreamFactory.java | 95 -
.../samtools/seekablestream/UserPasswordInput.java | 31 -
.../net/sf/samtools/util/AbstractAsyncWriter.java | 121 -
.../net/sf/samtools/util/AbstractIterator.java | 85 -
src/java/net/sf/samtools/util/AsciiWriter.java | 83 -
src/java/net/sf/samtools/util/BinaryCodec.java | 663 -
.../util/BlockCompressedFilePointerUtil.java | 101 -
.../samtools/util/BlockCompressedInputStream.java | 512 -
.../samtools/util/BlockCompressedOutputStream.java | 336 -
.../util/BlockCompressedStreamConstants.java | 118 -
src/java/net/sf/samtools/util/BlockGunzipper.java | 115 -
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.../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 -
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.../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 -
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.../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 -
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.../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 -
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.../picard/illumina/readerTests/s_1_1104_pos.txt | 0
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testdata/net/sf/picard/io/5newline5.txt | 2 -
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testdata/net/sf/picard/reference/testing.fai | 7 -
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.../Intensities/BaseCalls/L001/C35.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C36.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C36.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C37.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C37.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C38.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C38.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C39.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C39.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C4.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C4.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C40.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C40.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C41.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C41.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C42.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C42.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C43.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C43.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C44.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C44.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C45.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C45.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C46.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C46.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C47.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C47.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C48.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C48.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C49.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C49.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C5.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C5.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C50.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C50.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C51.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C51.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C52.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C52.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C53.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C53.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C54.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C54.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C55.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C55.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C56.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C56.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C57.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C57.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C58.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C58.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C6.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C6.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C7.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C7.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C8.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C8.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C9.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C9.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/s_1_1101.filter | Bin
.../Intensities/BaseCalls/L001/s_1_1201.filter | Bin
.../Intensities/BaseCalls/L001/s_1_2101.filter | Bin
.../Intensities/BaseCalls/s_1_1101_barcode.txt.gz | Bin
.../Intensities/BaseCalls/s_1_1201_barcode.txt.gz | Bin
.../Intensities/BaseCalls/s_1_2101_barcode.txt.gz | Bin
.../25T8B25T/Data/Intensities/L001/s_1_1101.clocs | Bin
.../25T8B25T/Data/Intensities/L001/s_1_1201.clocs | Bin
.../25T8B25T/Data/Intensities/L001/s_1_2101.clocs | Bin
.../illumina/25T8B25T/fastq/AAAAAAAA.1.fastq | 0
.../illumina/25T8B25T/fastq/AAAAAAAA.2.fastq | 0
.../25T8B25T/fastq/AAAAAAAA.barcode_1.fastq | 0
.../illumina/25T8B25T/fastq/AAAAGAAG.1.fastq | 0
.../illumina/25T8B25T/fastq/AAAAGAAG.2.fastq | 0
.../25T8B25T/fastq/AAAAGAAG.barcode_1.fastq | 0
.../illumina/25T8B25T/fastq/AACAATGG.1.fastq | 16 +
.../illumina/25T8B25T/fastq/AACAATGG.2.fastq | 16 +
.../25T8B25T/fastq/AACAATGG.barcode_1.fastq | 16 +
.../illumina/25T8B25T/fastq/AACGCATT.1.fastq | 28 +
.../illumina/25T8B25T/fastq/AACGCATT.2.fastq | 28 +
.../25T8B25T/fastq/AACGCATT.barcode_1.fastq | 28 +
.../illumina/25T8B25T/fastq/ACAAAATT.1.fastq | 0
.../illumina/25T8B25T/fastq/ACAAAATT.2.fastq | 0
.../25T8B25T/fastq/ACAAAATT.barcode_1.fastq | 0
.../illumina/25T8B25T/fastq/ACAGGTAT.1.fastq | 16 +
.../illumina/25T8B25T/fastq/ACAGGTAT.2.fastq | 16 +
.../25T8B25T/fastq/ACAGGTAT.barcode_1.fastq | 16 +
.../illumina/25T8B25T/fastq/ACAGTTGA.1.fastq | 8 +
.../illumina/25T8B25T/fastq/ACAGTTGA.2.fastq | 8 +
.../25T8B25T/fastq/ACAGTTGA.barcode_1.fastq | 8 +
.../illumina/25T8B25T/fastq/ACCAGTTG.1.fastq | 0
.../illumina/25T8B25T/fastq/ACCAGTTG.2.fastq | 0
.../25T8B25T/fastq/ACCAGTTG.barcode_1.fastq | 0
.../illumina/25T8B25T/fastq/ACGAAATC.1.fastq | 0
.../illumina/25T8B25T/fastq/ACGAAATC.2.fastq | 0
.../25T8B25T/fastq/ACGAAATC.barcode_1.fastq | 0
.../illumina/25T8B25T/fastq/ACTAAGAC.1.fastq | 16 +
.../illumina/25T8B25T/fastq/ACTAAGAC.2.fastq | 16 +
.../25T8B25T/fastq/ACTAAGAC.barcode_1.fastq | 16 +
.../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
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rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C13.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C130.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C131.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C132.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C133.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C134.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C135.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C136.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C137.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C138.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C139.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C14.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C140.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C141.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C142.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C143.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C144.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C145.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C146.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C147.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C148.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C149.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C15.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C150.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C151.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C152.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C153.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C154.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C155.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C156.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C157.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C158.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C159.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C16.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C160.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C161.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C162.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C163.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C164.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C165.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C166.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C167.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C168.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C169.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C17.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C170.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C171.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C172.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C173.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C174.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C175.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C176.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C177.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C178.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C179.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C18.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C180.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C181.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C182.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C183.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C184.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C185.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C186.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C187.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C188.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C189.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C19.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C190.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C191.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C192.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C193.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C194.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C195.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C196.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C197.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C198.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C199.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C2.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C20.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C200.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C201.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C202.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C203.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C204.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C205.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C206.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C207.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C208.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C209.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C21.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C210.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C211.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C212.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C213.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C214.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C215.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C216.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C217.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C218.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C219.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C22.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C220.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C221.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C222.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C223.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C224.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C225.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C226.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C227.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C228.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C229.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C23.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C230.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C231.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C232.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C233.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C234.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C235.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C236.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C237.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C238.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C239.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C24.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C240.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C241.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C242.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C243.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C244.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C245.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C246.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C247.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C248.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C249.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C25.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C250.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C26.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C27.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C28.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C29.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C3.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C30.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C31.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C32.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C33.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C34.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C35.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C36.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C37.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C38.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C39.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C4.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C40.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C41.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C42.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C43.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C44.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C45.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C46.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C47.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C48.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C49.1/s_2_1101.bcl (100%)
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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/C24.1/s_1_1101.bcl (100%)
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copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl (100%)
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copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl (100%)
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copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl (100%)
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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%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C45.1/s_1_2101.bcl (100%)
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%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C47.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C48.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C49.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C5.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C50.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C51.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C52.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C53.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C54.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C55.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C56.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C57.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C58.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1201.filter (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_2101.filter (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_1101_barcode.txt.gz (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_1201_barcode.txt.gz (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/s_1_2101_barcode.txt.gz (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_1101.clocs (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_1201.clocs (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/L001/s_1_2101.clocs (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/AAAAAAAA.1.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/AAAAAAAA.2.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/AAAAAAAA.barcode_1.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/AAAAGAAG.1.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/AAAAGAAG.2.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/AAAAGAAG.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/AACAATGG.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/AACAATGG.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/AACAATGG.barcode_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/AACGCATT.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/AACGCATT.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/AACGCATT.barcode_1.fastq
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/ACAAAATT.1.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/ACAAAATT.2.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/ACAAAATT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ACAGGTAT.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ACAGGTAT.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ACAGGTAT.barcode_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ACAGTTGA.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ACAGTTGA.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ACAGTTGA.barcode_1.fastq
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/ACCAGTTG.1.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/ACCAGTTG.2.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/ACCAGTTG.barcode_1.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/ACGAAATC.1.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/ACGAAATC.2.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/ACGAAATC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ACTAAGAC.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ACTAAGAC.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ACTAAGAC.barcode_1.fastq
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/ACTGTACC.1.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/ACTGTACC.2.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/ACTGTACC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ACTGTATC.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ACTGTATC.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ACTGTATC.barcode_1.fastq
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/AGAAAAGA.1.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/AGAAAAGA.2.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/AGAAAAGA.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/AGCATGGA.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/AGCATGGA.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/AGCATGGA.barcode_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/AGGTAAGG.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/AGGTAAGG.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/AGGTAAGG.barcode_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/AGGTCGCA.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/AGGTCGCA.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/AGGTCGCA.barcode_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ATTATCAA.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ATTATCAA.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ATTATCAA.barcode_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ATTCCTCT.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ATTCCTCT.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/ATTCCTCT.barcode_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/CAACTCTC.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/CAACTCTC.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/CAACTCTC.barcode_1.fastq
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/CAATAGAC.1.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/CAATAGAC.2.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/CAATAGAC.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/CAATAGTC.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/CAATAGTC.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/CAATAGTC.barcode_1.fastq
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/CAGCGGAT.1.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/CAGCGGAT.2.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/CAGCGGAT.barcode_1.fastq (100%)
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/CAGCGGTA.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/CAGCGGTA.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/CAGCGGTA.barcode_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/CCAACATT.1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/CCAGCACC.barcode_1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/CTAACTCG.barcode_1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/CTGTAATC.barcode_1.fastq
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rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/GAACGAT..1.fastq (100%)
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/GACCAGGA.barcode_1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/GACCGTTG.1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/GACCTAAC.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/GACCTAAC.barcode_1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/GCCGTCGA.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/GCCGTCGA.barcode_1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/GCCTAGCC.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/GCCTAGCC.barcode_1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/GTCCACAG.barcode_1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/N.barcode_1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TAAGCACA.barcode_1.fastq
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rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/TAGCGGTA.barcode_1.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/TATCAGCC.1.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/TATCAGCC.2.fastq (100%)
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TATCCAGG.1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TATCCAGG.barcode_1.fastq
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rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/TATCCATG.barcode_1.fastq (100%)
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TCGCTAGA.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TCGCTAGA.barcode_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TCTGCAAG.1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TCTGCAAG.barcode_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TGCAAGTA.1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TGCTGCTG.barcode_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TGTAACTC.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TGTAACTC.2.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TGTAACTC.barcode_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TGTAATCA.1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TGTAATCA.barcode_1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TTGTCTAT.1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/TTGTCTAT.barcode_1.fastq
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create mode 100644 testdata/picard/illumina/25T8B25T/fastq/nonBarcoded.1.fastq
create mode 100644 testdata/picard/illumina/25T8B25T/fastq/nonBarcoded.2.fastq
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rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/testMultiplex.barcode_1.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/testMultiplexRH.1.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/testMultiplexRH.2.fastq (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/fastq/testMultiplexRH.barcode_1.fastq (100%)
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create mode 100644 testdata/picard/illumina/25T8B25T/sams/nonBarcoded.sam
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rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B8B25T/Data/Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl (100%)
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%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C118.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C119.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C120.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C121.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C122.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C123.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C124.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C125.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C126.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C127.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C128.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C129.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C130.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C131.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C132.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C133.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C134.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C135.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C136.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C137.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C138.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C139.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C140.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C141.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C142.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C143.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C144.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C145.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C146.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C147.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C148.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C149.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C150.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C151.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C152.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C153.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C154.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C155.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C156.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C157.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C158.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C159.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C160.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C161.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C162.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C163.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C164.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C165.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C166.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C167.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C168.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C169.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C170.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C171.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C172.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C173.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C174.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C175.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C176.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C177.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C178.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C179.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C180.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C181.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C182.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C183.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C184.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C185.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C186.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C187.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C188.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C189.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C190.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C191.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C192.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C193.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C194.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C195.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C196.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C197.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C198.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C199.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C200.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C201.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C202.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C203.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C204.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C205.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C206.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C207.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C208.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C209.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C210.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C211.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C212.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C213.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C214.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C215.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C216.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C217.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C218.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C219.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C220.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C221.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C222.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C223.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C224.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C225.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C226.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C227.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C228.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C229.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C230.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C231.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C232.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C233.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C234.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C235.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C236.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C237.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C238.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C239.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C240.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C241.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C242.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C243.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C244.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C245.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C246.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C247.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C248.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C249.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C250.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C59.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C60.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C61.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C62.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C63.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C64.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C65.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C66.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C67.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C68.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C69.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C70.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C71.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C72.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C73.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C74.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C75.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C76.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C77.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C78.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C79.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C80.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C81.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C82.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C83.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C84.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C85.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C86.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C87.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C88.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C89.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C90.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C91.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C92.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C93.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C94.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C95.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C96.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C97.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C98.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/C99.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/BaseCalls/L001/s_1_1101.filter (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/125T125T/Data/Intensities/L001/s_1_1101.clocs (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C1.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C10.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C11.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C12.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C13.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C14.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C15.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C16.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C17.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C18.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C19.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C2.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C20.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C27.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C46.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C47.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C48.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C49.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C5.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C50.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C51.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C52.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C53.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C54.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C55.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C56.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C57.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C58.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C6.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C7.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C8.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/C9.1/s_1_1101.bcl (100%)
rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/BaseCalls/L001/s_1_1101.filter (100%)
create mode 100755 testdata/picard/illumina/CollectIlluminaBasecallingMetrics/25T8B25T/Data/Intensities/BaseCalls/barcodeData.1
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rename testdata/{net/sf/picard/illumina => picard/illumina/CollectIlluminaBasecallingMetrics}/25T8B25T/Data/Intensities/L001/s_1_1101.clocs (100%)
copy {src/java/org/broad/tribble/util/ftp => testdata/picard/illumina/CollectIlluminaLaneMetrics}/.gitignore (100%)
rename testdata/{net/sf => }/picard/illumina/Homo_sapiens_assembly18.seqdict.sam (100%)
create mode 100644 testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/130318_SL-HBB_0226_BFCC1WYMACXX.expected.lane_metrics
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create mode 100644 testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/tileRuns/H7H7RADXX/README
rename testdata/{net/sf => }/picard/illumina/parserTests/filterParser/L001/s_1_0001.filter (100%)
rename testdata/{net/sf => }/picard/illumina/parserTests/filterParser/L001/s_1_0002.filter (100%)
rename testdata/{net/sf => }/picard/illumina/parserTests/filterParser/L001/s_1_0003.filter (100%)
rename testdata/{net/sf => }/picard/illumina/parserTests/filterParser/L001/s_1_0004.filter (100%)
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rename testdata/{net/sf => }/picard/illumina/parserTests/posParser/s_9_3201_pos.txt (100%)
rename testdata/{net/sf => }/picard/illumina/parserTests/posParser/s_9_3202_pos.txt (100%)
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copy src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/illumina/readerTests/s_1_1104_pos.txt (100%)
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create mode 100644 testdata/picard/sam/CollectGcBiasMetrics/Mheader.dict
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rename testdata/{net/sf => }/picard/sam/CompareSAMs/genomic_sorted_5.sam (100%)
rename testdata/{net/sf => }/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam (100%)
rename testdata/{net/sf => }/picard/sam/CompareSAMs/group_same_coord.sam (100%)
rename testdata/{net/sf => }/picard/sam/CompareSAMs/group_same_coord_diff_order.sam (100%)
rename testdata/{net/sf => }/picard/sam/CompareSAMs/has_non_primary.sam (100%)
rename testdata/{net/sf => }/picard/sam/CompareSAMs/unmapped_first.sam (100%)
rename testdata/{net/sf => }/picard/sam/CompareSAMs/unmapped_second.sam (100%)
rename testdata/{net/sf => }/picard/sam/CompareSAMs/unsorted.sam (100%)
create mode 100644 testdata/picard/sam/GatherBamFiles/indUnknownChrom.bam
create mode 100644 testdata/picard/sam/GatherBamFiles/indchr1.bam
create mode 100644 testdata/picard/sam/GatherBamFiles/indchr2.bam
create mode 100644 testdata/picard/sam/GatherBamFiles/indchr3.bam
create mode 100644 testdata/picard/sam/GatherBamFiles/indchr4.bam
create mode 100644 testdata/picard/sam/GatherBamFiles/indchr5.bam
create mode 100644 testdata/picard/sam/GatherBamFiles/indchr6.bam
create mode 100644 testdata/picard/sam/GatherBamFiles/indchr7.bam
create mode 100644 testdata/picard/sam/GatherBamFiles/indchr8.bam
create mode 100644 testdata/picard/sam/GatherBamFiles/orig.bam
create mode 100644 testdata/picard/sam/MarkDuplicates/markDuplicatesWithMateCigar.pairSet.swap.sam
rename testdata/{net/sf => }/picard/sam/MarkDuplicates/merge1.sam (100%)
rename testdata/{net/sf => }/picard/sam/MarkDuplicates/merge2.sam (100%)
rename testdata/{net/sf => }/picard/sam/MarkDuplicates/merge3.sam (100%)
create mode 100644 testdata/picard/sam/MarkDuplicates/npe.perhaps.sam
create mode 100644 testdata/picard/sam/MarkDuplicates/optical_dupes.sam
create mode 100644 testdata/picard/sam/MarkDuplicates/optical_dupes_casava.sam
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/aligned.badorder.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/aligned.supplement.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/cliptest.aligned.sam (100%)
create mode 100644 testdata/picard/sam/MergeBamAlignment/cliptest.dict
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/cliptest.fasta (100%)
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/cliptest.unmapped.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/multihit.aligned.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/multihit.unmapped.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/unmapped.badorder.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeBamAlignment/unmapped.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeSamFiles/case1/chr11sub_file1.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeSamFiles/case1/chr11sub_file2.sam (100%)
create mode 100644 testdata/picard/sam/MergeSamFiles/case1/expected_output.sam
rename testdata/{net/sf => }/picard/sam/MergeSamFiles/case2/chr11sub_file1.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeSamFiles/case2/chr11sub_file2.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeSamFiles/case2/chr11sub_file3.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeSamFiles/case2/chr11sub_file4.sam (100%)
create mode 100644 testdata/picard/sam/MergeSamFiles/case2/expected_output.sam
rename testdata/{net/sf => }/picard/sam/MergeSamFiles/unsorted_input/1.sam (100%)
rename testdata/{net/sf => }/picard/sam/MergeSamFiles/unsorted_input/2.sam (100%)
create mode 100644 testdata/picard/sam/PositionalDownsampleSam/header.dict
create mode 100644 testdata/picard/sam/SamFileConverterTest/unmapped.bam
create mode 100644 testdata/picard/sam/SamFileConverterTest/unmapped.cram
create mode 100755 testdata/picard/sam/SamFileConverterTest/unmapped.sam
rename testdata/{net/sf => }/picard/sam/aligned.sam (100%)
rename testdata/{net/sf => }/picard/sam/aligned_queryname_sorted.bam (100%)
rename testdata/{net/sf => }/picard/sam/aligned_queryname_sorted.sam (100%)
copy {src/java/org/broad/tribble/util/ftp => testdata/picard/sam/bam2fastq/nonpaired}/.gitignore (100%)
rename testdata/{net/sf => }/picard/sam/bam2fastq/paired/bad/README.txt (100%)
rename testdata/{net/sf => }/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam (100%)
rename testdata/{net/sf => }/picard/sam/bam2fastq/paired/bad/unpaired-mate.sam (100%)
rename testdata/{net/sf => }/picard/sam/bam2fastq/paired/ok/README.txt (100%)
rename testdata/{net/sf => }/picard/sam/bam2fastq/paired/ok/clipping_test.sam (100%)
rename testdata/{net/sf => }/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam (100%)
rename testdata/{net/sf => }/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam (100%)
rename testdata/{net/sf => }/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam (100%)
rename testdata/{net/sf => }/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam (100%)
rename testdata/{net/sf => }/picard/sam/bam2fastq/paired/ok/sorted-pair.sam (100%)
rename testdata/{net/sf => }/picard/sam/basic.fasta (100%)
rename testdata/{net/sf => }/picard/sam/duplicate_sequence_names.fasta (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/README.txt (100%)
rename src/java/org/broad/tribble/util/ftp/.gitignore => testdata/picard/sam/fastq2bam/bad-format/0lines.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-format/1lines.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-format/2lines.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-format/3lines.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-format/bad-qual-header.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-format/bad-seq-header.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-format/extra-line.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-format/too-many-quals.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-format/tt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-paired/dott (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-paired/pair-a1.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-paired/pair-a2.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-paired/pair-b1.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-paired/pair-b2.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-paired/pair1-badnum.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-paired/pair1-nonum.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-paired/pair1-one-more-record.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-paired/pair1-onetoken.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-paired/pair2-badnum.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-paired/pair2-diff-name.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/bad-paired/pair2-one-more-record.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/fastq-illumina/README.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/fastq-illumina/illumina-sanger_full_range_as_sanger-62.fastq (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/fastq-illumina/s_1_1_sequence.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/fastq-illumina/s_1_sequence.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/fastq-sanger/README.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/fastq-sanger/sanger_full_range_as_sanger-63.fastq (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/fastq-solexa/README.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/fastq-solexa/bad1.fastq (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/fastq-solexa/s_1_sequence.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/fastq-solexa/solexa_full_range_as_sanger.fastq (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/fastq-solexa/solexa_full_range_as_solexa.fastq (100%)
copy testdata/{net/sf => }/picard/sam/fastq2bam/ok-paired/illumina-sanger_full_range_as_sanger-62.fastq (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/ok-paired/pair1.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/ok-paired/pair2.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/ok-paired/s_1_1_sequence.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/ok-paired/s_1_2_sequence.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/ok-paired/s_1_sequence.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/permissive-format/pair1.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/permissive-format/pair2.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt (100%)
rename testdata/{net/sf => }/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt (100%)
copy testdata/{net/sf/picard/sam/fastq2bam/ok-paired/illumina-sanger_full_range_as_sanger-62.fastq => picard/sam/fastq2bam/sequential-files/paired_end_R1_001.fastq} (100%)
copy testdata/{net/sf/picard/sam/fastq2bam/ok-paired/illumina-sanger_full_range_as_sanger-62.fastq => picard/sam/fastq2bam/sequential-files/paired_end_R1_002.fastq} (100%)
copy testdata/{net/sf/picard/sam/fastq2bam/ok-paired/illumina-sanger_full_range_as_sanger-62.fastq => picard/sam/fastq2bam/sequential-files/paired_end_R2_001.fastq} (100%)
copy testdata/{net/sf/picard/sam/fastq2bam/ok-paired/illumina-sanger_full_range_as_sanger-62.fastq => picard/sam/fastq2bam/sequential-files/paired_end_R2_002.fastq} (100%)
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%)
rename testdata/{net/sf/picard/sam/fastq2bam/ok-paired/illumina-sanger_full_range_as_sanger-62.fastq => picard/sam/fastq2bam/sequential-files/single_end_R1_002.fastq} (100%)
rename testdata/{net/sf => }/picard/sam/insert_size_metrics_test.sam (100%)
rename testdata/{net/sf/picard/sam/ValidateSamFileTest => picard/sam}/invalid_coord_sort_order.sam (100%)
rename testdata/{net/sf => }/picard/sam/merger.dict (100%)
rename testdata/{net/sf => }/picard/sam/merger.fasta (100%)
rename testdata/{net/sf => }/picard/sam/onehalfaligned.sam (100%)
rename testdata/{net/sf => }/picard/sam/otherhalfaligned.sam (100%)
rename testdata/{net/sf => }/picard/sam/revert_sam_basic.sam (100%)
rename testdata/{net/sf => }/picard/sam/revert_sam_negative.sam (100%)
create mode 100755 testdata/picard/sam/split_test.sam
create mode 100755 testdata/picard/sam/split_test2.sam
rename testdata/{net/sf => }/picard/sam/summary_alignment_bisulfite_test.sam (100%)
rename testdata/{net/sf => }/picard/sam/summary_alignment_stats_test.fasta (100%)
rename testdata/{net/sf => }/picard/sam/summary_alignment_stats_test.sam (100%)
rename testdata/{net/sf => }/picard/sam/summary_alignment_stats_test2.sam (100%)
rename testdata/{net/sf => }/picard/sam/summary_alignment_stats_test_multiple.sam (100%)
rename testdata/{net/sf => }/picard/sam/unmapped.sam (100%)
create mode 100644 testdata/picard/sam/viewsam_intervals_test.interval_list
create mode 100644 testdata/picard/sam/viewsam_intervals_test.sam
create mode 100644 testdata/picard/util/BedToIntervalListTest/end_after_chr.bed
create mode 100644 testdata/picard/util/BedToIntervalListTest/end_before_chr.bed
create mode 100644 testdata/picard/util/BedToIntervalListTest/extended.bed
create mode 100644 testdata/picard/util/BedToIntervalListTest/extended.bed.interval_list
create mode 100644 testdata/picard/util/BedToIntervalListTest/header.sam
create mode 100644 testdata/picard/util/BedToIntervalListTest/missing_chr.bed
create mode 100644 testdata/picard/util/BedToIntervalListTest/off_by_one_interval.bed
create mode 100644 testdata/picard/util/BedToIntervalListTest/one_base_interval.bed
create mode 100644 testdata/picard/util/BedToIntervalListTest/one_base_interval.bed.interval_list
create mode 100644 testdata/picard/util/BedToIntervalListTest/overlapping.bed
create mode 100644 testdata/picard/util/BedToIntervalListTest/overlapping.bed.interval_list
create mode 100644 testdata/picard/util/BedToIntervalListTest/seq_dict_test.bed
create mode 100644 testdata/picard/util/BedToIntervalListTest/seq_dict_test.bed.interval_list
create mode 100644 testdata/picard/util/BedToIntervalListTest/seq_dict_test.dictionary.bad
create mode 100644 testdata/picard/util/BedToIntervalListTest/seq_dict_test.dictionary.bad.vcf
create mode 100644 testdata/picard/util/BedToIntervalListTest/seq_dict_test.dictionary.dict
create mode 100644 testdata/picard/util/BedToIntervalListTest/seq_dict_test.dictionary.fasta
create mode 100644 testdata/picard/util/BedToIntervalListTest/seq_dict_test.dictionary.interval_list
create mode 100644 testdata/picard/util/BedToIntervalListTest/seq_dict_test.dictionary.sam
create mode 100644 testdata/picard/util/BedToIntervalListTest/seq_dict_test.dictionary.vcf
create mode 100644 testdata/picard/util/BedToIntervalListTest/simple.bed
create mode 100644 testdata/picard/util/BedToIntervalListTest/simple.bed.interval_list
create mode 100644 testdata/picard/util/BedToIntervalListTest/start_after_chr.bed
create mode 100644 testdata/picard/util/BedToIntervalListTest/start_before_chr.bed
create mode 100644 testdata/picard/util/BedToIntervalListTest/zero_base_interval.bed
create mode 100644 testdata/picard/util/BedToIntervalListTest/zero_base_interval.bed.interval_list
rename testdata/{net/sf => }/picard/util/all_ones_text_file.txt (100%)
rename testdata/{net/sf => }/picard/util/no_grouping_file.txt (100%)
create mode 100755 testdata/picard/util/scatterable.interval_list
rename testdata/{net/sf => }/picard/util/tabbed_text_file.txt (100%)
rename testdata/{net/sf/picard/util/whitepace_text_file.txt => picard/util/whitespace_text_file.txt} (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-indels-bad-samples.vcf (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-indels-bad-samples.vcf.idx (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-indels-dissimilar-contigs.vcf (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-indels-dissimilar-contigs.vcf.idx (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-indels-no-contigs.vcf (100%)
create mode 100644 testdata/picard/vcf/CEUTrio-indels-scrambled.1.vcf
rename testdata/{net/sf => }/picard/vcf/CEUTrio-indels.vcf (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-indels.vcf.idx (100%)
create mode 100644 testdata/picard/vcf/CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff.genotype_concordance_contingency_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff.genotype_concordance_detail_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-indels_vs_CEUTrio-indels_GtConcordanceDiff.genotype_concordance_summary_metrics
rename testdata/{net/sf => }/picard/vcf/CEUTrio-merged-indels-snps.vcf (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-merged-indels-snps.vcf.idx (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-random-scatter-0.vcf (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-random-scatter-0.vcf.idx (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-random-scatter-1.vcf (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-random-scatter-1.vcf.idx (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-random-scatter-2.vcf (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-random-scatter-2.vcf.idx (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-random-scatter-3.vcf (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-random-scatter-3.vcf.idx (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-random-scatter-4.vcf (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-random-scatter-4.vcf.idx (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-random-scatter-5.vcf (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-random-scatter-5.vcf.idx (100%)
create mode 100644 testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf
create mode 100644 testdata/picard/vcf/CEUTrio-snps-scrambled.2.vcf
rename testdata/{net/sf => }/picard/vcf/CEUTrio-snps.vcf (100%)
rename testdata/{net/sf => }/picard/vcf/CEUTrio-snps.vcf.idx (100%)
create mode 100644 testdata/picard/vcf/CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff.genotype_concordance_contingency_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff.genotype_concordance_detail_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_CEUTrio-snps_del_line_GtConcordanceDiff.genotype_concordance_summary_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff.genotype_concordance_contingency_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff.genotype_concordance_detail_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_CEUTrio-snps_first_line_GtConcordanceDiff.genotype_concordance_summary_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff.genotype_concordance_contingency_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff.genotype_concordance_detail_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_CEUTrio-snps_last_line_GtConcordanceDiff.genotype_concordance_summary_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_del_line.vcf
create mode 100644 testdata/picard/vcf/CEUTrio-snps_first_line_diff.vcf
create mode 100644 testdata/picard/vcf/CEUTrio-snps_last_line_diff.vcf
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff.genotype_concordance_contingency_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff.genotype_concordance_detail_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff.genotype_concordance_summary_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows.genotype_concordance_contingency_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows.genotype_concordance_detail_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_AllRows.genotype_concordance_summary_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp.genotype_concordance_contingency_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp.genotype_concordance_detail_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinDp.genotype_concordance_summary_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq.genotype_concordance_contingency_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq.genotype_concordance_detail_metrics
create mode 100644 testdata/picard/vcf/CEUTrio-snps_vs_CEUTrio-snps_GtConcordanceDiff_MinGq.genotype_concordance_summary_metrics
create mode 100644 testdata/picard/vcf/IntervalList1PerChrom.interval_list
create mode 100644 testdata/picard/vcf/IntervalListChr1Small.interval_list
create mode 100644 testdata/picard/vcf/NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff.genotype_concordance_contingency_metrics
create mode 100644 testdata/picard/vcf/NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff.genotype_concordance_detail_metrics
create mode 100644 testdata/picard/vcf/NIST-truth-snps_vs_CEUTrio-snps_GtConcordanceDiff.genotype_concordance_summary_metrics
create mode 100644 testdata/picard/vcf/NIST.selected.vcf
create mode 100644 testdata/picard/vcf/NIST.selected.vcf.idx
create mode 100644 testdata/picard/vcf/chunking/multi_allelic_at_10M.vcf
create mode 100644 testdata/picard/vcf/chunking/multi_allelic_at_10M.vcf.idx
create mode 100644 testdata/picard/vcf/filter/testFiltering.vcf
create mode 100755 testdata/picard/vcf/mini.dbsnp.vcf
create mode 100644 testdata/picard/vcf/mini.dbsnp.vcf.idx
create mode 100755 testdata/picard/vcf/mini.vcf
create mode 100644 testdata/picard/vcf/mini.vcf.idx
create mode 100644 testdata/picard/vcf/vcfFormatTest.bad_dict.vcf
rename testdata/{net/sf => }/picard/vcf/vcfFormatTest.bcf (100%)
rename testdata/{net/sf => }/picard/vcf/vcfFormatTest.bcf.idx (100%)
create mode 100644 testdata/picard/vcf/vcfFormatTest.scrambled.vcf
rename testdata/{net/sf => }/picard/vcf/vcfFormatTest.vcf (100%)
rename testdata/{net/sf => }/picard/vcf/vcfFormatTest.vcf.idx (100%)
delete mode 100644 testdata/tribble/Tb.vcf.idx
delete mode 100644 testdata/tribble/basicDbSNP.dbsnp
delete mode 100644 testdata/tribble/bed/NA12878.deletions.10kbp.het.gq99.hand_curated.hg19.bed
delete mode 100644 testdata/tribble/bed/NA12878.deletions.10kbp.het.gq99.hand_curated.hg19_fixed.bed
delete mode 100644 testdata/tribble/bed/Unigene.sample.bed
delete mode 100644 testdata/tribble/bed/disconcontigs.bed
delete mode 100644 testdata/tribble/bed/unsorted.bed
delete mode 100644 testdata/tribble/complexExample.vcf
delete mode 100644 testdata/tribble/fakeBed.bed
delete mode 100644 testdata/tribble/fakeVCF.vcf.gz
delete mode 100644 testdata/tribble/fakeVCF.vcf.gz.tbi
delete mode 100644 testdata/tribble/gwas/smallp.gwas
delete mode 100644 testdata/tribble/index/chrY_Y4_small.bed
delete mode 100644 testdata/tribble/large.txt
delete mode 100644 testdata/tribble/seekTest.txt
delete mode 100644 testdata/tribble/sites.bed
delete mode 100644 testdata/tribble/soapsnp.txt
delete mode 100644 testdata/tribble/split/test.bin.part1
delete mode 100644 testdata/tribble/split/test.bin.part2
delete mode 100644 testdata/tribble/split/test.bin.part3
delete mode 100644 testdata/tribble/split/test.bin.split
delete mode 100644 testdata/tribble/tabix/bigger.vcf.gz.tbi
delete mode 100644 testdata/tribble/tabix/trioDup.vcf
delete mode 100644 testdata/tribble/tabix/trioDup.vcf.gz
delete mode 100644 testdata/tribble/tabix/trioDup.vcf.gz.tbi
delete mode 100644 testdata/tribble/test.bed
delete mode 100644 testdata/tribble/test.gff
delete mode 100644 testdata/tribble/test.tabix.bed.gz
delete mode 100644 testdata/tribble/test.tabix.bed.gz.tbi
delete mode 100644 testdata/tribble/testGeliText.txt
delete mode 100644 testdata/tribble/testIntervalList.list
delete mode 100644 testdata/tribble/tmp/.gitignore
delete mode 100644 testdata/tribble/trio.vcf
delete mode 100644 testdata/tribble/trio.vcf.idx
delete mode 100644 testdata/tribble/trioDup.vcf
delete mode 100644 testdata/tribble/vcfexample.vcf
delete mode 100644 testdata/tribble/vcfexample.vcf.gz
delete mode 100644 testdata/tribble/vcfexample.vcf.gz.tbi
delete mode 100644 testdata/variant/HiSeq.10000.vcf
delete mode 100644 testdata/variant/ILLUMINA.wex.broad_phase2_baseline.20111114.both.exome.genotypes.1000.vcf
delete mode 100644 testdata/variant/VQSR.mixedTest.recal
delete mode 100644 testdata/variant/dbsnp_135.b37.1000.vcf
delete mode 100644 testdata/variant/diagnosis_targets_testfile.vcf
delete mode 100755 testdata/variant/ex2.bgzf.bcf
delete mode 100755 testdata/variant/ex2.bgzf.bcf.csi
delete mode 100755 testdata/variant/ex2.uncompressed.bcf
delete mode 100644 testdata/variant/ex2.vcf
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