[med-svn] [picard-tools] branch master updated (c073865 -> 47ecf00)
Vincent Danjean
vdanjean at debian.org
Mon Sep 7 23:48:12 UTC 2015
This is an automated email from the git hooks/post-receive script.
vdanjean pushed a change to branch master
in repository picard-tools.
from c073865 Upload to unstable
new 023d7a1 Update package with new upstream web site
new 688437a gbp import-orig --uscan does not work du to #796986
new 4957015 Imported Upstream version 1.138+dfsg.1
new d9e0f5a Merge tag 'upstream/1.138+dfsg.1' into sid
new 47ecf00 Rework the packaging due to the new sources layout
The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.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 +-
debian/PicardCommandLine.1 | 22 +
debian/README.source | 12 +
debian/bin/PicardCommandLine | 15 +
debian/bin/picard-tools | 79 -
debian/changelog | 7 +
debian/control | 120 +-
debian/copyright | 175 +-
debian/libpicard-java-doc.javadoc | 1 +
debian/libpicard-java.classpath | 1 +
debian/libpicard-java.jlibs | 1 +
debian/libsam-java.install | 1 -
debian/patches/00-for-upstream-fix-testsuite | 24 +
debian/patches/01-build.xml | 298 +-
debian/patches/02-snappy-java-compatibility.patch | 24 -
debian/patches/series | 3 +-
debian/patches/use_libjbzip2-java | 47 -
debian/picard-tools.1 | 58 -
debian/picard-tools.README.Debian | 8 -
debian/picard-tools.classpath | 1 -
debian/picard-tools.install | 4 +-
debian/picard-tools.links | 2 +
debian/picard-tools.manpages | 2 +-
debian/rules | 45 +-
debian/watch | 3 +-
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 -
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.../illumina/25T8B25T/fastq/AGGTAAGG.2.fastq | 16 -
.../25T8B25T/fastq/AGGTAAGG.barcode_1.fastq | 16 -
.../illumina/25T8B25T/fastq/AGGTCGCA.1.fastq | 16 -
.../illumina/25T8B25T/fastq/AGGTCGCA.2.fastq | 16 -
.../25T8B25T/fastq/AGGTCGCA.barcode_1.fastq | 16 -
.../illumina/25T8B25T/fastq/ATTATCAA.1.fastq | 20 -
.../illumina/25T8B25T/fastq/ATTATCAA.2.fastq | 20 -
.../25T8B25T/fastq/ATTATCAA.barcode_1.fastq | 20 -
.../illumina/25T8B25T/fastq/ATTCCTCT.1.fastq | 16 -
.../illumina/25T8B25T/fastq/ATTCCTCT.2.fastq | 16 -
.../25T8B25T/fastq/ATTCCTCT.barcode_1.fastq | 16 -
.../illumina/25T8B25T/fastq/CAACTCTC.1.fastq | 20 -
.../illumina/25T8B25T/fastq/CAACTCTC.2.fastq | 20 -
.../25T8B25T/fastq/CAACTCTC.barcode_1.fastq | 20 -
.../illumina/25T8B25T/fastq/CAATAGTC.1.fastq | 28 -
.../illumina/25T8B25T/fastq/CAATAGTC.2.fastq | 28 -
.../25T8B25T/fastq/CAATAGTC.barcode_1.fastq | 28 -
.../illumina/25T8B25T/fastq/CAGCGGTA.1.fastq | 20 -
.../illumina/25T8B25T/fastq/CAGCGGTA.2.fastq | 20 -
.../25T8B25T/fastq/CAGCGGTA.barcode_1.fastq | 20 -
.../illumina/25T8B25T/fastq/CCAACATT.1.fastq | 28 -
.../illumina/25T8B25T/fastq/CCAACATT.2.fastq | 28 -
.../25T8B25T/fastq/CCAACATT.barcode_1.fastq | 28 -
.../illumina/25T8B25T/fastq/CCAGCACC.1.fastq | 12 -
.../illumina/25T8B25T/fastq/CCAGCACC.2.fastq | 12 -
.../25T8B25T/fastq/CCAGCACC.barcode_1.fastq | 12 -
.../illumina/25T8B25T/fastq/CGCCTTCC.1.fastq | 8 -
.../illumina/25T8B25T/fastq/CGCCTTCC.2.fastq | 8 -
.../25T8B25T/fastq/CGCCTTCC.barcode_1.fastq | 8 -
.../illumina/25T8B25T/fastq/CGCTATGT.1.fastq | 20 -
.../illumina/25T8B25T/fastq/CGCTATGT.2.fastq | 20 -
.../25T8B25T/fastq/CGCTATGT.barcode_1.fastq | 20 -
.../illumina/25T8B25T/fastq/CTAACTCG.1.fastq | 16 -
.../illumina/25T8B25T/fastq/CTAACTCG.2.fastq | 16 -
.../25T8B25T/fastq/CTAACTCG.barcode_1.fastq | 16 -
.../illumina/25T8B25T/fastq/CTATGCGT.1.fastq | 28 -
.../illumina/25T8B25T/fastq/CTATGCGT.2.fastq | 28 -
.../25T8B25T/fastq/CTATGCGT.barcode_1.fastq | 28 -
.../illumina/25T8B25T/fastq/CTGCGGAT.1.fastq | 12 -
.../illumina/25T8B25T/fastq/CTGCGGAT.2.fastq | 12 -
.../25T8B25T/fastq/CTGCGGAT.barcode_1.fastq | 12 -
.../illumina/25T8B25T/fastq/CTGTAATC.1.fastq | 24 -
.../illumina/25T8B25T/fastq/CTGTAATC.2.fastq | 24 -
.../25T8B25T/fastq/CTGTAATC.barcode_1.fastq | 24 -
.../illumina/25T8B25T/fastq/GAAGGAAG.1.fastq | 12 -
.../illumina/25T8B25T/fastq/GAAGGAAG.2.fastq | 12 -
.../25T8B25T/fastq/GAAGGAAG.barcode_1.fastq | 12 -
.../illumina/25T8B25T/fastq/GACCAGGA.1.fastq | 28 -
.../illumina/25T8B25T/fastq/GACCAGGA.2.fastq | 28 -
.../25T8B25T/fastq/GACCAGGA.barcode_1.fastq | 28 -
.../illumina/25T8B25T/fastq/GACCGTTG.1.fastq | 16 -
.../illumina/25T8B25T/fastq/GACCGTTG.2.fastq | 16 -
.../25T8B25T/fastq/GACCGTTG.barcode_1.fastq | 16 -
.../illumina/25T8B25T/fastq/GACCTAAC.1.fastq | 4 -
.../illumina/25T8B25T/fastq/GACCTAAC.2.fastq | 4 -
.../25T8B25T/fastq/GACCTAAC.barcode_1.fastq | 4 -
.../illumina/25T8B25T/fastq/GATATCCA.1.fastq | 12 -
.../illumina/25T8B25T/fastq/GATATCCA.2.fastq | 12 -
.../25T8B25T/fastq/GATATCCA.barcode_1.fastq | 12 -
.../illumina/25T8B25T/fastq/GCCGTCGA.1.fastq | 20 -
.../illumina/25T8B25T/fastq/GCCGTCGA.2.fastq | 20 -
.../25T8B25T/fastq/GCCGTCGA.barcode_1.fastq | 20 -
.../illumina/25T8B25T/fastq/GCCTAGCC.1.fastq | 20 -
.../illumina/25T8B25T/fastq/GCCTAGCC.2.fastq | 20 -
.../25T8B25T/fastq/GCCTAGCC.barcode_1.fastq | 20 -
.../illumina/25T8B25T/fastq/GTAACATC.1.fastq | 8 -
.../illumina/25T8B25T/fastq/GTAACATC.2.fastq | 8 -
.../25T8B25T/fastq/GTAACATC.barcode_1.fastq | 8 -
.../illumina/25T8B25T/fastq/GTCCACAG.1.fastq | 8 -
.../illumina/25T8B25T/fastq/GTCCACAG.2.fastq | 8 -
.../25T8B25T/fastq/GTCCACAG.barcode_1.fastq | 8 -
.../sf/picard/illumina/25T8B25T/fastq/N.1.fastq | 64 -
.../sf/picard/illumina/25T8B25T/fastq/N.2.fastq | 64 -
.../illumina/25T8B25T/fastq/N.barcode_1.fastq | 64 -
.../illumina/25T8B25T/fastq/TAAGCACA.1.fastq | 8 -
.../illumina/25T8B25T/fastq/TAAGCACA.2.fastq | 8 -
.../25T8B25T/fastq/TAAGCACA.barcode_1.fastq | 8 -
.../illumina/25T8B25T/fastq/TATCCAGG.1.fastq | 16 -
.../illumina/25T8B25T/fastq/TATCCAGG.2.fastq | 16 -
.../25T8B25T/fastq/TATCCAGG.barcode_1.fastq | 16 -
.../illumina/25T8B25T/fastq/TATCTGCC.1.fastq | 28 -
.../illumina/25T8B25T/fastq/TATCTGCC.2.fastq | 28 -
.../25T8B25T/fastq/TATCTGCC.barcode_1.fastq | 28 -
.../illumina/25T8B25T/fastq/TCGCTAGA.1.fastq | 20 -
.../illumina/25T8B25T/fastq/TCGCTAGA.2.fastq | 20 -
.../25T8B25T/fastq/TCGCTAGA.barcode_1.fastq | 20 -
.../illumina/25T8B25T/fastq/TCTGCAAG.1.fastq | 4 -
.../illumina/25T8B25T/fastq/TCTGCAAG.2.fastq | 4 -
.../25T8B25T/fastq/TCTGCAAG.barcode_1.fastq | 4 -
.../illumina/25T8B25T/fastq/TGCAAGTA.1.fastq | 8 -
.../illumina/25T8B25T/fastq/TGCAAGTA.2.fastq | 8 -
.../25T8B25T/fastq/TGCAAGTA.barcode_1.fastq | 8 -
.../illumina/25T8B25T/fastq/TGCTGCTG.1.fastq | 16 -
.../illumina/25T8B25T/fastq/TGCTGCTG.2.fastq | 16 -
.../25T8B25T/fastq/TGCTGCTG.barcode_1.fastq | 16 -
.../illumina/25T8B25T/fastq/TGTAACTC.1.fastq | 4 -
.../illumina/25T8B25T/fastq/TGTAACTC.2.fastq | 4 -
.../25T8B25T/fastq/TGTAACTC.barcode_1.fastq | 4 -
.../illumina/25T8B25T/fastq/TGTAATCA.1.fastq | 12 -
.../illumina/25T8B25T/fastq/TGTAATCA.2.fastq | 12 -
.../25T8B25T/fastq/TGTAATCA.barcode_1.fastq | 12 -
.../illumina/25T8B25T/fastq/TTGTCTAT.1.fastq | 16 -
.../illumina/25T8B25T/fastq/TTGTCTAT.2.fastq | 16 -
.../25T8B25T/fastq/TTGTCTAT.barcode_1.fastq | 16 -
.../illumina/25T8B25T/fastq/nonBarcoded.1.fastq | 720 -
.../illumina/25T8B25T/fastq/nonBarcoded.2.fastq | 720 -
.../sf/picard/illumina/25T8B25T/sams/AAAAAAAA.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/AAAAGAAG.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/AACAATGG.sam | 10 -
.../sf/picard/illumina/25T8B25T/sams/AACGCATT.sam | 16 -
.../sf/picard/illumina/25T8B25T/sams/ACAAAATT.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/ACAGGTAT.sam | 10 -
.../sf/picard/illumina/25T8B25T/sams/ACAGTTGA.sam | 6 -
.../sf/picard/illumina/25T8B25T/sams/ACCAGTTG.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/ACGAAATC.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/ACTAAGAC.sam | 10 -
.../sf/picard/illumina/25T8B25T/sams/ACTGTACC.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/ACTGTATC.sam | 10 -
.../sf/picard/illumina/25T8B25T/sams/AGAAAAGA.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/AGCATGGA.sam | 8 -
.../sf/picard/illumina/25T8B25T/sams/AGGTAAGG.sam | 10 -
.../sf/picard/illumina/25T8B25T/sams/AGGTCGCA.sam | 10 -
.../sf/picard/illumina/25T8B25T/sams/ATTATCAA.sam | 12 -
.../sf/picard/illumina/25T8B25T/sams/ATTCCTCT.sam | 10 -
.../sf/picard/illumina/25T8B25T/sams/CAACTCTC.sam | 12 -
.../sf/picard/illumina/25T8B25T/sams/CAATAGAC.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/CAATAGTC.sam | 16 -
.../sf/picard/illumina/25T8B25T/sams/CAGCGGAT.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/CAGCGGTA.sam | 12 -
.../sf/picard/illumina/25T8B25T/sams/CCAACATT.sam | 16 -
.../sf/picard/illumina/25T8B25T/sams/CCAGCACC.sam | 8 -
.../sf/picard/illumina/25T8B25T/sams/CCATGCGT.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/CGCCTTCC.sam | 6 -
.../sf/picard/illumina/25T8B25T/sams/CGCTATGT.sam | 12 -
.../sf/picard/illumina/25T8B25T/sams/CTAACTCG.sam | 10 -
.../sf/picard/illumina/25T8B25T/sams/CTATGCGC.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/CTATGCGT.sam | 16 -
.../sf/picard/illumina/25T8B25T/sams/CTGCGGAT.sam | 8 -
.../sf/picard/illumina/25T8B25T/sams/CTGTAATC.sam | 14 -
.../sf/picard/illumina/25T8B25T/sams/GAAAAAAA.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/GAACGAT..sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/GAAGGAAG.sam | 8 -
.../sf/picard/illumina/25T8B25T/sams/GACCAGGA.sam | 16 -
.../sf/picard/illumina/25T8B25T/sams/GACCAGGC.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/GACCGTTG.sam | 10 -
.../sf/picard/illumina/25T8B25T/sams/GACCTAAC.sam | 4 -
.../sf/picard/illumina/25T8B25T/sams/GATATCCA.sam | 8 -
.../sf/picard/illumina/25T8B25T/sams/GCCGTCGA.sam | 12 -
.../sf/picard/illumina/25T8B25T/sams/GCCTAGCC.sam | 12 -
.../sf/picard/illumina/25T8B25T/sams/GTAACATC.sam | 6 -
.../sf/picard/illumina/25T8B25T/sams/GTCCACAG.sam | 6 -
.../net/sf/picard/illumina/25T8B25T/sams/N.sam | 34 -
.../sf/picard/illumina/25T8B25T/sams/TAAGCACA.sam | 6 -
.../sf/picard/illumina/25T8B25T/sams/TACCGTCT.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/TAGCGGTA.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/TATCAGCC.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/TATCCAGG.sam | 10 -
.../sf/picard/illumina/25T8B25T/sams/TATCCATG.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/TATCTCGG.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/TATCTGCC.sam | 16 -
.../sf/picard/illumina/25T8B25T/sams/TCCGTCTA.sam | 2 -
.../sf/picard/illumina/25T8B25T/sams/TCGCTAGA.sam | 12 -
.../sf/picard/illumina/25T8B25T/sams/TCTGCAAG.sam | 4 -
.../sf/picard/illumina/25T8B25T/sams/TGCAAGTA.sam | 6 -
.../sf/picard/illumina/25T8B25T/sams/TGCTGCTG.sam | 10 -
.../sf/picard/illumina/25T8B25T/sams/TGTAACTC.sam | 4 -
.../sf/picard/illumina/25T8B25T/sams/TGTAATCA.sam | 8 -
.../sf/picard/illumina/25T8B25T/sams/TTGTCTAT.sam | 10 -
.../picard/illumina/25T8B25T/sams/nonBarcoded.sam | 182 -
.../25T8B8B25T/fastq/AACTTGACGCTCTCTT.1.fastq | 4 -
.../25T8B8B25T/fastq/AACTTGACGCTCTCTT.2.fastq | 4 -
.../fastq/AACTTGACGCTCTCTT.barcode_1.fastq | 4 -
.../fastq/AACTTGACGCTCTCTT.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/AAGACACTAGTCACCT.1.fastq | 4 -
.../25T8B8B25T/fastq/AAGACACTAGTCACCT.2.fastq | 4 -
.../fastq/AAGACACTAGTCACCT.barcode_1.fastq | 4 -
.../fastq/AAGACACTAGTCACCT.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/ACAGGTATCACTTCAT.1.fastq | 4 -
.../25T8B8B25T/fastq/ACAGGTATCACTTCAT.2.fastq | 4 -
.../fastq/ACAGGTATCACTTCAT.barcode_1.fastq | 4 -
.../fastq/ACAGGTATCACTTCAT.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/ACAGTTGAATCTTCTC.1.fastq | 8 -
.../25T8B8B25T/fastq/ACAGTTGAATCTTCTC.2.fastq | 8 -
.../fastq/ACAGTTGAATCTTCTC.barcode_1.fastq | 8 -
.../fastq/ACAGTTGAATCTTCTC.barcode_2.fastq | 8 -
.../25T8B8B25T/fastq/ACCAACTGCATCACTT.1.fastq | 4 -
.../25T8B8B25T/fastq/ACCAACTGCATCACTT.2.fastq | 4 -
.../fastq/ACCAACTGCATCACTT.barcode_1.fastq | 4 -
.../fastq/ACCAACTGCATCACTT.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/ACTAAGACGTCCTCAT.1.fastq | 4 -
.../25T8B8B25T/fastq/ACTAAGACGTCCTCAT.2.fastq | 4 -
.../fastq/ACTAAGACGTCCTCAT.barcode_1.fastq | 4 -
.../fastq/ACTAAGACGTCCTCAT.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/AGGTGCGAGACATTAA.1.fastq | 4 -
.../25T8B8B25T/fastq/AGGTGCGAGACATTAA.2.fastq | 4 -
.../fastq/AGGTGCGAGACATTAA.barcode_1.fastq | 4 -
.../fastq/AGGTGCGAGACATTAA.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/AGGTTATCTTAGCCAG.1.fastq | 4 -
.../25T8B8B25T/fastq/AGGTTATCTTAGCCAG.2.fastq | 4 -
.../fastq/AGGTTATCTTAGCCAG.barcode_1.fastq | 4 -
.../fastq/AGGTTATCTTAGCCAG.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/AGTTGCTTTGACTTGG.1.fastq | 4 -
.../25T8B8B25T/fastq/AGTTGCTTTGACTTGG.2.fastq | 4 -
.../fastq/AGTTGCTTTGACTTGG.barcode_1.fastq | 4 -
.../fastq/AGTTGCTTTGACTTGG.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.1.fastq | 4 -
.../25T8B8B25T/fastq/ATAGCGTCTTGGTCTG.2.fastq | 4 -
.../fastq/ATAGCGTCTTGGTCTG.barcode_1.fastq | 4 -
.../fastq/ATAGCGTCTTGGTCTG.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/CAATAGTCCGACTCTC.1.fastq | 4 -
.../25T8B8B25T/fastq/CAATAGTCCGACTCTC.2.fastq | 4 -
.../fastq/CAATAGTCCGACTCTC.barcode_1.fastq | 4 -
.../fastq/CAATAGTCCGACTCTC.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/CAGCAAGGGCGATATT.1.fastq | 4 -
.../25T8B8B25T/fastq/CAGCAAGGGCGATATT.2.fastq | 4 -
.../fastq/CAGCAAGGGCGATATT.barcode_1.fastq | 4 -
.../fastq/CAGCAAGGGCGATATT.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/CAGCGGTAAGTACTGC.1.fastq | 4 -
.../25T8B8B25T/fastq/CAGCGGTAAGTACTGC.2.fastq | 4 -
.../fastq/CAGCGGTAAGTACTGC.barcode_1.fastq | 4 -
.../fastq/CAGCGGTAAGTACTGC.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/CATGCTTATAGCATTG.1.fastq | 8 -
.../25T8B8B25T/fastq/CATGCTTATAGCATTG.2.fastq | 8 -
.../fastq/CATGCTTATAGCATTG.barcode_1.fastq | 8 -
.../fastq/CATGCTTATAGCATTG.barcode_2.fastq | 8 -
.../25T8B8B25T/fastq/CCAGAGCTCAACTGAT.1.fastq | 8 -
.../25T8B8B25T/fastq/CCAGAGCTCAACTGAT.2.fastq | 8 -
.../fastq/CCAGAGCTCAACTGAT.barcode_1.fastq | 8 -
.../fastq/CCAGAGCTCAACTGAT.barcode_2.fastq | 8 -
.../25T8B8B25T/fastq/CCCGATTTTCTCTCCC.1.fastq | 0
.../25T8B8B25T/fastq/CCCGATTTTCTCTCCC.2.fastq | 0
.../fastq/CCCGATTTTCTCTCCC.barcode_1.fastq | 0
.../fastq/CCCGATTTTCTCTCCC.barcode_2.fastq | 0
.../25T8B8B25T/fastq/CCTATGCCAATTGGCC.1.fastq | 4 -
.../25T8B8B25T/fastq/CCTATGCCAATTGGCC.2.fastq | 4 -
.../fastq/CCTATGCCAATTGGCC.barcode_1.fastq | 4 -
.../fastq/CCTATGCCAATTGGCC.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/CCTATTCTTCGTTTTC.1.fastq | 0
.../25T8B8B25T/fastq/CCTATTCTTCGTTTTC.2.fastq | 0
.../fastq/CCTATTCTTCGTTTTC.barcode_1.fastq | 0
.../fastq/CCTATTCTTCGTTTTC.barcode_2.fastq | 0
.../25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.1.fastq | 0
.../25T8B8B25T/fastq/CCTCTTCTCTCGCTTT.2.fastq | 0
.../fastq/CCTCTTCTCTCGCTTT.barcode_1.fastq | 0
.../fastq/CCTCTTCTCTCGCTTT.barcode_2.fastq | 0
.../25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.1.fastq | 0
.../25T8B8B25T/fastq/CCTCTTTCTTCTGCTC.2.fastq | 0
.../fastq/CCTCTTTCTTCTGCTC.barcode_1.fastq | 0
.../fastq/CCTCTTTCTTCTGCTC.barcode_2.fastq | 0
.../25T8B8B25T/fastq/CCTTCGCAGAATCGAC.1.fastq | 4 -
.../25T8B8B25T/fastq/CCTTCGCAGAATCGAC.2.fastq | 4 -
.../fastq/CCTTCGCAGAATCGAC.barcode_1.fastq | 4 -
.../fastq/CCTTCGCAGAATCGAC.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/CCTTCTTTTATCATTT.1.fastq | 0
.../25T8B8B25T/fastq/CCTTCTTTTATCATTT.2.fastq | 0
.../fastq/CCTTCTTTTATCATTT.barcode_1.fastq | 0
.../fastq/CCTTCTTTTATCATTT.barcode_2.fastq | 0
.../25T8B8B25T/fastq/CGCTATGTTTCACCTT.1.fastq | 4 -
.../25T8B8B25T/fastq/CGCTATGTTTCACCTT.2.fastq | 4 -
.../fastq/CGCTATGTTTCACCTT.barcode_1.fastq | 4 -
.../fastq/CGCTATGTTTCACCTT.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/CGCTATGTTTCTCCTT.1.fastq | 0
.../25T8B8B25T/fastq/CGCTATGTTTCTCCTT.2.fastq | 0
.../fastq/CGCTATGTTTCTCCTT.barcode_1.fastq | 0
.../fastq/CGCTATGTTTCTCCTT.barcode_2.fastq | 0
.../25T8B8B25T/fastq/CTACCAGGTTCTTGGC.1.fastq | 4 -
.../25T8B8B25T/fastq/CTACCAGGTTCTTGGC.2.fastq | 4 -
.../fastq/CTACCAGGTTCTTGGC.barcode_1.fastq | 4 -
.../fastq/CTACCAGGTTCTTGGC.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.1.fastq | 0
.../25T8B8B25T/fastq/CTCCCTCTTCCTTCTT.2.fastq | 0
.../fastq/CTCCCTCTTCCTTCTT.barcode_1.fastq | 0
.../fastq/CTCCCTCTTCCTTCTT.barcode_2.fastq | 0
.../25T8B8B25T/fastq/CTGTAATCCTATTAGC.1.fastq | 4 -
.../25T8B8B25T/fastq/CTGTAATCCTATTAGC.2.fastq | 4 -
.../fastq/CTGTAATCCTATTAGC.barcode_1.fastq | 4 -
.../fastq/CTGTAATCCTATTAGC.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/GACCAGGACCATCACA.1.fastq | 4 -
.../25T8B8B25T/fastq/GACCAGGACCATCACA.2.fastq | 4 -
.../fastq/GACCAGGACCATCACA.barcode_1.fastq | 4 -
.../fastq/GACCAGGACCATCACA.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/GCCGTCGAAGGTACCA.1.fastq | 8 -
.../25T8B8B25T/fastq/GCCGTCGAAGGTACCA.2.fastq | 8 -
.../fastq/GCCGTCGAAGGTACCA.barcode_1.fastq | 8 -
.../fastq/GCCGTCGAAGGTACCA.barcode_2.fastq | 8 -
.../25T8B8B25T/fastq/GCCGTCGAAGGTACCC.1.fastq | 0
.../25T8B8B25T/fastq/GCCGTCGAAGGTACCC.2.fastq | 0
.../fastq/GCCGTCGAAGGTACCC.barcode_1.fastq | 0
.../fastq/GCCGTCGAAGGTACCC.barcode_2.fastq | 0
.../25T8B8B25T/fastq/GCCGTCGATGGTACCC.1.fastq | 0
.../25T8B8B25T/fastq/GCCGTCGATGGTACCC.2.fastq | 0
.../fastq/GCCGTCGATGGTACCC.barcode_1.fastq | 0
.../fastq/GCCGTCGATGGTACCC.barcode_2.fastq | 0
.../25T8B8B25T/fastq/GCCTAGCCCTTGAATC.1.fastq | 4 -
.../25T8B8B25T/fastq/GCCTAGCCCTTGAATC.2.fastq | 4 -
.../fastq/GCCTAGCCCTTGAATC.barcode_1.fastq | 4 -
.../fastq/GCCTAGCCCTTGAATC.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/GCTATCCACCTCCCCC.1.fastq | 0
.../25T8B8B25T/fastq/GCTATCCACCTCCCCC.2.fastq | 0
.../fastq/GCTATCCACCTCCCCC.barcode_1.fastq | 0
.../fastq/GCTATCCACCTCCCCC.barcode_2.fastq | 0
.../25T8B8B25T/fastq/GTATAACAAATTCAAC.1.fastq | 4 -
.../25T8B8B25T/fastq/GTATAACAAATTCAAC.2.fastq | 4 -
.../fastq/GTATAACAAATTCAAC.barcode_1.fastq | 4 -
.../fastq/GTATAACAAATTCAAC.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/GTATAACATATTCAAC.1.fastq | 0
.../25T8B8B25T/fastq/GTATAACATATTCAAC.2.fastq | 0
.../fastq/GTATAACATATTCAAC.barcode_1.fastq | 0
.../fastq/GTATAACATATTCAAC.barcode_2.fastq | 0
.../25T8B8B25T/fastq/GTCTGATGGAACTTCG.1.fastq | 4 -
.../25T8B8B25T/fastq/GTCTGATGGAACTTCG.2.fastq | 4 -
.../fastq/GTCTGATGGAACTTCG.barcode_1.fastq | 4 -
.../fastq/GTCTGATGGAACTTCG.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/GTCTGATGTCACTTCC.1.fastq | 0
.../25T8B8B25T/fastq/GTCTGATGTCACTTCC.2.fastq | 0
.../fastq/GTCTGATGTCACTTCC.barcode_1.fastq | 0
.../fastq/GTCTGATGTCACTTCC.barcode_2.fastq | 0
.../sf/picard/illumina/25T8B8B25T/fastq/NN.1.fastq | 76 -
.../sf/picard/illumina/25T8B8B25T/fastq/NN.2.fastq | 76 -
.../illumina/25T8B8B25T/fastq/NN.barcode_1.fastq | 76 -
.../illumina/25T8B8B25T/fastq/NN.barcode_2.fastq | 76 -
.../25T8B8B25T/fastq/TACTTAGCGTCTGCAC.1.fastq | 8 -
.../25T8B8B25T/fastq/TACTTAGCGTCTGCAC.2.fastq | 8 -
.../fastq/TACTTAGCGTCTGCAC.barcode_1.fastq | 8 -
.../fastq/TACTTAGCGTCTGCAC.barcode_2.fastq | 8 -
.../25T8B8B25T/fastq/TCCCCGTTCCAACTTC.1.fastq | 0
.../25T8B8B25T/fastq/TCCCCGTTCCAACTTC.2.fastq | 0
.../fastq/TCCCCGTTCCAACTTC.barcode_1.fastq | 0
.../fastq/TCCCCGTTCCAACTTC.barcode_2.fastq | 0
.../25T8B8B25T/fastq/TCCTTGGTGCTGCACT.1.fastq | 4 -
.../25T8B8B25T/fastq/TCCTTGGTGCTGCACT.2.fastq | 4 -
.../fastq/TCCTTGGTGCTGCACT.barcode_1.fastq | 4 -
.../fastq/TCCTTGGTGCTGCACT.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/TCGCCTTGCCAACGCT.1.fastq | 4 -
.../25T8B8B25T/fastq/TCGCCTTGCCAACGCT.2.fastq | 4 -
.../fastq/TCGCCTTGCCAACGCT.barcode_1.fastq | 4 -
.../fastq/TCGCCTTGCCAACGCT.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/TGCAAGTACGAACTTC.1.fastq | 8 -
.../25T8B8B25T/fastq/TGCAAGTACGAACTTC.2.fastq | 8 -
.../fastq/TGCAAGTACGAACTTC.barcode_1.fastq | 8 -
.../fastq/TGCAAGTACGAACTTC.barcode_2.fastq | 8 -
.../25T8B8B25T/fastq/TGCTCGACTTCACAGA.1.fastq | 4 -
.../25T8B8B25T/fastq/TGCTCGACTTCACAGA.2.fastq | 4 -
.../fastq/TGCTCGACTTCACAGA.barcode_1.fastq | 4 -
.../fastq/TGCTCGACTTCACAGA.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/TGCTCGACTTCACAGT.1.fastq | 0
.../25T8B8B25T/fastq/TGCTCGACTTCACAGT.2.fastq | 0
.../fastq/TGCTCGACTTCACAGT.barcode_1.fastq | 0
.../fastq/TGCTCGACTTCACAGT.barcode_2.fastq | 0
.../25T8B8B25T/fastq/TGTAATCACCTCTAAC.1.fastq | 4 -
.../25T8B8B25T/fastq/TGTAATCACCTCTAAC.2.fastq | 4 -
.../fastq/TGTAATCACCTCTAAC.barcode_1.fastq | 4 -
.../fastq/TGTAATCACCTCTAAC.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/TGTATCTCTTACTCTT.1.fastq | 0
.../25T8B8B25T/fastq/TGTATCTCTTACTCTT.2.fastq | 0
.../fastq/TGTATCTCTTACTCTT.barcode_1.fastq | 0
.../fastq/TGTATCTCTTACTCTT.barcode_2.fastq | 0
.../25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.1.fastq | 0
.../25T8B8B25T/fastq/TGTCGGTTTTTTGCTT.2.fastq | 0
.../fastq/TGTCGGTTTTTTGCTT.barcode_1.fastq | 0
.../fastq/TGTCGGTTTTTTGCTT.barcode_2.fastq | 0
.../25T8B8B25T/fastq/TGTTCCGAAACCTCTT.1.fastq | 4 -
.../25T8B8B25T/fastq/TGTTCCGAAACCTCTT.2.fastq | 4 -
.../fastq/TGTTCCGAAACCTCTT.barcode_1.fastq | 4 -
.../fastq/TGTTCCGAAACCTCTT.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/TTAATCAGCTGGTATT.1.fastq | 4 -
.../25T8B8B25T/fastq/TTAATCAGCTGGTATT.2.fastq | 4 -
.../fastq/TTAATCAGCTGGTATT.barcode_1.fastq | 4 -
.../fastq/TTAATCAGCTGGTATT.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/TTATATCTTCATGTCT.1.fastq | 4 -
.../25T8B8B25T/fastq/TTATATCTTCATGTCT.2.fastq | 4 -
.../fastq/TTATATCTTCATGTCT.barcode_1.fastq | 4 -
.../fastq/TTATATCTTCATGTCT.barcode_2.fastq | 4 -
.../25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.1.fastq | 0
.../25T8B8B25T/fastq/TTCCCCAGTGCTTTTA.2.fastq | 0
.../fastq/TTCCCCAGTGCTTTTA.barcode_1.fastq | 0
.../fastq/TTCCCCAGTGCTTTTA.barcode_2.fastq | 0
.../25T8B8B25T/fastq/TTCCTCCTCACCATCC.1.fastq | 0
.../25T8B8B25T/fastq/TTCCTCCTCACCATCC.2.fastq | 0
.../fastq/TTCCTCCTCACCATCC.barcode_1.fastq | 0
.../fastq/TTCCTCCTCACCATCC.barcode_2.fastq | 0
.../25T8B8B25T/fastq/TTCTCATCTTCCTTCC.1.fastq | 0
.../25T8B8B25T/fastq/TTCTCATCTTCCTTCC.2.fastq | 0
.../fastq/TTCTCATCTTCCTTCC.barcode_1.fastq | 0
.../fastq/TTCTCATCTTCCTTCC.barcode_2.fastq | 0
.../25T8B8B25T/fastq/TTGAATAGATATCCGA.1.fastq | 4 -
.../25T8B8B25T/fastq/TTGAATAGATATCCGA.2.fastq | 4 -
.../fastq/TTGAATAGATATCCGA.barcode_1.fastq | 4 -
.../fastq/TTGAATAGATATCCGA.barcode_2.fastq | 4 -
.../picard/illumina/25T8B8B25T/sams/AACTTGAC.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/AAGACACT.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/ACAGGTAT.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/ACAGTTGA.sam | 6 -
.../picard/illumina/25T8B8B25T/sams/ACCAACTG.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/ACCTACTG.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/ACTAAGAC.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/AGGTCGCA.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/AGGTGCGA.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/AGGTTATC.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/AGTTGCTT.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/ATAGCGTC.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/ATTATCAA.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/ATTGTCTG.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/CAATAGTC.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/CAGCAAGG.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/CAGCGGTA.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/CATGCTTA.sam | 6 -
.../picard/illumina/25T8B8B25T/sams/CATGCTTT.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/CATGTTCG.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/CCAGAGCT.sam | 6 -
.../picard/illumina/25T8B8B25T/sams/CCCGATTT.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/CCTATGCC.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/CCTATTCT.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/CCTCTTCT.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/CCTCTTTC.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/CCTTCGCA.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/CCTTCTTT.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/CGCTATGT.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/CTACCAGG.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/CTCCCTCT.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/CTGTAATC.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/GACCAGGA.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/GCCGTCGA.sam | 6 -
.../picard/illumina/25T8B8B25T/sams/GCCTAGCC.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/GCTATCCA.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/GTATAACA.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/GTCTGATG.sam | 4 -
.../net/sf/picard/illumina/25T8B8B25T/sams/N.sam | 40 -
.../picard/illumina/25T8B8B25T/sams/TACTTAGC.sam | 6 -
.../picard/illumina/25T8B8B25T/sams/TCCCCGTT.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/TCCTTGGT.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/TCGCCTTG.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/TGCAAGTA.sam | 6 -
.../picard/illumina/25T8B8B25T/sams/TGCTCGAC.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/TGTAATCA.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/TGTATCTC.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/TGTCGGTT.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/TGTTCCGA.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/TTAATCAG.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/TTATATCT.sam | 4 -
.../picard/illumina/25T8B8B25T/sams/TTCCCCAG.sam | 2 -
.../picard/illumina/25T8B8B25T/sams/TTCCTCCT.sam | 2 -
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.../picard/illumina/25T8B8B25T/sams/TTGAATAG.sam | 4 -
.../picard/illumina/readerTests/s_1_1104_pos.txt | 0
.../intervallist/IntervalListFromVCFTest.vcf | 53 -
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.../IntervalListchr123_empty.interval_list | 4 -
testdata/net/sf/picard/io/5newline5.txt | 2 -
testdata/net/sf/picard/io/empty.txt | 0
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.../Homo_sapiens_assembly18.trimmed.fasta | 16946 ----------
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testdata/net/sf/picard/reference/testing.fai | 7 -
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.../Intensities/BaseCalls/L001/C30.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C30.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C31.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C31.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C32.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C32.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C33.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C33.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C34.1/s_1_1201.bcl | Bin
.../Intensities/BaseCalls/L001/C34.1/s_1_2101.bcl | Bin
.../Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl | Bin
.../Intensities/BaseCalls/L001/C35.1/s_1_1201.bcl | Bin
.../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
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rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C117.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C118.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C119.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C12.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C120.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C121.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C122.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C123.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C124.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C125.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C126.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C127.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C128.1/s_2_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/125T125T/Data/Intensities/BaseCalls/L002/C129.1/s_2_1101.bcl (100%)
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%)
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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/C13.1/s_1_1101.bcl (100%)
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copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C21.1/s_1_1101.bcl (100%)
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copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C22.1/s_1_1101.bcl (100%)
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copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C23.1/s_1_1101.bcl (100%)
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copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C24.1/s_1_1101.bcl (100%)
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copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C25.1/s_1_1101.bcl (100%)
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copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C26.1/s_1_1101.bcl (100%)
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copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C28.1/s_1_1201.bcl (100%)
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copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C29.1/s_1_1101.bcl (100%)
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copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C3.1/s_1_1101.bcl (100%)
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rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C3.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C30.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C30.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C31.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C31.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C32.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C32.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C33.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C33.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C34.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C34.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C35.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C35.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C36.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C36.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C37.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C37.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C38.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C38.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C39.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C39.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C4.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C4.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C40.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C40.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C41.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C41.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C42.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C42.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C43.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C43.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C44.1/s_1_1201.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C44.1/s_1_2101.bcl (100%)
copy testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1101.bcl (100%)
rename testdata/{net/sf => }/picard/illumina/25T8B25T/Data/Intensities/BaseCalls/L001/C45.1/s_1_1201.bcl (100%)
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
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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%)
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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/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%)
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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%)
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create mode 100644 testdata/picard/illumina/IlluminaLaneMetricsCollectorTest/130318_SL-HBB_0226_BFCC1WYMACXX.expected.lane_metrics
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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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rename testdata/{net/sf => }/picard/illumina/readerTests/s_1_1101_pos.txt (100%)
rename testdata/{net/sf => }/picard/illumina/readerTests/s_1_1102_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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rename testdata/{net/sf => }/picard/illumina/readerTests/s_3_2103.clocs (100%)
rename testdata/{net/sf => }/picard/illumina/readerTests/s_3_2104.clocs (100%)
rename testdata/{net/sf => }/picard/illumina/readerTests/s_3_2105.clocs (100%)
create mode 100644 testdata/picard/metrics/chrM.reference.fasta
create mode 100644 testdata/picard/metrics/chrMReads.sam
create mode 100644 testdata/picard/quality/chrM.part.intervallist
create mode 100644 testdata/picard/quality/chrM.reference.fasta
create mode 100644 testdata/picard/quality/chrMReads.sam
create mode 100644 testdata/picard/quality/chrMReadsDiffereingLengths.sam
create mode 100644 testdata/picard/quality/chrMReadsMateUnmapped.sam
create mode 100644 testdata/picard/quality/chrMReadsMated.sam
create mode 100644 testdata/picard/quality/chrMReadsMatedRev.sam
create mode 100644 testdata/picard/quality/chrMReadsMatedRevOrder.sam
create mode 100644 testdata/picard/quality/chrMReadsMatedSameStrand.sam
create mode 100644 testdata/picard/quality/chrMReadsSecondaryAlignSoft.sam
create mode 100644 testdata/picard/quality/chrMReadsSupplementalAlignSoft.sam
create mode 100644 testdata/picard/quality/chrMReadsUnMated.sam
rename testdata/{net/sf => }/picard/sam/CleanSam/fits_with_deletion.sam (100%)
rename testdata/{net/sf => }/picard/sam/CleanSam/long_trailing_insertion.sam (100%)
rename testdata/{net/sf => }/picard/sam/CleanSam/overhang_with_deletion.sam (100%)
rename testdata/{net/sf => }/picard/sam/CleanSam/simple_fits.sam (100%)
rename testdata/{net/sf => }/picard/sam/CleanSam/simple_overhang.sam (100%)
rename testdata/{net/sf => }/picard/sam/CleanSam/trailing_insertion.sam (100%)
create mode 100644 testdata/picard/sam/CollectGcBiasMetrics/Mheader.dict
rename testdata/{net/sf => }/picard/sam/CompareSAMs/bigger_seq_dict.sam (100%)
rename testdata/{net/sf => }/picard/sam/CompareSAMs/chr21.sam (100%)
rename testdata/{net/sf => }/picard/sam/CompareSAMs/diff_coords.sam (100%)
rename testdata/{net/sf => }/picard/sam/CompareSAMs/example2.sam (100%)
rename testdata/{net/sf => }/picard/sam/CompareSAMs/genomic_sorted.sam (100%)
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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